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Python: drop EOL versions (#33898)

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This PR removes [end of life](https://endoflife.date/python) versions of Python from Spack. Specifically, this includes all versions of Python older than 3.7.

See https://github.com/spack/spack/discussions/31824 for rationale. Deprecated in #32615. And #28003.

For anyone using software that relies on Python 2, you have a few options:

* Upgrade the software to support Python 3. The `3to2` tool may get you most of the way there, although more complex libraries may need manual tweaking.
* Add Python 2 as an [external package](https://spack.readthedocs.io/en/latest/build_settings.html#external-packages). Many Python libraries do not support Python 2, but you may be able to add older versions that did once upon a time.
* Use Spack 0.19. Spack 0.19 is the last release to officially support Python 3.6 and older
* Create and maintain your own [custom repository](https://spack.readthedocs.io/en/latest/repositories.html). Basically, you would need a package for Python 2 and any other Python 2-specific libraries you need.
This commit is contained in:
Adam J. Stewart 2022-11-22 17:02:30 -06:00 committed by GitHub
parent 4bf964e6b3
commit c5883fffd7
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
542 changed files with 315 additions and 8279 deletions
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11
var/spack/repos/builtin/packages/alps/alps_climit.patch
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@ -1,11 +0,0 @@
diff -u -r -N e/alps/src/alps/osiris/xdrcore.C h/alps/src/alps/osiris/xdrcore.C
--- e/alps/src/alps/osiris/xdrcore.C 2020-11-04 12:59:46.000000000 +0900
+++ h/alps/src/alps/osiris/xdrcore.C 2020-12-16 11:45:16.000000000 +0900
@@ -66,6 +66,7 @@
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
+#include <climits>
#include <alps/osiris/xdrcore.h>

11
var/spack/repos/builtin/packages/alps/alps_cmake_time.patch
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@ -1,11 +0,0 @@
--- a/alps/config/run_test.cmake 2020-12-10 10:05:48.925076699 +0900
+++ b/alps/config/run_test.cmake 2020-12-10 11:37:18.180959480 +0900
@@ -3,7 +3,7 @@
# (See accompanying file LICENSE_1_0.txt or copy at
# http://www.boost.org/LICENSE_1_0.txt)
-find_program(cmd_path ${cmd} ${binarydir} ${dllexedir})
+find_program(cmd_path ${cmd} ${binarydir} ${dllexedir} NO_SYSTEM_ENVIRONMENT_PATH)
find_file(input_path ${input}.input ${binarydir} ${sourcedir})
if(NOT input_path)

59
var/spack/repos/builtin/packages/alps/alps_newgcc.patch
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@ -1,59 +0,0 @@
diff -u -r -N a/alps/applications/dmrg/dmrg/dmtk/system.h b/alps/applications/dmrg/dmrg/dmtk/system.h
--- a/alps/applications/dmrg/dmrg/dmtk/system.h 2020-10-20 15:38:28.000000000 +0900
+++ b/alps/applications/dmrg/dmrg/dmtk/system.h 2020-10-20 15:40:15.000000000 +0900
@@ -577,8 +577,11 @@
{
s.write((const char *)&_numsweeps, sizeof(size_t));
for(int i = 1; i <= _numsweeps; i++){
- s.write((const char *)&_sweeps(0,i), sizeof(double));
- s.write((const char *)&_sweeps(1,i), sizeof(double));
+ double x;
+ x = _sweeps(0,i);
+ s.write((const char *)&x, sizeof(double));
+ x = _sweeps(1,i);
+ s.write((const char *)&x, sizeof(double));
}
s.write((const char *)&_in_warmup, sizeof(bool));
s.write((const char *)&_sweep, sizeof(int));
diff -u -r -N a/alps/applications/dmrg/mps/framework/dmrg/mp_tensors/twositetensor.hpp b/alps/applications/dmrg/mps/framework/dmrg/mp_tensors/twositetensor.hpp
--- a/alps/applications/dmrg/mps/framework/dmrg/mp_tensors/twositetensor.hpp 2020-10-20 14:47:06.000000000 +0900
+++ b/alps/applications/dmrg/mps/framework/dmrg/mp_tensors/twositetensor.hpp 2020-10-20 14:47:53.000000000 +0900
@@ -216,8 +216,8 @@
swap(this->left_i, b.left_i);
swap(this->right_i, b.right_i);
swap(this->data_, b.data_);
- swap(this->cur_storage, b.cur_storage);
- swap(this->cur_normalization, b.cur_normalization);
+ this->swap(this->cur_storage, b.cur_storage);
+ this->swap(this->cur_normalization, b.cur_normalization);
}
template<class Matrix, class SymmGroup>
diff -u -r -N a/alps/applications/qmc/sse4/model.h b/alps/applications/qmc/sse4/model.h
--- a/alps/applications/qmc/sse4/model.h 2020-10-20 15:12:20.000000000 +0900
+++ b/alps/applications/qmc/sse4/model.h 2020-12-15 14:56:27.000000000 +0900
@@ -140,11 +140,6 @@
return diag_vertex_indices[e_index(state, utype, sites)];
}
- double max_diag_me() const
- {
- return _max_diag_me;
- }
-
double c(unsigned unit_type) const
{
return epsilon + _max_diag_me[unit_type];
diff -u -r -N a/alps/src/alps/alea/histogram.h b/alps/src/alps/alea/histogram.h
--- a/alps/src/alps/alea/histogram.h 2020-10-20 14:49:19.000000000 +0900
+++ b/alps/src/alps/alea/histogram.h 2020-12-15 14:56:59.000000000 +0900
@@ -85,9 +85,7 @@
// forward a few things from container
const_iterator begin() const { return histogram_.begin();}
- const_iterator rbegin() const { return histogram_.rbegin();}
const_iterator end() const { return histogram_.end();}
- const_iterator rend() const { return histogram_.rend();}
size_type size() const { return histogram_.size();}
value_type operator[](size_type i) const { return histogram_[i];}
value_type at(size_type i) const { return histogram_.at(i);}

13
var/spack/repos/builtin/packages/alps/mpi.patch
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@ -1,13 +0,0 @@
diff --git a/alps/src/alps/CMakeLists.txt b/alps/src/alps/CMakeLists.txt
index ae73f13..0d1ba34 100644
--- a/alps/src/alps/CMakeLists.txt
+++ b/alps/src/alps/CMakeLists.txt
@@ -93,7 +93,7 @@ if (Boost_FOUND)
set(ALPS_LINK_LIBS ${ALPS_LINK_LIBS} ${PYTHON_LIBRARY} ${PYTHON_EXTRA_LIBS})
endif(PYTHONLIBS_FOUND)
if(MPI_FOUND)
- set(ALPS_LINK_LIBS ${ALPS_LINK_LIBS} ${MPI_LIBRARIES} ${MPI_EXTRA_LIBRARY})
+ set(ALPS_LINK_LIBS ${ALPS_LINK_LIBS} ${MPI_LIBRARIES})
endif(MPI_FOUND)
target_link_libraries(alps ${ALPS_LINK_LIBS})
else (Boost_FOUND)

85
var/spack/repos/builtin/packages/alps/package.py
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@ -1,85 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
# Refs for building from source and recipes
# https://alps.comp-phys.org/mediawiki/index.php/Building_ALPS_from_source
# https://github.com/easybuilders/easybuild-easyconfigs/tree/master/easybuild/easyconfigs/a/ALPS
# https://github.com/conda-forge/alps-feedstock/tree/master/recipe
class Alps(CMakePackage):
"""Algorithms for Physics Simulations
Tags: Condensed Matter Physics, Computational Physics
"""
homepage = "https://alps.comp-phys.org"
url = "https://alps.comp-phys.org/static/software/releases/alps-2.3.0-src.tar.gz"
version("2.3.0", sha256="e64208d1e5acdd6f569277413c4867e1fa366cf4a224570eacbf1e9939fca2d2")
# Package failed to build with boost version >= 1.64
depends_on(
"boost@:1.63.0"
"+chrono +date_time +filesystem +iostreams +mpi +numpy +program_options"
"+python +regex +serialization +system +test +thread +timer"
)
depends_on("fftw")
depends_on("hdf5 ~mpi+hl")
depends_on("lapack")
# build fails for latest python@3.7
depends_on("python@:3.6", type=("build", "link", "run"))
depends_on("py-numpy", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
# use depends_on to help with dependency resolution
depends_on("py-numpy@:1.19", when="^python@:3.6")
depends_on("py-scipy@:1.5", when="^python@:3.6")
# fix for gcc@7:
patch("alps_newgcc.patch", when="%gcc@7:")
# remove a problematic build variable
patch("mpi.patch")
# include climits to use INT_MAX
patch("alps_climit.patch")
# ctest tries to test '/usr/bin/time'
patch("alps_cmake_time.patch")
extends("python")
root_cmakelists_dir = "alps"
def cmake_args(self):
args = []
args.append("Boost_ROOT_DIR=" + self.spec["boost"].prefix)
args.append("-DCMAKE_CXX_FLAGS={0}".format(self.compiler.cxx98_flag))
return args
def _single_test(self, target, exename, dataname, opts=[]):
troot = self.prefix.tutorials
copy_tree(join_path(troot, target), target)
if target == "dmrg-01-dmrg":
test_dir = self.test_suite.current_test_data_dir
copy(join_path(test_dir, dataname), target)
self.run_test("parameter2xml", options=[dataname, "SEED=123456"], work_dir=target)
options = []
options.extend(opts)
options.extend(["--write-xml", "{0}.in.xml".format(dataname)])
self.run_test(
exename, options=options, expected=["Finished with everything."], work_dir=target
)
def test(self):
self._single_test("mc-02-susceptibilities", "spinmc", "parm2a", ["--Tmin", "10"])
self._single_test("ed-01-sparsediag", "sparsediag", "parm1a")
self._single_test("dmrg-01-dmrg", "dmrg", "spin_one_half")

9
var/spack/repos/builtin/packages/alps/test/spin_one_half
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@ -1,9 +0,0 @@
LATTICE="open chain lattice"
MODEL="spin"
CONSERVED_QUANTUMNUMBERS="N,Sz"
Sz_total=0
J=1
SWEEPS=4
NUMBER_EIGENVALUES=1
L=32
{MAXSTATES=100}

6
var/spack/repos/builtin/packages/alquimia/package.py
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@ -20,8 +20,6 @@ class Alquimia(CMakePackage):
version("1.0.9", commit="2ee3bcfacc63f685864bcac2b6868b48ad235225") # tag v.1.0.9
version("xsdk-0.6.0", commit="9a0aedd3a927d4d5e837f8fd18b74ad5a78c3821")
version("xsdk-0.5.0", commit="8397c3b00a09534c5473ff3ab21f0e32bb159380")
version("xsdk-0.4.0", commit="2edad6733106142d014bb6e6a73c2b21d5e3cf2d")
version("xsdk-0.3.0", tag="xsdk-0.3.0")
variant("shared", default=True, description="Enables the build of shared libraries")
@ -31,11 +29,7 @@ class Alquimia(CMakePackage):
depends_on("pflotran@3.0.2", when="@1.0.9")
depends_on("pflotran@xsdk-0.6.0", when="@xsdk-0.6.0")
depends_on("pflotran@xsdk-0.5.0", when="@xsdk-0.5.0")
depends_on("pflotran@xsdk-0.4.0", when="@xsdk-0.4.0")
depends_on("pflotran@xsdk-0.3.0", when="@xsdk-0.3.0")
depends_on("pflotran@develop", when="@develop")
depends_on("petsc@3.10.0:3.10", when="@xsdk-0.4.0")
depends_on("petsc@3.8.0:3.8", when="@xsdk-0.3.0")
depends_on("petsc@3.10:", when="@develop")
@when("@1.0.10")

25
var/spack/repos/builtin/packages/ambari/package.py
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@ -1,25 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Ambari(PythonPackage):
"""Apache Ambari is a tool for provisioning, managing, and monitoring
Apache Hadoop clusters. Ambari consists of a set of RESTful APIs and
a browser-based management interface."""
homepage = "https://cwiki.apache.org/confluence/display/AMBARI/Ambari"
url = "https://github.com/apache/ambari/archive/release-2.7.5.tar.gz"
version("2.7.5", sha256="f8c8687b7a61b633b92f83b1c104fd75b1e13836cd8a0e0df6db7b483b23a354")
version("2.7.4", sha256="d6796c7ea913d39c93dad52b4cb74ef411a7dce4ebf68f11b12718117f2c01a4")
version("2.7.3", sha256="30fe72e60fa6b62fe032bd193ebd0cef20b65c54b57cad92f6f44daabd3771cf")
version("2.7.1", sha256="ea4eb28f377ce9d0b9b7648f2020dda4be974c6d9a22ebaafbf1bc97890e4e42")
depends_on("python@:2.7", type=("build", "run"))
depends_on("py-setuptools@:44", type="build")
depends_on("py-mock", type="test")
depends_on("py-coilmq", type=("build", "run"))

1
var/spack/repos/builtin/packages/amdlibm/package.py
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@ -34,7 +34,6 @@ class Amdlibm(SConsPackage):
variant("verbose", default=False, description="Building with verbosity")
# Mandatory dependencies
depends_on("python@3.6.2", when="%aocc@3.2.0:", type=("build", "run"))
depends_on("python@3.6.1:", type=("build", "run"))
depends_on("scons@3.1.2:", type=("build"))
depends_on("mpfr", type=("link"))

8
var/spack/repos/builtin/packages/aomp/package.py
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@ -90,19 +90,11 @@ class Aomp(Package):
version("3.10.0", sha256=versions_dict["3.10.0"]["aomp"])
version("3.9.0", sha256=versions_dict["3.9.0"]["aomp"])
version("3.8.0", sha256=versions_dict["3.8.0"]["aomp"])
version("3.7.0", sha256=versions_dict["3.7.0"]["aomp"])
version("3.5.0", sha256=versions_dict["3.5.0"]["aomp"])
# Cmake above 3.18 would fail the build on 3.5.0
depends_on("cmake@3:", type="build")
depends_on("cmake@3:3.17", when="@3.5.0", type="build")
# Python 2 is needed for 3.5.0 and 3.8.0, limit py-setuptools
# to avoid spec error
depends_on("python@2.7:2.8", when="@3.5.0:3.8.0", type="build")
depends_on("py-setuptools@:44", when="@3.5.0:3.8.0", type="build")
depends_on("python@3:", type="build", when="@3.9.0:")
depends_on("py-setuptools", when="@3.9.0:", type="build")

15
var/spack/repos/builtin/packages/asciidoc/package.py
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@ -22,25 +22,12 @@ class Asciidoc(AutotoolsPackage):
version("9.0.3", sha256="b6ef4accd7959f51b532ab4d3aaa211e15f18fd544c4c3cc3ed712f5590a50de")
version("9.0.2", sha256="93fbe32d56380afee2f26389d8ebfdf33de72536449d53308120d3c20d2c1e17")
version("8.6.10", sha256="22d6793d4f48cefb4a6963853212a214591a591ece1bcbc56af3c67c642003ea")
version("8.6.9", sha256="45e95bed1e341980f7de0a66fdc467090956fe55d4625bdad8057cd926e0c6c6")
depends_on("libxml2", type=("build", "run"))
depends_on("libxslt", type=("build", "run"))
depends_on("docbook-xml", type=("build", "run"))
depends_on("docbook-xsl", type=("build", "run"))
depends_on("python@2.3.0:2.7", when="@:8.6.9", type=("build", "run"))
depends_on("python@3.5:", when="@9.0.2:", type=("build", "run"))
depends_on("python@3.5:", type=("build", "run"))
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
@when("@:8.6.9")
def install(self, spec, prefix):
# Old release demands python2
mpythpath = spec["python"].command.path
exes = ["asciidoc", "a2x"]
for exe in exes:
fthfile = FileFilter(exe + ".py")
fthfile.filter("#!/usr/bin/env python", "#!" + mpythpath)
make("install")

17
var/spack/repos/builtin/packages/aws-parallelcluster/enum34.patch
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@ -1,17 +0,0 @@
diff -Naur a/setup.py b/setup.py
--- a/setup.py 2020-02-06 15:40:26.000000000 -0600
+++ b/setup.py 2020-02-06 15:41:17.000000000 -0600
@@ -27,10 +27,12 @@
"future>=0.16.0,<=0.18.2",
"tabulate>=0.8.2,<=0.8.3",
"ipaddress>=1.0.22",
- "enum34>=1.1.6",
"PyYAML>=5.1.2",
]
+if sys.version_info < (3, 4):
+ REQUIRES.append("enum34>=1.1.6")
+
if sys.version_info[0] == 2:
REQUIRES.append("configparser>=3.5.0,<=3.8.1")

23
var/spack/repos/builtin/packages/aws-parallelcluster/package.py
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@ -57,23 +57,17 @@ class AwsParallelcluster(PythonPackage):
depends_on("py-ipaddress@1.0.22:", type=("build", "run"))
depends_on("py-configparser@3.5.0:3.8.1", when="^python@:2", type=("build", "run"))
depends_on("py-tabulate@0.8.3:0.8.10", when="@2.11: ^python@:2,3.5:3.9", type=("build", "run"))
depends_on("py-tabulate@0.8.3:0.8.10", when="@2.11: ^python@:3.9", type=("build", "run"))
depends_on("py-tabulate@0.8.8:0.8.10", when="@2.11: ^python@3.10:", type=("build", "run"))
depends_on("py-tabulate@0.8.2:0.8.3", when="@:2.8", type=("build", "run"))
depends_on("py-tabulate@0.8.5", when="@2.9: ^python@3.0:3.4", type=("build", "run"))
depends_on("py-tabulate@0.8.2:0.8.7", when="@2.9: ^python@:2,3.5:", type=("build", "run"))
depends_on("py-tabulate@0.8.2:0.8.7", when="@2.9:", type=("build", "run"))
depends_on("py-pyyaml@5.3.1:", when="@2.11:", type=("build", "run"))
depends_on("py-pyyaml@5.3.1:", when="@2.9:2.10 ^python@:2,3.5:", type=("build", "run"))
depends_on("py-pyyaml@5.2", when="@2.6:2.10 ^python@3.0:3.4", type=("build", "run"))
depends_on("py-pyyaml@5.1.2:", when="@2.6:2.8 ^python@:2,3.5:", type=("build", "run"))
depends_on("py-pyyaml@5.1.2:", when="@:2.5", type=("build", "run"))
depends_on("py-pyyaml@5.3.1:", when="@2.9:", type=("build", "run"))
depends_on("py-pyyaml@5.2", when="@2.6:2.10", type=("build", "run"))
depends_on("py-pyyaml@5.1.2:", when="@:2.8", type=("build", "run"))
depends_on("py-jinja2@2.11.3:", when="@2.11:", type=("build", "run"))
depends_on("py-jinja2@2.10.1", when="@2.9: ^python@3.0:3.4", type=("build", "run"))
depends_on("py-jinja2@2.11.0:", when="@2.9: ^python@:2,3.5:", type=("build", "run"))
depends_on("py-jinja2@2.11.0:", when="@2.9:", type=("build", "run"))
depends_on("py-boto3@1.17.27:", when="@2.11:", type=("build", "run"))
depends_on("py-boto3@1.16.14:", when="@2.10:", type=("build", "run"))
@ -82,11 +76,6 @@ class AwsParallelcluster(PythonPackage):
depends_on("py-setuptools", type=("build", "run"))
depends_on("py-enum34@1.1.6:", when="^python@:3.3", type=("build", "run"))
# https://github.com/aws/aws-parallelcluster/pull/1633
patch("enum34.patch", when="@:2.5.1")
@run_after("install")
@on_package_attributes(run_tests=True)
def install_test(self):

7
var/spack/repos/builtin/packages/awscli/package.py
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@ -22,10 +22,7 @@ class Awscli(PythonPackage):
depends_on("py-docutils@0.10:0.15", type=("build", "run"))
depends_on("py-rsa@3.1.2:3.5.0", type=("build", "run"))
depends_on("py-s3transfer@0.2.0:0.2", type=("build", "run"))
depends_on("py-argparse@1.1:", when="^python@:2.6,3.0:3.1", type=("build", "run"))
depends_on("py-pyyaml@3.10:3.13", when="^python@:2.6,3.0:3.3", type=("build", "run"))
depends_on("py-pyyaml@3.10:5.2", when="^python@3.4:", type=("build", "run"))
depends_on("py-colorama@0.2.5:0.3.9", when="^python@:2.6,3.0:3.3", type=("build", "run"))
depends_on("py-colorama@0.2.5:0.4.1", when="^python@3.4:", type=("build", "run"))
depends_on("py-pyyaml@3.10:5.2", type=("build", "run"))
depends_on("py-colorama@0.2.5:0.4.1", type=("build", "run"))
depends_on("py-nose", type="test")
depends_on("py-mock@1.3.0:", type="test")

6
var/spack/repos/builtin/packages/berkeleygw/package.py
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@ -37,7 +37,6 @@ class Berkeleygw(MakefilePackage):
variant("mpi", default=True, description="Builds with MPI support")
variant("elpa", default=True, description="Build with ELPA support")
variant("python", default=False, description="Build with Python support")
variant("openmp", default=True, description="Build with OpenMP support")
variant("scalapack", default=True, description="Build with ScaLAPACK support")
variant("hdf5", default=True, description="Builds with HDF5 support")
@ -56,11 +55,6 @@ class Berkeleygw(MakefilePackage):
depends_on("fftw-api@3+openmp", when="+openmp")
depends_on("fftw-api@3~openmp", when="~openmp")
depends_on("python@:2", type=("build", "run"), when="+python")
depends_on("py-numpy@:1.16", type=("build", "run"), when="+python")
depends_on("py-setuptools@:44", type=("build", "run"), when="+python")
depends_on("py-h5py@:2", type=("build", "run"), when="+hdf5+python")
depends_on("perl", type="test")
conflicts(

3
var/spack/repos/builtin/packages/bigdft-atlab/package.py
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@ -17,7 +17,6 @@ class BigdftAtlab(AutotoolsPackage):
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
version("1.8.3", sha256="f112bb08833da4d11dd0f14f7ab10d740b62bc924806d77c985eb04ae0629909")
variant("mpi", default=True, description="Enable MPI support")
variant("openmp", default=True, description="Enable OpenMP support")
@ -26,7 +25,7 @@ class BigdftAtlab(AutotoolsPackage):
depends_on("mpi", when="+mpi")
depends_on("openbabel", when="+openbabel")
for vers in ["1.8.1", "1.8.2", "1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-futile@{0}".format(vers), when="@{0}".format(vers))
build_directory = "atlab"

13
var/spack/repos/builtin/packages/bigdft-chess/package.py
View file

@ -18,9 +18,6 @@ class BigdftChess(AutotoolsPackage, CudaPackage):
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
version("1.8.3", sha256="f112bb08833da4d11dd0f14f7ab10d740b62bc924806d77c985eb04ae0629909")
version("1.8.2", sha256="042e5a3b478b1a4c050c450a9b1be7bcf8e13eacbce4759b7f2d79268b298d61")
version("1.8.1", sha256="e09ff0ba381f6ffbe6a3c0cb71db5b73117874beb41f22a982a7e5ba32d018b3")
variant("mpi", default=True, description="Enable MPI support")
variant("openmp", default=True, description="Enable OpenMP support")
@ -28,9 +25,7 @@ class BigdftChess(AutotoolsPackage, CudaPackage):
variant("ntpoly", default=False, description="Option to use NTPoly")
# variant('minpack', default=False, description='Give the link-line for MINPACK')
depends_on("python@:2.8", type=("build", "run"), when="@:1.8.3")
depends_on("python@3.0:", type=("build", "run"), when="@1.9.0:")
depends_on("python@3.0:", type=("build", "run"), when="@develop")
depends_on("python@3.0:", type=("build", "run"))
depends_on("blas")
depends_on("lapack")
@ -40,9 +35,8 @@ class BigdftChess(AutotoolsPackage, CudaPackage):
depends_on("ntpoly", when="+ntpoly")
# depends_on('netlib-minpack', when='+minpack')
for vers in ["1.8.1", "1.8.2", "1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-futile@{0}".format(vers), when="@{0}".format(vers))
for vers in ["1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-atlab@{0}".format(vers), when="@{0}".format(vers))
build_directory = "chess"
@ -93,8 +87,7 @@ def configure_args(self):
else:
args.append("--without-openmp")
if spec.satisfies("@1.8.3:") or spec.satisfies("@develop"):
args.append("--with-atlab-libs=%s" % spec["bigdft-atlab"].prefix.lib)
args.append("--with-atlab-libs=%s" % spec["bigdft-atlab"].prefix.lib)
if "+cuda" in spec:
args.append("--enable-cuda-gpu")

9
var/spack/repos/builtin/packages/bigdft-core/package.py
View file

@ -18,18 +18,13 @@ class BigdftCore(AutotoolsPackage, CudaPackage):
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
version("1.8.3", sha256="f112bb08833da4d11dd0f14f7ab10d740b62bc924806d77c985eb04ae0629909")
version("1.8.2", sha256="042e5a3b478b1a4c050c450a9b1be7bcf8e13eacbce4759b7f2d79268b298d61")
version("1.8.1", sha256="e09ff0ba381f6ffbe6a3c0cb71db5b73117874beb41f22a982a7e5ba32d018b3")
variant("mpi", default=True, description="Enable MPI support")
variant("openmp", default=True, description="Enable OpenMP support")
variant("scalapack", default=True, description="Enable SCALAPACK support")
variant("openbabel", default=False, description="Enable detection of openbabel compilation")
depends_on("python@:2.8", type=("build", "run"), when="@:1.8.3")
depends_on("python@3.0:", type=("build", "run"), when="@1.9.0:")
depends_on("python@3.0:", type=("build", "run"), when="@develop")
depends_on("python@3.0:", type=("build", "run"))
depends_on("blas")
depends_on("lapack")
@ -42,7 +37,7 @@ class BigdftCore(AutotoolsPackage, CudaPackage):
depends_on("libxc@:4.3.4", when="@1.9.2:")
depends_on("libxc@:4.3.4", when="@develop")
for vers in ["1.8.1", "1.8.2", "1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-futile@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-chess@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-psolver@{0}".format(vers), when="@{0}".format(vers))

7
var/spack/repos/builtin/packages/bigdft-futile/package.py
View file

@ -21,16 +21,11 @@ class BigdftFutile(AutotoolsPackage, CudaPackage):
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
version("1.8.3", sha256="f112bb08833da4d11dd0f14f7ab10d740b62bc924806d77c985eb04ae0629909")
version("1.8.2", sha256="042e5a3b478b1a4c050c450a9b1be7bcf8e13eacbce4759b7f2d79268b298d61")
version("1.8.1", sha256="e09ff0ba381f6ffbe6a3c0cb71db5b73117874beb41f22a982a7e5ba32d018b3")
variant("mpi", default=True, description="Enable MPI support")
variant("openmp", default=True, description="Enable OpenMP support")
depends_on("python@:2.8", type=("build", "run"), when="@:1.8.3")
depends_on("python@3.0:", type=("build", "run"), when="@1.9.0:")
depends_on("python@3.0:", type=("build", "run"), when="@develop")
depends_on("python@3.0:", type=("build", "run"))
depends_on("blas")
depends_on("lapack")

222
var/spack/repos/builtin/packages/bigdft-libabinit/m_libpaw_mpi.F90.patch
View file

@ -1,222 +0,0 @@
--- a/libABINIT/src/libpaw/m_libpaw_mpi.F90
+++ b/libABINIT/src/libpaw/m_libpaw_mpi.F90
@@ -54,6 +54,24 @@
integer,public,parameter :: xpaw_mpi_comm_null = 0
#endif
+ type xpaw_mpi_attr
+ integer :: attr_data
+ end type
+
+ interface xpaw_mpi_attr
+ module procedure new_xpaw_mpi_attr
+ end interface
+
+ interface mod
+ module procedure mod_xpaw_mpi_attr
+ end interface
+
+#ifdef HAVE_MPI
+ type(xpaw_mpi_attr),public,parameter :: xpaw_mpi_tag_ub = xpaw_mpi_attr(MPI_TAG_UB)
+#else
+ integer,public,parameter :: xpaw_mpi_tag_ub = 1
+#endif
+
!----------------------------------------------------------------------
!MPI public procedures.
@@ -180,6 +198,32 @@
CONTAINS !===========================================================
!!***
+function new_xpaw_mpi_attr(key_val)
+ type(xpaw_mpi_attr) :: new_xpaw_mpi_attr
+ integer, intent(in) :: key_val
+!Local variables-------------------
+ integer :: mpierr
+#ifdef HAVE_MPI
+ integer :: attribute_val
+ logical :: lflag
+#endif
+
+ ! Deprecated in MPI2 but not all MPI2 implementations provide MPI_Comm_get_attr !
+ call MPI_ATTR_GET(xpaw_mpi_world, key_val, attribute_val, lflag, mpierr)
+ !call MPI_Comm_get_attr(xpaw_mpi_world, key_val, attribute_val, lflag, mpierr)
+
+ if (lflag) new_xpaw_mpi_attr%attr_data = attribute_val
+end function
+
+
+function mod_xpaw_mpi_attr(a, p)
+ integer :: mod_xpaw_mpi_attr
+ integer, intent(in) :: a
+ type(xpaw_mpi_attr), intent(in) :: p
+
+ mod_xpaw_mpi_attr = mod(a, p%attr_data)
+end function
+
!!****f* m_libpaw_mpi/xpaw_mpi_abort
!! NAME
!! xpaw_mpi_abort
@@ -2297,7 +2341,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1)
- my_tag = MOD(tag,MPI_TAG_UB)
+ my_tag = MOD(tag,xpaw_mpi_tag_ub)
call MPI_RECV(xval,n1,MPI_INTEGER,source,my_tag,spaceComm,MPI_STATUS_IGNORE,ier)
end if
#endif
@@ -2358,7 +2402,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1)
- my_tag = MOD(tag,MPI_TAG_UB)
+ my_tag = MOD(tag,xpaw_mpi_tag_ub)
call MPI_RECV(xval,n1,MPI_DOUBLE_PRECISION,source,my_tag,spaceComm,MPI_STATUS_IGNORE,ier)
end if
#endif
@@ -2419,7 +2463,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1) ; n2=size(xval,dim=2)
- my_tag=MOD(tag,MPI_TAG_UB)
+ my_tag=MOD(tag,xpaw_mpi_tag_ub)
call MPI_RECV(xval,n1*n2,MPI_DOUBLE_PRECISION,source,my_tag,spaceComm,MPI_STATUS_IGNORE,ier)
end if
#endif
@@ -2480,7 +2524,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1) ; n2=size(xval,dim=2) ; n3=size(xval,dim=3)
- my_tag=MOD(tag,MPI_TAG_UB)
+ my_tag=MOD(tag,xpaw_mpi_tag_ub)
call MPI_RECV(xval,n1*n2*n3,MPI_DOUBLE_PRECISION,source,my_tag,spaceComm,MPI_STATUS_IGNORE,ier)
end if
#endif
@@ -2541,7 +2585,7 @@
ierr=0
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
- my_tag=MOD(tag,MPI_TAG_UB)
+ my_tag=MOD(tag,xpaw_mpi_tag_ub)
n1=size(xval)
call MPI_IRECV(xval,n1,MPI_INTEGER,source,my_tag,spaceComm,request,ier)
ierr=ier
@@ -2604,7 +2648,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1)
- my_tag=MOD(tag,MPI_TAG_UB)
+ my_tag=MOD(tag,xpaw_mpi_tag_ub)
call MPI_IRECV(xval,n1,MPI_DOUBLE_PRECISION,source,my_tag,spaceComm,request,ier)
ierr=ier
end if
@@ -2666,7 +2710,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1);n2=size(xval,dim=2)
- my_tag=MOD(tag,MPI_TAG_UB)
+ my_tag=MOD(tag,xpaw_mpi_tag_ub)
call MPI_IRECV(xval,n1*n2,MPI_DOUBLE_PRECISION,source,my_tag,spaceComm,request,ier)
ierr=ier
end if
@@ -2727,7 +2771,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1)
- my_tag = MOD(tag,MPI_TAG_UB)
+ my_tag = MOD(tag,xpaw_mpi_tag_ub)
call MPI_SEND(xval,n1,MPI_INTEGER,dest,my_tag,spaceComm,ier)
end if
#endif
@@ -2785,7 +2829,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1)
- my_tag = MOD(tag,MPI_TAG_UB)
+ my_tag = MOD(tag,xpaw_mpi_tag_ub)
call MPI_SEND(xval,n1,MPI_DOUBLE_PRECISION,dest,my_tag,spaceComm,ier)
end if
#endif
@@ -2843,7 +2887,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1) ; n2=size(xval,dim=2)
- my_tag = MOD(tag,MPI_TAG_UB)
+ my_tag = MOD(tag,xpaw_mpi_tag_ub)
call MPI_SEND(xval,n1*n2,MPI_DOUBLE_PRECISION,dest,my_tag,spaceComm,ier)
end if
#endif
@@ -2901,7 +2945,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1) ; n2=size(xval,dim=2) ; n3=size(xval,dim=3)
- my_tag = MOD(tag,MPI_TAG_UB)
+ my_tag = MOD(tag,xpaw_mpi_tag_ub)
call MPI_SEND(xval,n1*n2*n3,MPI_DOUBLE_PRECISION,dest,my_tag,spaceComm,ier)
end if
#endif
@@ -2961,7 +3005,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1)
- my_tag = MOD(tag,MPI_TAG_UB)
+ my_tag = MOD(tag,xpaw_mpi_tag_ub)
call MPI_ISEND(xval,n1,MPI_INTEGER,dest,my_tag,spaceComm,request,ier)
ierr=ier
end if
@@ -3020,7 +3064,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1)
- my_tag = MOD(tag,MPI_TAG_UB)
+ my_tag = MOD(tag,xpaw_mpi_tag_ub)
call MPI_ISEND(xval,n1,MPI_DOUBLE_PRECISION,dest,my_tag,spaceComm,request,ier)
ierr=ier
end if
@@ -3079,7 +3123,7 @@
#if defined HAVE_MPI
if (spaceComm /= xpaw_mpi_comm_self .and. spaceComm /= xpaw_mpi_comm_null) then
n1=size(xval,dim=1) ; n1=size(xval,dim=2)
- my_tag = MOD(tag,MPI_TAG_UB)
+ my_tag = MOD(tag,xpaw_mpi_tag_ub)
call MPI_ISEND(xval,n1*n2,MPI_DOUBLE_PRECISION,dest,my_tag,spaceComm,request,ier)
ierr=ier
end if
@@ -3145,7 +3189,7 @@
#if defined HAVE_MPI
if (sender==recever.or.spaceComm==xpaw_mpi_comm_null.or.(n1==0)) return
call MPI_COMM_RANK(spaceComm,me,ier)
- tag = MOD(n1,MPI_TAG_UB)
+ tag = MOD(n1,xpaw_mpi_tag_ub)
if (recever==me) then
call MPI_RECV(vrecv,n1,MPI_INTEGER,sender,tag,spaceComm,status,ier)
end if
@@ -3212,7 +3256,7 @@
#if defined HAVE_MPI
if (sender==recever.or.spaceComm==xpaw_mpi_comm_null.or.(n1==0)) return
call MPI_COMM_RANK(spaceComm,me,ier)
- tag = MOD(n1,MPI_TAG_UB)
+ tag = MOD(n1,xpaw_mpi_tag_ub)
if (recever==me) then
call MPI_RECV(vrecv,n1,MPI_DOUBLE_PRECISION,sender,tag,spaceComm,status,ier)
end if
@@ -3279,7 +3323,7 @@
#if defined HAVE_MPI
if (sender==recever.or.spaceComm==xpaw_mpi_comm_null.or.(nt==0)) return
call MPI_COMM_RANK(spaceComm,me,ier)
- tag=MOD(nt,MPI_TAG_UB)
+ tag=MOD(nt,xpaw_mpi_tag_ub)
if (recever==me) then
call MPI_RECV(vrecv,nt,MPI_DOUBLE_PRECISION,sender,tag,spaceComm,status,ier)
end if
@@ -3346,7 +3390,7 @@
#if defined HAVE_MPI
if (sender==recever.or.spaceComm==xpaw_mpi_comm_null.or.(nt==0)) return
call MPI_COMM_RANK(spaceComm,me,ier)
- tag=MOD(nt,MPI_TAG_UB)
+ tag=MOD(nt,xpaw_mpi_tag_ub)
if (recever==me) then
call MPI_RECV(vrecv,nt,MPI_DOUBLE_PRECISION,sender,tag,spaceComm,status,ier)
end if

17
var/spack/repos/builtin/packages/bigdft-libabinit/package.py
View file

@ -20,36 +20,25 @@ class BigdftLibabinit(AutotoolsPackage):
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
version("1.8.3", sha256="f112bb08833da4d11dd0f14f7ab10d740b62bc924806d77c985eb04ae0629909")
version("1.8.2", sha256="042e5a3b478b1a4c050c450a9b1be7bcf8e13eacbce4759b7f2d79268b298d61")
version("1.8.1", sha256="e09ff0ba381f6ffbe6a3c0cb71db5b73117874beb41f22a982a7e5ba32d018b3")
variant("mpi", default=True, description="Enable MPI support")
depends_on("python@:2.8", type=("build", "run"), when="@:1.8.3")
depends_on("python@3.0:", type=("build", "run"), when="@1.9.0:")
depends_on("python@3.0:", type=("build", "run"), when="@develop")
depends_on("python@3.0:", type=("build", "run"))
depends_on("mpi", when="+mpi")
depends_on("libxc@:2.2.2", when="@:1.9.1")
depends_on("libxc@:4.3.4", when="@1.9.1:")
depends_on("libxc@:4.3.4", when="@develop")
for vers in ["1.8.1", "1.8.2", "1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-futile@{0}".format(vers), when="@{0}".format(vers))
patch("m_libpaw_mpi.F90.patch", when="@:1.8.2")
build_directory = "libABINIT"
def autoreconf(self, spec, prefix):
autoreconf = which("autoreconf")
with working_dir(self.build_directory):
if spec.satisfies("@:1.8.2"):
autoreconf("-i")
else:
autoreconf("-fi")
autoreconf("-fi")
def configure_args(self):
spec = self.spec

13
var/spack/repos/builtin/packages/bigdft-psolver/package.py
View file

@ -19,17 +19,12 @@ class BigdftPsolver(AutotoolsPackage, CudaPackage):
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
version("1.8.3", sha256="f112bb08833da4d11dd0f14f7ab10d740b62bc924806d77c985eb04ae0629909")
version("1.8.2", sha256="042e5a3b478b1a4c050c450a9b1be7bcf8e13eacbce4759b7f2d79268b298d61")
version("1.8.1", sha256="e09ff0ba381f6ffbe6a3c0cb71db5b73117874beb41f22a982a7e5ba32d018b3")
variant("mpi", default=True, description="Enable MPI support")
variant("openmp", default=True, description="Enable OpenMP support")
variant("scalapack", default=True, description="Enable SCALAPACK support")
depends_on("python@:2.8", type=("build", "run"), when="@:1.8.3")
depends_on("python@3.0:", type=("build", "run"), when="@1.9.0:")
depends_on("python@3.0:", type=("build", "run"), when="@develop")
depends_on("python@3.0:", type=("build", "run"))
depends_on("blas")
depends_on("lapack")
@ -37,9 +32,8 @@ class BigdftPsolver(AutotoolsPackage, CudaPackage):
depends_on("mpi", when="+mpi")
depends_on("scalapack", when="+scalapack")
for vers in ["1.8.1", "1.8.2", "1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-futile@{0}".format(vers), when="@{0}".format(vers))
for vers in ["1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-atlab@{0}".format(vers), when="@{0}".format(vers))
build_directory = "psolver"
@ -92,8 +86,7 @@ def configure_args(self):
else:
args.append("--without-openmp")
if spec.satisfies("@1.8.3:") or spec.satisfies("@develop"):
args.append("--with-atlab-libs=%s" % spec["bigdft-atlab"].prefix.lib)
args.append("--with-atlab-libs=%s" % spec["bigdft-atlab"].prefix.lib)
if "+cuda" in spec:
args.append("--enable-cuda-gpu")

9
var/spack/repos/builtin/packages/bigdft-spred/package.py
View file

@ -18,17 +18,12 @@ class BigdftSpred(AutotoolsPackage):
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
version("1.8.3", sha256="f112bb08833da4d11dd0f14f7ab10d740b62bc924806d77c985eb04ae0629909")
version("1.8.2", sha256="042e5a3b478b1a4c050c450a9b1be7bcf8e13eacbce4759b7f2d79268b298d61")
version("1.8.1", sha256="e09ff0ba381f6ffbe6a3c0cb71db5b73117874beb41f22a982a7e5ba32d018b3")
variant("mpi", default=True, description="Enable MPI support")
variant("openmp", default=True, description="Enable OpenMP support")
variant("scalapack", default=True, description="Enable SCALAPACK support")
depends_on("python@:2.8", type=("build", "run"), when="@:1.8.3")
depends_on("python@3.0:", type=("build", "run"), when="@1.9.0:")
depends_on("python@3.0:", type=("build", "run"), when="@develop")
depends_on("python@3.0:", type=("build", "run"))
depends_on("blas")
depends_on("lapack")
@ -36,7 +31,7 @@ class BigdftSpred(AutotoolsPackage):
depends_on("mpi", when="+mpi")
depends_on("scalapack", when="+scalapack")
for vers in ["1.8.1", "1.8.2", "1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-futile@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-psolver@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-core@{0}".format(vers), when="@{0}".format(vers))

11
var/spack/repos/builtin/packages/bigdft-suite/package.py
View file

@ -18,22 +18,15 @@ class BigdftSuite(BundlePackage):
version("1.9.2", sha256="dc9e49b68f122a9886fa0ef09970f62e7ba21bb9ab1b86be9b7d7e22ed8fbe0f")
version("1.9.1", sha256="3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41")
version("1.9.0", sha256="4500e505f5a29d213f678a91d00a10fef9dc00860ea4b3edf9280f33ed0d1ac8")
version("1.8.3", sha256="f112bb08833da4d11dd0f14f7ab10d740b62bc924806d77c985eb04ae0629909")
version("1.8.2", sha256="042e5a3b478b1a4c050c450a9b1be7bcf8e13eacbce4759b7f2d79268b298d61")
version("1.8.1", sha256="e09ff0ba381f6ffbe6a3c0cb71db5b73117874beb41f22a982a7e5ba32d018b3")
depends_on("python@:2.8", type=("run"), when="@:1.8.3")
depends_on("python@3.0:", type=("run"), when="@1.9.0:")
depends_on("python@3.0:", type=("run"), when="@develop")
depends_on("python@3.0:", type=("run"))
for vers in ["1.8.1", "1.8.2", "1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-futile@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-psolver@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-libabinit@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-chess@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-core@{0}".format(vers), when="@{0}".format(vers))
depends_on("bigdft-spred@{0}".format(vers), when="@{0}".format(vers))
for vers in ["1.8.3", "1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("bigdft-atlab@{0}".format(vers), when="@{0}".format(vers))
for vers in ["1.9.0", "1.9.1", "1.9.2", "develop"]:
depends_on("py-bigdft@{0}".format(vers), when="@{0}".format(vers))

59
var/spack/repos/builtin/packages/blasr-libcpp/package.py
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@ -1,59 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack.package import *
class BlasrLibcpp(Package):
"""Blasr_libcpp is a library used by blasr
and other executables such as samtoh5,
loadPulses for analyzing PacBio sequences."""
homepage = "https://github.com/PacificBiosciences/blasr_libcpp"
url = "https://github.com/PacificBiosciences/blasr_libcpp/archive/5.3.1.tar.gz"
maintainers = ["robqiao"]
version("5.3.1", sha256="45a673255bfe7e29ed1f5bdb6410aa45cb6b907400d038c3da9daf1058b09156")
depends_on("pbbam")
depends_on("hdf5+cxx@1.8.12:1.8")
# maximum version is 1.8.20 currently. There doesn't appear to be a
# major version 1.9 and the 1.10.1 version doesn't build correctly.
# https://github.com/PacificBiosciences/blasr/issues/355
depends_on("python@2.7:2.8", type="build")
@run_before("install")
def configure(self, spec, prefix):
configure_args = [
"PBBAM_INC={0}".format(self.spec["pbbam"].prefix.include),
"PBBAM_LIB={0}".format(self.spec["pbbam"].prefix.lib),
"HDF5_INC={0}".format(self.spec["hdf5"].prefix.include),
"HDF5_LIB={0}".format(self.spec["hdf5"].prefix.lib),
]
python("configure.py", *configure_args)
@run_before("install")
def build(self, spec, prefix):
os.environ["CPLUS_INCLUDE_PATH"] = self.stage.source_path
make()
def install(self, spec, prefix):
install_tree("alignment", prefix.alignment)
install_tree("hdf", prefix.hdf)
install_tree("pbdata", prefix.pbdata)
def setup_dependent_build_environment(self, env, dependent_spec):
env.prepend_path("LD_LIBRARY_PATH", self.spec.prefix.hdf)
env.prepend_path("LD_LIBRARY_PATH", self.spec.prefix.alignment)
env.prepend_path("LD_LIBRARY_PATH", self.spec.prefix.pbdata)
def setup_run_environment(self, env):
env.prepend_path("LD_LIBRARY_PATH", self.spec["blasr-libcpp"].prefix.pbdata)
env.prepend_path("LD_LIBRARY_PATH", self.spec["blasr-libcpp"].prefix.alignment)
env.prepend_path("LD_LIBRARY_PATH", self.spec["blasr-libcpp"].prefix.hdf)

78
var/spack/repos/builtin/packages/blasr/package.py
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@ -1,78 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack.package import *
from spack.pkg.builtin.boost import Boost
class Blasr(Package):
"""The PacBio long read aligner."""
homepage = "https://github.com/PacificBiosciences/blasr/wiki"
url = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz"
version("5.3.1", sha256="ff7da5a03096294572e6c64340354da5c5ee1c86c277e7b899f2c170c1ac4049")
depends_on("ncurses")
depends_on("hdf5+cxx@1.8.12:1.8")
depends_on("htslib")
depends_on("zlib")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
depends_on("pbbam")
depends_on("blasr-libcpp")
depends_on("python", type="build")
def setup_build_environment(self, env):
env.prepend_path("CPATH", self.spec["blasr-libcpp"].prefix)
env.prepend_path("CPATH", self.spec["blasr-libcpp"].prefix.pbdata)
env.prepend_path("CPATH", self.spec["blasr-libcpp"].prefix.alignment)
env.prepend_path("CPATH", self.spec["blasr-libcpp"].prefix.hdf)
# hdf has +mpi by default, so handle that possibility
if "+mpi" in self.spec["hdf5"]:
env.set("CC", self.spec["mpi"].mpicc)
env.set("CXX", self.spec["mpi"].mpicxx)
def setup_run_environment(self, env):
env.prepend_path("PATH", self.spec.prefix.utils)
@run_before("install")
def configure(self, spec, prefix):
configure_args = [
"LIBPBDATA_INC={0}".format(self.spec["blasr-libcpp"].prefix),
"LIBPBDATA_LIB={0}".format(self.spec["blasr-libcpp"].prefix.pbdata),
"LIBBLASR_LIB={0}".format(self.spec["blasr-libcpp"].prefix.alignment),
"LIBBLASR_INC={0}".format(self.spec["blasr-libcpp"].prefix),
"LIBPBIHDF_INC={0}".format(self.spec["blasr-libcpp"].prefix),
"LIBPBIHDF_LIB={0}".format(self.spec["blasr-libcpp"].prefix.hdf),
"HDF5_INC={0}".format(self.spec["hdf5"].prefix.include),
"HDF5_LIB={0}".format(self.spec["hdf5"].prefix.lib),
"--shared",
]
python("configure.py", *configure_args)
@run_before("install")
def build(self, spec, prefix):
os.environ["CPLUS_INCLUDE_PATH"] = join_path(self.stage.source_path, "include")
make()
def install(self, spec, prefix):
mkdir(prefix.utils)
mkdir(prefix.bin)
install("blasr", prefix.bin.blasr)
install("utils/loadPulses", prefix.utils)
install("utils/pls2fasta", prefix.utils)
install("utils/samFilter", prefix.utils)
install("utils/samtoh5", prefix.utils)
install("utils/samtom4", prefix.utils)
install("utils/sawriter", prefix.utils)
install("utils/sdpMatcher", prefix.utils)
install("utils/toAfg", prefix.utils)

5
var/spack/repos/builtin/packages/blitz/package.py
View file

@ -13,11 +13,8 @@ class Blitz(AutotoolsPackage):
url = "https://github.com/blitzpp/blitz/archive/1.0.2.tar.gz"
version("1.0.2", sha256="500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2")
version("1.0.1", sha256="b62fc3f07b64b264307b01fec5e4f2793e09a68dcb5378984aedbc2e4b3adcef")
version("1.0.0", sha256="79c06ea9a0585ba0e290c8140300e3ad19491c45c1d90feb52819abc3b58a0c1")
depends_on("python@:2.7", type="build", when="@:1.0.1")
depends_on("python@3:", type="build", when="@1.0.2:")
depends_on("python@3:", type="build")
build_targets = ["lib"]

2
var/spack/repos/builtin/packages/cantera/package.py
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@ -45,8 +45,6 @@ class Cantera(SConsPackage):
depends_on("py-numpy", when="+python", type=("build", "run"))
depends_on("py-scipy", when="+python", type=("build", "run"))
depends_on("py-3to2", when="+python", type=("build", "run"))
depends_on("py-unittest2", when="+python^python@2.6.0:2.6", type=("build", "run"))
depends_on("py-unittest2py3k", when="+python^python@3.1.0:3.1", type=("build", "run"))
# Matlab toolbox dependencies
extends("matlab", when="+matlab")

68
var/spack/repos/builtin/packages/catalyst/package.py
View file

@ -21,26 +21,13 @@ class Catalyst(CMakePackage):
"""
homepage = "http://www.paraview.org"
url = "https://www.paraview.org/files/v5.5/ParaView-v5.5.2.tar.gz"
_urlfmt_gz = "https://www.paraview.org/files/v{0}/ParaView-v{1}{2}.tar.gz"
_urlfmt_xz = "https://www.paraview.org/files/v{0}/ParaView-v{1}{2}.tar.xz"
url = "https://www.paraview.org/files/v5.6/ParaView-v5.6.0.tar.xz"
maintainers = ["chuckatkins", "danlipsa"]
version("5.6.0", sha256="5b49cb96ab78eee0427e25200530ac892f9a3da7725109ce1790f8010cb5b377")
version("5.5.2", sha256="64561f34c4402b88f3cb20a956842394dde5838efd7ebb301157a837114a0e2d")
version("5.5.1", sha256="a6e67a95a7a5711a2b5f95f38ccbff4912262b3e1b1af7d6b9afe8185aa85c0d")
version("5.5.0", sha256="1b619e326ff574de808732ca9a7447e4cd14e94ae6568f55b6581896cd569dff")
version("5.4.1", sha256="390d0f5dc66bf432e202a39b1f34193af4bf8aad2355338fa5e2778ea07a80e4")
version("5.4.0", sha256="f488d84a53b1286d2ee1967e386626c8ad05a6fe4e6cbdaa8d5e042f519f94a9")
version("5.3.0", sha256="046631bbf00775edc927314a3db207509666c9c6aadc7079e5159440fd2f88a0")
version("5.2.0", sha256="894e42ef8475bb49e4e7e64f4ee2c37c714facd18bfbb1d6de7f69676b062c96")
version("5.1.2", sha256="ff02b7307a256b7c6e8ad900dee5796297494df7f9a0804fe801eb2f66e6a187")
version("5.0.1", sha256="caddec83ec284162a2cbc46877b0e5a9d2cca59fb4ab0ea35b0948d2492950bb")
version("4.4.0", sha256="c2dc334a89df24ce5233b81b74740fc9f10bc181cd604109fd13f6ad2381fc73")
variant("python", default=False, description="Enable Python support")
variant("python3", default=False, description="Enable Python3 support")
variant("essentials", default=False, description="Enable Essentials support")
variant("extras", default=False, description="Enable Extras support. Implies Essentials.")
variant(
@ -51,61 +38,24 @@ class Catalyst(CMakePackage):
variant("osmesa", default=True, description="Use offscreen rendering")
conflicts("+osmesa", when="~rendering")
conflicts("+python", when="+python3")
conflicts("+python", when="@5.6:")
conflicts("+python3", when="@:5.5")
# Workaround for
# adding the following to your packages.yaml
# packages:
# python:
# version: [3, 2]
# without this you'll get:
# paraview requires python version 3:, but spec asked for 2.7.16
# for `spack spec paraview+python`
# see spack pull request #11539
# extends('python', when='+python')
extends("python", when="+python")
extends("python", when="+python3")
# VTK < 8.2.1 can't handle Python 3.8
# This affects Paraview <= 5.7 (VTK 8.2.0)
# https://gitlab.kitware.com/vtk/vtk/-/issues/17670
depends_on("python@3:3.7", when="@:5.7 +python3", type=("build", "run"))
depends_on("python@3:", when="@5.8:+python3", type=("build", "run"))
depends_on("python@2.7:2.8", when="+python", type=("build", "link", "run"))
depends_on("python@3:3.7", when="@:5.7 +python", type=("build", "run"))
depends_on("python@3:", when="@5.8:+python", type=("build", "run"))
depends_on("git", type="build")
depends_on("mpi")
depends_on("py-numpy", when="+python", type=("build", "run"))
depends_on("py-numpy", when="+python3", type=("build", "run"))
depends_on("py-mpi4py", when="+python", type=("build", "run"))
depends_on("py-mpi4py", when="+python3", type=("build", "run"))
depends_on("gl@3.2:", when="+rendering")
depends_on("osmesa", when="+osmesa")
depends_on("glx", when="~osmesa")
depends_on("cmake@3.3:", type="build")
@when("@5.5.0:5.5.2")
def patch(self):
"""Apply the patch (it should be fixed in Paraview 5.6)
at the package dir to the source code in
root_cmakelists_dir."""
patch_name = "vtkm-catalyst-pv551.patch"
patch = which("patch", required=True)
with working_dir(self.root_cmakelists_dir):
patch("-s", "-p", "1", "-i", join_path(self.package_dir, patch_name), "-d", ".")
def url_for_version(self, version):
"""Handle ParaView version-based custom URLs."""
if version < Version("5.1.0"):
return self._urlfmt_gz.format(version.up_to(2), version, "-source")
elif version < Version("5.6.0"):
return self._urlfmt_gz.format(version.up_to(2), version, "")
else:
return self._urlfmt_xz.format(version.up_to(2), version, "")
@property
def paraview_subdir(self):
"""The paraview subdirectory name as paraview-major.minor"""
@ -116,7 +66,7 @@ def editions(self):
"""Transcribe spack variants into names of Catalyst Editions"""
selected = ["Base"] # Always required
if "+python" in self.spec or "+python3" in self.spec:
if "+python" in self.spec:
selected.append("Enable-Python")
if "+essentials" in self.spec:
@ -144,9 +94,7 @@ def do_stage(self, mirror_only=False):
catalyst_source_dir = os.path.abspath(self.root_cmakelists_dir)
python_path = os.path.realpath(
self.spec["python"].command.path
if ("+python3" in self.spec or "+python" in self.spec)
else sys.executable
self.spec["python"].command.path if "+python" in self.spec else sys.executable
)
command = [
@ -178,13 +126,11 @@ def setup_run_environment(self, env):
else:
lib_dir = self.prefix.lib
if self.spec.version <= Version("5.4.1"):
lib_dir = join_path(lib_dir, paraview_subdir)
env.set("ParaView_DIR", self.prefix)
env.prepend_path("LIBRARY_PATH", lib_dir)
env.prepend_path("LD_LIBRARY_PATH", lib_dir)
if "+python" in self.spec or "+python3" in self.spec:
if "+python" in self.spec:
python_version = self.spec["python"].version.up_to(2)
env.prepend_path(
"PYTHONPATH",
@ -234,7 +180,7 @@ def nvariant_bool(feature):
"-DVTK_USE_OFFSCREEN:BOOL=%s" % variant_bool("+osmesa"),
"-DVTK_OPENGL_HAS_OSMESA:BOOL=%s" % variant_bool("+osmesa"),
]
if "+python" in spec or "+python3" in spec:
if "+python" in spec:
cmake_args.extend(
[
"-DPARAVIEW_ENABLE_PYTHON:BOOL=ON",

14
var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py
View file

@ -18,7 +18,6 @@ class CbtfArgonavisGui(QMakePackage):
git = "https://github.com/OpenSpeedShop/cbtf-argonavis-gui.git"
version("develop", branch="master")
version("1.3.0.0", branch="1.3.0.0")
depends_on("cmake@3.0.2:", type="build")
@ -33,28 +32,20 @@ class CbtfArgonavisGui(QMakePackage):
# For MRNet
depends_on("mrnet@5.0.1-3:+lwthreads", when="@develop")
depends_on("mrnet@5.0.1-3+lwthreads", when="@1.3.0.0:9999")
# Dependencies for the openspeedshop cbtf packages.
depends_on("cbtf@develop", when="@develop")
depends_on("cbtf@1.9.3:9999", when="@1.3.0.0:9999")
depends_on("cbtf-krell@develop", when="@develop")
depends_on("cbtf-krell@1.9.3:9999", when="@1.3.0.0:9999")
depends_on("cbtf-argonavis@develop", when="@develop")
depends_on("cbtf-argonavis@1.9.3:9999", when="@1.3.0.0:9999")
depends_on("cuda")
depends_on("openspeedshop-utils+cuda@develop", when="@develop")
depends_on("openspeedshop-utils@2.4.0:+cuda", when="@1.3.0.0:9999")
# For Xerces-C
depends_on("xerces-c")
depends_on("graphviz@2.40.1:", when="@develop")
depends_on("graphviz@2.40.1", when="@1.3.0.0:9999")
depends_on("qtgraph")
@ -66,7 +57,6 @@ def setup_build_environment(self, env):
env.set("CBTF_ROOT", self.spec["cbtf"].prefix)
env.set("CBTF_KRELL_ROOT", self.spec["cbtf-krell"].prefix)
env.set("CBTF_ARGONAVIS_ROOT", self.spec["cbtf-argonavis"].prefix)
env.set("OSS_CBTF_ROOT", self.spec["openspeedshop-utils"].prefix)
env.set("GRAPHVIZ_ROOT", self.spec["graphviz"].prefix)
env.set("QTGRAPHLIB_ROOT", self.spec["qtgraph"].prefix)
env.set("KRELL_ROOT_MRNET", self.spec["mrnet"].prefix)
@ -89,10 +79,6 @@ def setup_run_environment(self, env):
join_path(qtgraph_lib_dir, "{0}".format(self.spec["qt"].version.up_to(3))),
)
# The openspeedshop libraries are needed to actually load the
# performance information into the GUI.
env.prepend_path("LD_LIBRARY_PATH", self.spec["openspeedshop-utils"].prefix.lib64)
def qmake_args(self):
options = ["-o", "Makefile", "openss-gui.pro"]
return options

12
var/spack/repos/builtin/packages/cbtf-argonavis/package.py
View file

@ -16,9 +16,6 @@ class CbtfArgonavis(CMakePackage):
git = "https://github.com/OpenSpeedShop/cbtf-argonavis.git"
version("develop", branch="master")
version("1.9.4.1", branch="1.9.4.1")
version("1.9.4", branch="1.9.4")
version("1.9.3", branch="1.9.3")
variant(
"crayfe",
@ -54,17 +51,12 @@ class CbtfArgonavis(CMakePackage):
# For MRNet
depends_on("mrnet@5.0.1-3:+lwthreads", when="@develop", type=("build", "link", "run"))
depends_on("mrnet@5.0.1-3+lwthreads", when="@1.9.3:9999", type=("build", "link", "run"))
# For CBTF
depends_on("cbtf@develop", when="@develop", type=("build", "link", "run"))
depends_on("cbtf@1.9.3:9999", when="@1.9.3:9999", type=("build", "link", "run"))
# For CBTF with runtime
depends_on("cbtf@develop+runtime", when="@develop+runtime", type=("build", "link", "run"))
depends_on(
"cbtf@1.9.3:9999+runtime", when="@1.9.3:9999+runtime", type=("build", "link", "run")
)
# For libmonitor
depends_on("libmonitor@2013.02.18+commrank", type=("build", "link", "run"))
@ -74,14 +66,10 @@ class CbtfArgonavis(CMakePackage):
# For CBTF-KRELL
depends_on("cbtf-krell@develop", when="@develop", type=("build", "link", "run"))
depends_on("cbtf-krell@1.9.3:9999", when="@1.9.3:9999", type=("build", "link", "run"))
depends_on(
"cbtf-krell@develop+runtime", when="@develop+runtime", type=("build", "link", "run")
)
depends_on(
"cbtf-krell@1.9.3:9999+runtime", when="@1.9.3:9999+runtime", type=("build", "link", "run")
)
# For CUDA
depends_on("cuda")

11
var/spack/repos/builtin/packages/cbtf-krell/package.py
View file

@ -19,9 +19,6 @@ class CbtfKrell(CMakePackage):
git = "https://github.com/OpenSpeedShop/cbtf-krell.git"
version("develop", branch="master")
version("1.9.4.1", branch="1.9.4.1")
version("1.9.4", branch="1.9.4")
version("1.9.3", branch="1.9.3")
# MPI variants
variant(
@ -70,30 +67,23 @@ class CbtfKrell(CMakePackage):
# For Dyninst
depends_on("dyninst@10.1.0", when="@develop")
depends_on("dyninst@10.1.0", when="@1.9.3:9999")
# For MRNet
depends_on("mrnet@5.0.1-3:+lwthreads", when="@develop", type=("build", "link", "run"))
depends_on("mrnet@5.0.1-3+lwthreads", when="@1.9.3:9999", type=("build", "link", "run"))
# For Xerces-C
depends_on("xerces-c")
# For CBTF
depends_on("cbtf@develop", when="@develop", type=("build", "link", "run"))
depends_on("cbtf@1.9.3:9999", when="@1.9.3:9999", type=("build", "link", "run"))
# For CBTF with runtime
depends_on("cbtf@develop+runtime", when="@develop+runtime", type=("build", "link", "run"))
depends_on(
"cbtf@1.9.3:9999+runtime", when="@1.9.3:9999+runtime", type=("build", "link", "run")
)
# for services and collectors
depends_on("libmonitor@2013.02.18+commrank", type=("build", "link", "run"))
depends_on("libunwind", when="@develop")
depends_on("libunwind@1.2.1", when="@1.9.3:9999")
depends_on("papi@5.4.1:", type=("build", "link", "run"))
@ -106,7 +96,6 @@ class CbtfKrell(CMakePackage):
depends_on("mpt", when="+mpt")
depends_on("python", when="@develop", type=("build", "run"))
depends_on("python@2.7.14:2.7.15", when="@2.3.1.3:9999", type=("build", "run"))
depends_on("gotcha")

8
var/spack/repos/builtin/packages/cbtf-lanl/package.py
View file

@ -14,9 +14,6 @@ class CbtfLanl(CMakePackage):
git = "https://github.com/OpenSpeedShop/cbtf-lanl.git"
version("develop", branch="master")
version("1.9.4.1", branch="1.9.4.1")
version("1.9.4", branch="1.9.4")
version("1.9.3", branch="1.9.3")
variant(
"build_type",
@ -33,25 +30,20 @@ class CbtfLanl(CMakePackage):
# For MRNet
depends_on("mrnet@5.0.1-3:+lwthreads", when="@develop")
depends_on("mrnet@5.0.1-3+lwthreads", when="@1.9.3:9999")
# For Xerces-C
depends_on("xerces-c")
# For CBTF
depends_on("cbtf@develop", when="@develop")
depends_on("cbtf@1.9.3:9999", when="@1.9.3:9999")
# For CBTF with runtime
depends_on("cbtf@develop+runtime", when="@develop+runtime")
depends_on("cbtf@1.9.3:9999+runtime", when="@1.9.3:9999+runtime")
# For CBTF-KRELL
depends_on("cbtf-krell@develop", when="@develop")
depends_on("cbtf-krell@1.9.3:9999", when="@1.9.3:9999")
depends_on("cbtf-krell@develop+runtime", when="@develop+runtime")
depends_on("cbtf-krell@1.9.3:9999+runtime", when="@1.9.3:9999+runtime")
parallel = False

26
var/spack/repos/builtin/packages/cctools/package.py
View file

@ -75,29 +75,15 @@ def configure_args(self):
# make sure we do not pick a python outside spack:
if self.spec.satisfies("@6.1.1"):
if self.spec.satisfies("^python@3:"):
args.extend(
["--with-python3-path", self.spec["python"].prefix, "--with-python-path", "no"]
)
elif self.spec.satisfies("^python@:2.9"):
args.extend(
["--with-python-path", self.spec["python"].prefix, "--with-python3-path", "no"]
)
else:
args.extend(["--with-python-path", "no", "--with-python3-path", "no"])
args.extend(
["--with-python3-path", self.spec["python"].prefix, "--with-python-path", "no"]
)
else:
# versions 7 and above, where --with-python-path recognized the
# python version:
if self.spec.satisfies("^python@3:"):
args.extend(
["--with-python-path", self.spec["python"].prefix, "--with-python2-path", "no"]
)
elif self.spec.satisfies("^python@:2.9"):
args.extend(
["--with-python-path", self.spec["python"].prefix, "--with-python3-path", "no"]
)
else:
args.extend(["--with-python2-path", "no", "--with-python3-path", "no"])
args.extend(
["--with-python-path", self.spec["python"].prefix, "--with-python2-path", "no"]
)
# disable these bits
for p in ["mysql", "xrootd"]:

8
var/spack/repos/builtin/packages/ceed/package.py
View file

@ -27,7 +27,7 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
variant("mfem", default=True, description="Build MFEM, Laghos and Remhos")
variant("nek", default=True, description="Build Nek5000, GSLIB, Nekbone, and NekCEM")
variant("occa", default=True, description="Enable OCCA support")
variant("petsc", default=True, description="Build PETSc and HPGMG")
variant("petsc", default=True, description="Build PETSc and HPGMG", when="@2:")
variant("pumi", default=True, description="Build PUMI")
variant("omega-h", default=True, description="Build Omega_h")
variant(
@ -202,14 +202,8 @@ class Ceed(BundlePackage, CudaPackage, ROCmPackage):
depends_on("petsc@3.11.1+mpi+hypre+suite-sparse+mumps+double~int64", when="@2.0.0+petsc+mfem")
depends_on("hpgmg@0.4+fe", when="@2.0.0+petsc")
# ceed-1.0
# For a +quickbuild we disable hdf5, and superlu-dist in PETSc.
# Ideally, these can be turned into recommendations to Spack for
# concretizing the PETSc spec, if Spack ever supports recommendations.
depends_on("petsc@3.8.3~hdf5~superlu-dist", when="@1.0.0+petsc+quickbuild")
depends_on("petsc@3.8.3+mpi+double~int64", when="@1.0.0+petsc~mfem")
# The mfem petsc examples need the petsc variants +hypre, +suite-sparse,
# and +mumps:
depends_on("petsc@3.8.3+mpi+hypre+suite-sparse+mumps+double~int64", when="@1.0.0+petsc+mfem")
depends_on("hpgmg@a0a5510df23b+fe", when="@1.0.0+petsc")
# MAGMA

1
var/spack/repos/builtin/packages/cget/package.py
View file

@ -17,4 +17,3 @@ class Cget(PythonPackage):
depends_on("py-setuptools", type="build")
depends_on("py-six@1.10:", type=("build", "run"))
depends_on("py-click@6.6:", type=("build", "run"))
depends_on("py-subprocess32", when="^python@:2", type=("build", "run"))

25
var/spack/repos/builtin/packages/chill/Add-GCC-libquadmath-for-rose.patch
View file

@ -1,25 +0,0 @@
From 15c3cc127d8f48324b00fd654d9630724eedcfcd Mon Sep 17 00:00:00 2001
From: John Jolly <john.jolly@gmail.com>
Date: Fri, 5 Jun 2020 23:54:13 -0600
Subject: [PATCH] Add GCC libquadmath for rose
---
Makefile.am | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Makefile.am b/Makefile.am
index 7dd92b0..a8daba1 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -7,7 +7,7 @@ core_cxxflags =-g --std=c++11
## Core Libraries ##
core_libs = -lcodegen -lomega
-core_libs += -lm -lrose -lrt -lutil -ldl
+core_libs += -lm -lrose -lrt -lutil -ldl -lquadmath
core_libs += -lboost_date_time -lboost_filesystem -lboost_program_options
core_libs += -lboost_regex -lboost_system -lboost_wave -lboost_iostreams
--
2.25.1

53
var/spack/repos/builtin/packages/chill/Add-GMPHOME-option.patch
View file

@ -1,53 +0,0 @@
From 336dfb3a1c314b6eec23ab4f99114be94c5e518e Mon Sep 17 00:00:00 2001
From: John Jolly <john.jolly@gmail.com>
Date: Fri, 5 Jun 2020 23:45:39 -0600
Subject: [PATCH] Add GMPHOME option
---
Makefile.am | 4 ++++
configure.ac | 7 +++++++
2 files changed, 11 insertions(+)
diff --git a/Makefile.am b/Makefile.am
index 541cb99..7dd92b0 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -16,6 +16,8 @@ core_libs += -liegenlib -lisl -lgmp
core_libdirs = -Lomega/code_gen/obj -Lomega/omega_lib/obj
core_libdirs += -L$(ROSEHOME)/lib -L$(BOOSTHOME)/lib
+core_libdirs += -L$(GMPHOME)/lib
+
core_libdirs += -L$(ISLHOME)/lib
core_libdirs += -L$(IEGENHOME)/lib
@@ -32,6 +34,8 @@ core_includes += -I$(srcdir)/include/chill
core_includes += -I$(ROSEHOME)/include/rose
core_includes += -I$(BOOSTHOME)/include
+core_includes += -I$(GSLHOME)/include
+
core_includes += -I$(ISLHOME)/include
core_includes += -I$(IEGENHOME)/include/iegenlib
diff --git a/configure.ac b/configure.ac
index e146839..18ecf76 100644
--- a/configure.ac
+++ b/configure.ac
@@ -58,6 +58,13 @@ AC_ARG_WITH([boost],[
],[
AC_SUBST([BOOSTHOME], ["${BOOSTHOME}"])])
+AC_ARG_WITH([gmp],[
+ AS_HELP_STRING([--with-gmp],[set path to gmp])
+ ],[
+ AC_SUBST([GMPHOME], [$withval])
+ ],[
+ AC_SUBST([GMPHOME], ["${GMPHOME}"])])
+
AC_ARG_WITH([iegen],[
AS_HELP_STRING([--with-iegen],[set path to iegenlib])
],[
--
2.25.1

53
var/spack/repos/builtin/packages/chill/Add-ISLHOME-option.patch
View file

@ -1,53 +0,0 @@
From 3b4094b9cf1beec0b870e9ca0c3e51ed9b10dc39 Mon Sep 17 00:00:00 2001
From: John Jolly <john.jolly@gmail.com>
Date: Fri, 5 Jun 2020 23:21:18 -0600
Subject: [PATCH] Add ISLHOME option
---
Makefile.am | 4 ++++
configure.ac | 7 +++++++
2 files changed, 11 insertions(+)
diff --git a/Makefile.am b/Makefile.am
index 30667a8..541cb99 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -16,6 +16,8 @@ core_libs += -liegenlib -lisl -lgmp
core_libdirs = -Lomega/code_gen/obj -Lomega/omega_lib/obj
core_libdirs += -L$(ROSEHOME)/lib -L$(BOOSTHOME)/lib
+core_libdirs += -L$(ISLHOME)/lib
+
core_libdirs += -L$(IEGENHOME)/lib
core_libdirs += -L$(IEGENHOME)/../lib/installed/lib
@@ -30,6 +32,8 @@ core_includes += -I$(srcdir)/include/chill
core_includes += -I$(ROSEHOME)/include/rose
core_includes += -I$(BOOSTHOME)/include
+core_includes += -I$(ISLHOME)/include
+
core_includes += -I$(IEGENHOME)/include/iegenlib
core_includes += -I$(IEGENHOME)/../lib/installed/include
diff --git a/configure.ac b/configure.ac
index 8e163cd..e146839 100644
--- a/configure.ac
+++ b/configure.ac
@@ -65,6 +65,13 @@ AC_ARG_WITH([iegen],[
],[
AC_SUBST([IEGENHOME], ["${IEGENHOME}"])])
+AC_ARG_WITH([isl],[
+ AS_HELP_STRING([--with-isl],[set path to isl])
+ ],[
+ AC_SUBST([ISLHOME], [$withval])
+ ],[
+ AC_SUBST([ISLHOME], ["${ISLHOME}"])])
+
AC_ARG_WITH([omega],[
AS_HELP_STRING([--with-omega],[set omega home])],[
AC_SUBST([OMEGAHOME], [$withval])],[
--
2.25.1

92
var/spack/repos/builtin/packages/chill/package.py
View file

@ -1,92 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
from spack.pkg.builtin.boost import Boost
class Chill(AutotoolsPackage):
"""A polyheadral compiler for autotuning"""
homepage = "https://github.com/CtopCsUtahEdu/chill"
url = "https://github.com/CtopCsUtahEdu/chill/archive/v0.3.tar.gz"
git = "https://github.com/CtopCsUtahEdu/chill.git"
maintainers = ["dhuth"]
version("master", branch="master")
version("0.3", sha256="574b622368a6bfaadbe9c1fa02fabefdc6c006069246f67d299f943b7e1d8aa3")
depends_on("boost@1.66.0 cxxstd=11", type="build")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants, type="build")
depends_on("rose@0.9.13.0: +cxx11", type=("build", "run"))
depends_on("autoconf", type="build")
depends_on("automake@1.14:", type="build")
depends_on("libtool", type="build")
depends_on("m4", type="build")
depends_on("iegenlib", type=("build", "run"))
depends_on("bison@3.4.2:", type="build")
depends_on("flex", type="build")
# Does not currrently work with Python3
depends_on("python@2.7:2.8")
depends_on("isl", type="build")
depends_on("gmp", type="build")
patch("Add-ISLHOME-option.patch")
patch("Add-GMPHOME-option.patch")
patch("Add-GCC-libquadmath-for-rose.patch")
build_directory = "spack-build"
def autoreconf(self, spec, prefix):
bash = which("bash")
bash("./bootstrap")
def setup_build_environment(self, env):
rose_home = self.spec["rose"].prefix
boost_home = self.spec["boost"].prefix
iegen_home = self.spec["iegenlib"].prefix
isl_home = self.spec["isl"].prefix
gmp_home = self.spec["gmp"].prefix
env.set("ROSEHOME", rose_home)
env.set("BOOSTHOME", boost_home)
env.set("IEGENHOME", iegen_home)
env.set("ISLHOME", isl_home)
env.set("GMPHOME", gmp_home)
env.append_path("LD_LIBRARY_PATH", rose_home.lib)
env.append_path("LD_LIBRARY_PATH", boost_home.lib)
env.append_path("LD_LIBRARY_PATH", iegen_home.lib)
env.append_path("LD_LIBRARY_PATH", isl_home.lib)
env.append_path("LD_LIBRARY_PATH", gmp_home.lib)
def setup_run_environment(self, env):
rose_home = self.spec["rose"].prefix
boost_home = self.spec["boost"].prefix
iegen_home = self.spec["iegenlib"].prefix
isl_home = self.spec["isl"].prefix
gmp_home = self.spec["gmp"].prefix
env.append_path("LD_LIBRARY_PATH", rose_home.lib)
env.append_path("LD_LIBRARY_PATH", boost_home.lib)
env.append_path("LD_LIBRARY_PATH", iegen_home.lib)
env.append_path("LD_LIBRARY_PATH", isl_home.lib)
env.append_path("LD_LIBRARY_PATH", gmp_home.lib)
def configure_args(self):
args = [
"--with-rose={0}".format(self.spec["rose"].prefix),
"--with-boost={0}".format(self.spec["boost"].prefix),
"--with-iegen={0}".format(self.spec["iegenlib"].prefix),
"--with-isl={0}".format(self.spec["isl"].prefix),
"--with-gmp={0}".format(self.spec["gmp"].prefix),
]
return args

1
var/spack/repos/builtin/packages/citcoms/package.py
View file

@ -27,7 +27,6 @@ class Citcoms(AutotoolsPackage):
# Required dependencies
depends_on("mpi")
depends_on("zlib")
depends_on("python@:2", type="run") # needed for post-processing scripts
depends_on("automake", when="@master", type="build")
depends_on("autoconf", when="@master", type="build")
depends_on("libtool", when="@master", type="build")

3
var/spack/repos/builtin/packages/cmor/package.py
View file

@ -24,7 +24,7 @@ class Cmor(AutotoolsPackage):
version("3.1.2", sha256="ee58b6d405f081e4e0633af931b7992f1a570953b71ece17c01ab9e15889211a")
variant("fortran", default=True, description="Enable Fortran API")
variant("python", default=False, description="Enable PYTHON support")
variant("python", default=False, description="Enable PYTHON support", when="@3.4:")
# older releases require another implementation providing uuid_create()
# 3.6.1 requires libuuid(only the lib) or util-linux-uuid providing uuid_generate()
@ -37,7 +37,6 @@ class Cmor(AutotoolsPackage):
depends_on("udunits")
extends("python", when="+python")
depends_on("python@:2", when="@:3.3 +python", type=("build", "run"))
depends_on("py-pip", when="+python", type="build")
depends_on("py-wheel", when="+python", type="build")
depends_on("py-numpy", type=("build", "run"), when="+python")

41
var/spack/repos/builtin/packages/couchdb/package.py
View file

@ -1,41 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Couchdb(AutotoolsPackage):
"""A CouchDB server hosts named databases, which store documents. Each document
is uniquely named in the database, and CouchDB provides a RESTful HTTP API
for reading and updating (add, edit, delete) database documents."""
homepage = "https://couchdb.apache.org/"
url = "https://archive.apache.org/dist/couchdb/source/3.1.0/apache-couchdb-3.1.0.tar.gz"
version("3.1.0", sha256="4867c796a1ff6f0794b7bd3863089ea6397bd5c47544f9b97db8cdacff90f8ed")
version("3.0.1", sha256="08d61d5c779957d074d5097f28a2dfc9eb518af3c479d5318135ff31212cc522")
version("3.0.0", sha256="d109bb1a70fe746c04a9bf79a2bb1096cb949c750c29dbd196e9c2efd4167fd9")
depends_on("icu4c")
depends_on("openssl")
depends_on("curl")
depends_on("node-js@6:")
depends_on("mozjs@1.8.5")
depends_on("gmake", type="build")
depends_on("help2man", type="build")
depends_on("python", type=("build", "run"))
depends_on("erlang@:22", type=("build", "run"))
def setup_build_environment(self, env):
env.set("CPATH", self.spec["mozjs"].prefix.include.js)
def configure_args(self):
args = ["--disable-docs"]
return args
def install(self, spec, prefix):
make("release")
with working_dir("rel/couchdb/"):
install_tree(".", prefix)

8
var/spack/repos/builtin/packages/cp2k/package.py
View file

@ -53,7 +53,10 @@ class Cp2k(MakefilePackage, CudaPackage):
description=("Enable the alternative PEXSI method" "for density matrix evaluation"),
)
variant(
"elpa", default=False, description="Enable optimised diagonalisation routines from ELPA"
"elpa",
default=False,
description="Enable optimised diagonalisation routines from ELPA",
when="@8.3:",
)
variant(
"sirius",
@ -164,9 +167,6 @@ class Cp2k(MakefilePackage, CudaPackage):
conflicts("~mpi", msg="elpa requires MPI")
depends_on("elpa+openmp", when="+openmp")
depends_on("elpa~openmp", when="~openmp")
depends_on("elpa@2011.12:2016.13", when="@:5")
depends_on("elpa@2011.12:2017.11", when="@6.0:6")
depends_on("elpa@2018.05:2020.11.001", when="@7.0:8.2")
depends_on("elpa@2021.05:", when="@8.3:")
depends_on("elpa@2021.11.001:", when="@9.1:")

2
var/spack/repos/builtin/packages/damaris/package.py
View file

@ -51,7 +51,7 @@ class Damaris(CMakePackage):
depends_on("xsd")
depends_on("xerces-c")
depends_on("hdf5@1.8.20:", when="+hdf5")
depends_on("paraview+python3", when="+catalyst")
depends_on("paraview+python", when="+catalyst")
depends_on("visit+mpi", when="+visit")
depends_on("boost+thread+log+filesystem+date_time+python+numpy @1.67:", when="+python")

2
var/spack/repos/builtin/packages/dealii/package.py
View file

@ -182,10 +182,8 @@ class Dealii(CMakePackage, CudaPackage):
depends_on("p4est", when="+p4est+mpi")
depends_on("petsc+mpi~int64", when="+petsc+mpi~int64")
depends_on("petsc+mpi+int64", when="+petsc+mpi+int64")
depends_on("petsc@:3.6.4", when="@:8.4.1+petsc+mpi")
depends_on("scalapack", when="@9.0:+scalapack")
depends_on("slepc", when="+slepc+petsc+mpi")
depends_on("slepc@:3.6.3", when="@:8.4.1+slepc+petsc+mpi")
depends_on("slepc~arpack", when="+slepc+petsc+mpi+int64")
depends_on("sundials@:3~pthread", when="@9.0:9.2+sundials")
depends_on("sundials@5:5.8", when="@9.3:9.3.3+sundials")

62
var/spack/repos/builtin/packages/draco/d710-python2.patch
View file

@ -1,62 +0,0 @@
diff --git a/config/ApplicationUnitTest.cmake b/config/ApplicationUnitTest.cmake
index a0a79858..0c47b72a 100644
--- a/config/ApplicationUnitTest.cmake
+++ b/config/ApplicationUnitTest.cmake
@@ -249,7 +249,7 @@ macro( aut_register_test )
endif(VERBOSE_DEBUG)
# Look for python, which is used to drive application unit tests
- if( NOT PYTHONINTERP_FOUND )
+ if( NOT Python_Interpreter_FOUND )
# python should have been found when vendor_libraries.cmake was run.
message( FATAL_ERROR "Draco requires python. Python not found in PATH.")
endif()
@@ -289,7 +289,7 @@ macro( aut_register_test )
if (${PYTHON_TEST})
add_test(
NAME ${ctestname_base}${argname}
- COMMAND "${PYTHON_EXECUTABLE}"
+ COMMAND "${Python_EXECUTABLE}"
${aut_DRIVER}
${SHARED_ARGUMENTS}
)
diff --git a/config/draco-config-install.cmake.in b/config/draco-config-install.cmake.in
index c5bf1c75..a16f72f4 100644
--- a/config/draco-config-install.cmake.in
+++ b/config/draco-config-install.cmake.in
@@ -107,8 +107,9 @@ set( WITH_CUDA "@WITH_CUDA@" )
#endif()
# Python
-set( PYTHONINTERP_FOUND "@PYTHONINTERP_FOUND@" )
-set( PYTHON_EXECUTABLE "@PYTHON_EXECUTABLE@" )
+set( Python_FOUND "@Python_FOUND@" )
+set( Python_Interpreter_FOUND "@Python_Interpreter_FOUND@" )
+set( Python_EXECUTABLE "@Python_EXECUTABLE@" )
## ---------------------------------------------------------------------------
## Set useful general variables
diff --git a/config/vendor_libraries.cmake b/config/vendor_libraries.cmake
index c3e079bc..6b393eb4 100644
--- a/config/vendor_libraries.cmake
+++ b/config/vendor_libraries.cmake
@@ -16,7 +16,7 @@ include( setupMPI ) # defines the macros setupMPILibrariesUnix|Windows
macro( setupPython )
message( STATUS "Looking for Python...." )
- find_package(PythonInterp 2.7 QUIET REQUIRED)
+ find_package(Python 2.7 QUIET REQUIRED COMPONENTS Interpreter)
# PYTHONINTERP_FOUND - Was the Python executable found
# PYTHON_EXECUTABLE - path to the Python interpreter
set_package_properties( PythonInterp PROPERTIES
@@ -25,8 +25,8 @@ macro( setupPython )
TYPE REQUIRED
PURPOSE "Required for running tests and accessing features that rely on matplotlib."
)
- if( PYTHONINTERP_FOUND )
- message( STATUS "Looking for Python....found ${PYTHON_EXECUTABLE}" )
+ if( Python_Interpreter_FOUND )
+ message( STATUS "Looking for Python....found ${Python_EXECUTABLE}" )
else()
message( STATUS "Looking for Python....not found" )
endif()

3
var/spack/repos/builtin/packages/draco/package.py
View file

@ -88,8 +88,7 @@ class Draco(CMakePackage):
conflicts("+caliper", when="@:7.7")
# Fix python discovery.
patch("d710.patch", when="@7.1.0^python@3:")
patch("d710-python2.patch", when="@7.1.0^python@2.7:2")
patch("d710.patch", when="@7.1.0")
patch("d730.patch", when="@7.3.0:7.3")
patch("d740.patch", when="@7.4.0:7.4")
patch("d750-intel17.patch", when="@7.5.0:7.6.99%intel@17.0.0:18.0.0")

4
var/spack/repos/builtin/packages/easybuild/package.py
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@ -16,14 +16,12 @@ class Easybuild(PythonPackage):
maintainers = ["boegel"]
version("4.0.0", sha256="21bcc1048525ad6219667cc97a7421b5388068c670cabba356712e474896de40")
version("3.1.2", sha256="a966a08e41d3557d7fd3dc5322180c006d27281d9ecc1b1fce1b4518c32664d4")
depends_on("python@2.6:2.8", when="@:3", type=("build", "run"))
depends_on("python@2.6:2.8,3.5:", when="@4:", type=("build", "run"))
# pip silently replaces distutils with setuptools
depends_on("py-setuptools", type="build")
for v in ["@4.0.0", "@3.1.2"]:
for v in ["@4.0.0"]:
depends_on("py-easybuild-framework" + v, when=v, type="run")
depends_on("py-easybuild-easyblocks" + v, when=v, type="run")
depends_on("py-easybuild-easyconfigs" + v, when=v, type="run")

22
var/spack/repos/builtin/packages/eccodes/package.py
View file

@ -77,7 +77,6 @@ class Eccodes(CMakePackage):
variant(
"memfs", default=False, description="Enable memory based access to definitions/samples"
)
variant("python", default=False, description="Enable the Python 2 interface")
variant("fortran", default=False, description="Enable the Fortran support")
variant("shared", default=True, description="Build shared versions of the libraries")
@ -114,12 +113,6 @@ class Eccodes(CMakePackage):
depends_on("libaec", when="+aec")
# Can be built with Python 2 or Python 3.
depends_on("python", when="+memfs", type="build")
# The interface is available only for Python 2.
# Python 3 interface is available as a separate packages:
# https://confluence.ecmwf.int/display/ECC/Python+3+interface+for+ecCodes
depends_on("python@2.6:2", when="+python", type=("build", "link", "run"))
depends_on("py-numpy", when="+python", type=("build", "run"))
extends("python", when="+python")
depends_on("cmake@3.6:", type="build")
depends_on("cmake@3.12:", when="@2.19:", type="build")
@ -149,7 +142,7 @@ class Eccodes(CMakePackage):
name=center,
destination="spack-definitions",
placement="definitions.{0}".format(center),
**kwargs
**kwargs,
)
# Enforce linking against the specified JPEG2000 backend, see also
@ -236,13 +229,13 @@ def patch(self):
r"(^\s*kind_of_double\s*=\s*)(\d{1,2})(\s*$)",
"\\1kind(real\\2)\\3",
"fortran/grib_types.f90",
**kwargs
**kwargs,
)
filter_file(
r"(^\s*kind_of_\w+\s*=\s*)(\d{1,2})(\s*$)",
"\\1kind(x\\2)\\3",
"fortran/grib_types.f90",
**kwargs
**kwargs,
)
# Replace integer kinds:
@ -251,7 +244,7 @@ def patch(self):
r"(^\s*integer\((?:kind=)?){0}(\).*)".format(size),
"\\1selected_int_kind({0})\\2".format(r),
*patch_kind_files,
**kwargs
**kwargs,
)
# Replace real kinds:
@ -260,7 +253,7 @@ def patch(self):
r"(^\s*real\((?:kind=)?){0}(\).*)".format(size),
"\\1selected_real_kind({0}, {1})\\2".format(p, r),
*patch_kind_files,
**kwargs
**kwargs,
)
# Enable getarg and exit subroutines:
@ -268,7 +261,7 @@ def patch(self):
r"(^\s*program\s+\w+)(\s*$)",
"\\1; use f90_unix_env; use f90_unix_proc\\2",
*patch_unix_ext_files,
**kwargs
**kwargs,
)
@property
@ -332,9 +325,6 @@ def cmake_args(self):
self.define_from_variant("ENABLE_ECCODES_THREADS", "pthreads"),
self.define_from_variant("ENABLE_ECCODES_OMP_THREADS", "openmp"),
self.define_from_variant("ENABLE_MEMFS", "memfs"),
self.define_from_variant(
"ENABLE_PYTHON{0}".format("2" if self.spec.satisfies("@2.20.0:") else ""), "python"
),
self.define_from_variant("ENABLE_FORTRAN", "fortran"),
self.define("BUILD_SHARED_LIBS", "BOTH" if "+shared" in self.spec else "OFF"),
self.define("ENABLE_TESTS", self.run_tests),

2
var/spack/repos/builtin/packages/ecp-data-vis-sdk/package.py
View file

@ -156,7 +156,7 @@ class EcpDataVisSdk(BundlePackage, CudaPackage, ROCmPackage):
depends_on("py-cinemasci", when="+cinema")
dav_sdk_depends_on(
"paraview@5.10:+mpi+python3+kits+shared", when="+paraview", propagate=["hdf5", "adios2"]
"paraview@5.10:+mpi+python+kits+shared", when="+paraview", propagate=["hdf5", "adios2"]
)
# ParaView needs @5.11: in order to use cuda and be compatible with other
# SDK packages.

7
var/spack/repos/builtin/packages/elemental/package.py
View file

@ -27,7 +27,6 @@ class Elemental(CMakePackage):
"openmp_blas", default=False, description="Use OpenMP for threading in the BLAS library"
)
variant("c", default=False, description="Build C interface")
variant("python", default=False, description="Install Python interface")
variant("parmetis", default=False, description="Enable ParMETIS")
variant("quad", default=False, description="Enable quad precision")
variant("int64", default=False, description="Use 64bit integers")
@ -83,8 +82,6 @@ class Elemental(CMakePackage):
depends_on("mpi")
# Allow Elemental to build internally when using 8-byte ints
depends_on("scalapack", when="+scalapack ~int64_blas")
extends("python", when="+python")
depends_on("python@:2.8", when="+python")
depends_on("gmp", when="+mpfr")
depends_on("mpc", when="+mpfr")
depends_on("mpfr", when="+mpfr")
@ -117,7 +114,6 @@ def cmake_args(self):
"-DBUILD_SHARED_LIBS:BOOL=%s" % ("+shared" in spec),
"-DEL_HYBRID:BOOL=%s" % ("+hybrid" in spec),
"-DEL_C_INTERFACE:BOOL=%s" % ("+c" in spec),
"-DINSTALL_PYTHON_PACKAGE:BOOL=%s" % ("+python" in spec),
"-DEL_DISABLE_PARMETIS:BOOL=%s" % ("~parmetis" in spec),
"-DEL_DISABLE_QUAD:BOOL=%s" % ("~quad" in spec),
"-DEL_USE_64BIT_INTS:BOOL=%s" % ("+int64" in spec),
@ -175,7 +171,4 @@ def cmake_args(self):
args.extend(["-DMATH_LIBS:STRING={0}".format(math_libs.ld_flags)])
if "+python" in spec:
args.extend(["-DPYTHON_SITE_PACKAGES:STRING={0}".format(python_platlib)])
return args

54
var/spack/repos/builtin/packages/elpa/package.py
View file

@ -24,47 +24,6 @@ class Elpa(AutotoolsPackage, CudaPackage, ROCmPackage):
version(
"2021.05.001", sha256="a4f1a4e3964f2473a5f8177f2091a9da5c6b5ef9280b8272dfefcbc3aad44d41"
)
version(
"2020.05.001", sha256="66ff1cf332ce1c82075dc7b5587ae72511d2bcb3a45322c94af6b01996439ce5"
)
version(
"2019.11.001", sha256="10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357"
)
version(
"2019.05.002", sha256="d2eab5e5d74f53601220b00d18185670da8c00c13e1c1559ecfb0cd7cb2c4e8d"
)
version(
"2018.11.001", sha256="cc27fe8ba46ce6e6faa8aea02c8c9983052f8e73a00cfea38abf7613cb1e1b16"
)
version(
"2018.05.001.rc1",
sha256="598c01da20600a4514ea4d503b93e977ac0367e797cab7a7c1b0e0e3e86490db",
)
version(
"2017.11.001", sha256="59f99c3abe2190fac0db8a301d0b9581ee134f438669dbc92551a54f6f861820"
)
version(
"2017.05.003", sha256="bccd49ce35a323bd734b17642aed8f2588fea4cc78ee8133d88554753bc3bf1b"
)
version(
"2017.05.002", sha256="568b71024c094d667b5cbb23045ad197ed5434071152ac608dae490ace5eb0aa"
)
version(
"2017.05.001", sha256="28f7edad60984d93da299016ad33571dc6db1cdc9fab0ceaef05dc07de2c7dfd"
)
version(
"2016.11.001.pre",
sha256="69b67f0f6faaa2b3b5fd848127b632be32771636d2ad04583c5269d550956f92",
)
version(
"2016.05.004", sha256="08c59dc9da458bab856f489d779152e5506e04f0d4b8d6dcf114ca5fbbe46c58"
)
version(
"2016.05.003", sha256="c8da50c987351514e61491e14390cdea4bdbf5b09045261991876ed5b433fca4"
)
version(
"2015.11.001", sha256="c0761a92a31c08a4009c9688c85fc3fc8fde9b6ce05e514c3e1587cf045e9eba"
)
variant("openmp", default=True, description="Activates OpenMP support")
variant("mpi", default=True, description="Activates MPI support")
@ -75,8 +34,7 @@ class Elpa(AutotoolsPackage, CudaPackage, ROCmPackage):
depends_on("scalapack", when="+mpi")
depends_on("rocblas", when="+rocm")
depends_on("libtool", type="build")
depends_on("python@:2", type="build", when="@:2020.05.001")
depends_on("python@3:", type="build", when="@2020.11.001:")
depends_on("python@3:", type="build")
with when("@2021.11.01:"):
variant(
@ -84,15 +42,12 @@ class Elpa(AutotoolsPackage, CudaPackage, ROCmPackage):
)
depends_on("scalapack", when="+autotune")
patch("python_shebang.patch", when="@:2020.05.001")
# fails to build due to broken type-bound procedures in OMP parallel regions
conflicts(
"+openmp",
when="@2021.05.001: %gcc@:7",
msg="ELPA-2021.05.001+ requires GCC-8+ for OpenMP support",
)
conflicts("+rocm", when="@:2020", msg="ROCm support was introduced in ELPA 2021.05.001")
conflicts("+mpi", when="+rocm", msg="ROCm support and MPI are not yet compatible")
def url_for_version(self, version):
@ -158,11 +113,6 @@ def configure_args(self):
gcc_options = []
gfortran_options = ["-ffree-line-length-none"]
if self.compiler.version >= Version("10.0.0") and spec.version <= Version(
"2019.11.001"
):
gfortran_options.append("-fallow-argument-mismatch")
space_separator = " "
options.extend(
[
@ -174,7 +124,7 @@ def configure_args(self):
if "%aocc" in spec:
options.extend(["FCFLAGS=-O3", "CFLAGS=-O3"])
cuda_flag = "nvidia-gpu" if "@2021.05.001:" in self.spec else "gpu"
cuda_flag = "nvidia-gpu"
if "+cuda" in spec:
prefix = spec["cuda"].prefix
options.append("--enable-{0}".format(cuda_flag))

8
var/spack/repos/builtin/packages/elpa/python_shebang.patch
View file

@ -1,8 +0,0 @@
--- a/manual_cpp 2021-01-27 20:21:23.897206207 +0100
+++ b/manual_cpp 2021-01-27 20:13:08.743822289 +0100
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python
from __future__ import print_function
import os
import sys

34
var/spack/repos/builtin/packages/find-circ/package.py
View file

@ -1,34 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class FindCirc(Package):
"""Find-circ is a collection of python scripts
detecting head-to-tail spliced (back-spliced) sequencing reads,
indicative of circular RNA (circRNA) in RNA-seq data."""
homepage = "https://github.com/marvin-jens/find_circ"
url = "https://github.com/marvin-jens/find_circ/archive/v1.2.tar.gz"
version("1.2", sha256="f88bf9b5d0cc818313074982d4460c96706f555d924e2821832c3d03bf67743e")
depends_on("python@2.7:2.8", type=("build", "run"))
depends_on("py-pysam", type=("build", "run"))
# Higher version of py-pandas and py-numpy
# depends on python@3: which conflicts with py-rnacocktail
depends_on("py-numpy@:1.16.5", type=("build", "run"))
def install(self, spec, prefix):
mkdir(prefix.bin)
install("cmp_bed.py", prefix.bin)
install("find_circ.py", prefix.bin)
install("maxlength.py", prefix.bin)
install("unmapped2anchors.py", prefix.bin)
install("README.md", prefix)
install("README.pdf", prefix)
install("LICENSE", prefix)
install_tree("test_data", prefix.test_data)

5
var/spack/repos/builtin/packages/fplo/package.py
View file

@ -128,10 +128,7 @@ def build(self, spec, prefix):
# build python
with working_dir("PYTHON"):
if "^python@:2" in self.spec:
make()
else:
make("python3")
make("python3")
def install(self, spec, prefix):
with working_dir(self.stage.source_path):

35
var/spack/repos/builtin/packages/ganglia/package.py
View file

@ -1,35 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Ganglia(AutotoolsPackage):
"""Ganglia is a scalable distributed monitoring system for high-performance
computing systems such as clusters and Grids. It is based on a hierarchical
design targeted at federations of clusters. Supports clusters up to 2000
nodes in size."""
homepage = "http://ganglia.sourceforge.net/"
url = "https://jaist.dl.sourceforge.net/project/ganglia/ganglia%20monitoring%20core/3.7.2/ganglia-3.7.2.tar.gz"
list_url = "http://jaist.dl.sourceforge.net/project/ganglia/ganglia%20monitoring%20core"
list_depth = 1
version("3.7.2", sha256="042dbcaf580a661b55ae4d9f9b3566230b2232169a0898e91a797a4c61888409")
depends_on("m4", type="build")
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("libtool", type="build")
depends_on("apr")
depends_on("libconfuse")
depends_on("python@:2.7")
depends_on("pcre")
depends_on("libtirpc")
depends_on("expat")
def setup_build_environment(self, env):
env.prepend_path("CPATH", self.spec["libtirpc"].prefix.include.tirpc)
env.append_flags("LDFLAGS", "-ltirpc")

7
var/spack/repos/builtin/packages/gaudi/package.py
View file

@ -31,8 +31,6 @@ class Gaudi(CMakePackage):
version("33.1", sha256="7eb6b2af64aeb965228d4b6ea66c7f9f57f832f93d5b8ad55c9105235af5b042")
version("33.0", sha256="76a967c41f579acc432593d498875dd4dc1f8afd5061e692741a355a9cf233c8")
version("32.2", sha256="e9ef3eb57fd9ac7b9d5647e278a84b2e6263f29f0b14dbe1321667d44d969d2e")
version("31.0", commit="aeb156f0c40571b5753a9e1dab31e331491b2f3e")
version("30.5", commit="2c70e73ee5b543b26197b90dd59ea4e4d359d230")
maintainers = ["drbenmorgan", "vvolkl"]
@ -71,10 +69,7 @@ class Gaudi(CMakePackage):
depends_on("nlohmann-json", when="@35.0:")
depends_on("python", type=("build", "run"))
depends_on("python@:3.7", when="@32.2:34", type=("build", "run"))
depends_on("python@:2", when="@:32.1", type=("build", "run"))
depends_on("py-networkx@:2.2", when="^python@:2.7")
depends_on("py-networkx", when="^python@3.0.0:")
depends_on("py-setuptools@:45", when="^python@:2.7", type="build")
depends_on("py-networkx", type=("build", "run"))
depends_on("py-six", type=("build", "run"))
depends_on("py-xenv@1:", when="@:34.9", type=("build", "run"))
depends_on("range-v3")

3
var/spack/repos/builtin/packages/gdb/package.py
View file

@ -37,7 +37,7 @@ class Gdb(AutotoolsPackage, GNUMirrorPackage):
version("7.11.1", sha256="57e9e9aa3172ee16aa1e9c66fef08b4393b51872cc153e3f1ffdf18a57440586")
version("7.10.1", sha256="ff14f8050e6484508c73cbfa63731e57901478490ca1672dc0b5e2b03f6af622")
variant("python", default=True, description="Compile with Python support")
variant("python", default=True, description="Compile with Python support", when="@8.2:")
variant("xz", default=True, description="Compile with lzma support")
variant("source-highlight", default=False, description="Compile with source-highlight support")
variant("lto", default=False, description="Enable lto")
@ -73,7 +73,6 @@ class Gdb(AutotoolsPackage, GNUMirrorPackage):
# Optional dependencies
depends_on("python", when="+python", type=("build", "link", "run"))
depends_on("python@:3.6", when="@:8.1+python", type=("build", "link", "run"))
# gdb@9.2 will segmentation fault if it builds with python@3.9.
# https://bugzilla.redhat.com/show_bug.cgi?id=1829702
depends_on("python@:3.8", when="@:9.2+python", type=("build", "link", "run"))

10
var/spack/repos/builtin/packages/gdl/package.py
View file

@ -26,7 +26,6 @@ class Gdl(CMakePackage):
variant("hdf5", default=True, description="Enable HDF5")
variant("openmp", default=True, description="Enable OpenMP")
variant("proj", default=True, description="Enable LIBPROJ4")
variant("embed_python", default=False, description="Ability to embed Python within GDL")
variant("python", default=False, description="Build the GDL Python module")
variant("wx", default=False, description="Enable WxWidgets")
variant("x11", default=False, description="Enable X11")
@ -44,8 +43,6 @@ class Gdl(CMakePackage):
# Too many dependencies to test if GDL supports PROJ.6,
# so restricting to old API
depends_on("proj@:5", when="+proj")
depends_on("py-numpy", type=("build", "run"), when="+embed_python")
depends_on("python@2.7:2.8", type=("build", "run"), when="+embed_python")
depends_on("wxwidgets", when="+wx")
depends_on("eigen")
@ -62,8 +59,6 @@ class Gdl(CMakePackage):
depends_on("libtirpc", type="link")
depends_on("libgeotiff", type="link")
conflicts("+python", when="~embed_python")
# Building the Python module requires patches currently targetting 0.9.8
# othwerwise asking for the Python module *only* builds the Python module
conflicts("+python", when="@:0.9.7,0.9.9:")
@ -113,11 +108,6 @@ def cmake_args(self):
else:
args += ["-DLIBPROJ4=OFF"]
if "+embed_python" in self.spec:
args += ["-DPYTHON=ON"]
else:
args += ["-DPYTHON=OFF"]
if "+python" in self.spec:
args += ["-DPYTHON_MODULE=ON"]
else:

23
var/spack/repos/builtin/packages/genesis/package.py
View file

@ -17,7 +17,6 @@ class Genesis(AutotoolsPackage, CudaPackage):
url = "https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/09/genesis-1.5.1.tar.bz2"
git = "https://github.com/genesis-release-r-ccs/genesis-2.0.git"
version("master", branch="master")
version(
"1.6.0",
sha256="d0185a5464ed4231f6ee81f6dcaa15935a99fa30b96658d2b7c25d7fbc5b38e9",
@ -63,7 +62,6 @@ class Genesis(AutotoolsPackage, CudaPackage):
depends_on("mpi", type=("build", "run"))
depends_on("lapack")
depends_on("python@2.6.9:2.8.0", type=("build", "run"), when="@master")
patch("fj_compiler.patch", when="@master %fj")
patch("fj_compiler_1.5.1.patch", when="@1.5.1 %fj")
@ -115,24 +113,3 @@ def cache_test_sources(self):
"""Copy test files after the package is installed for test()."""
if self.spec.satisfies("@master"):
self.cache_extra_test_sources(["tests"])
def test(self):
"""Perform stand-alone/smoke tests using installed package."""
if not self.spec.satisfies("@master"):
print("Skipping: Tests are only available for the master branch")
return
test_name = join_path(self.cached_tests_work_dir, "regression_test", "test.py")
bin_name = join_path(self.prefix.bin, "spdyn")
opts = [
test_name,
self.spec["mpi"].prefix.bin.mpirun + " -np 8 " + bin_name,
]
env["OMP_NUM_THREADS"] = "1"
self.run_test(
self.spec["python"].command.path,
options=opts,
expected="Passed 53 / 53",
purpose="test: running regression test",
work_dir=self.cached_tests_work_dir,
)

1
var/spack/repos/builtin/packages/git-imerge/package.py
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@ -31,7 +31,6 @@ class GitImerge(MakefilePackage):
version("1.0.0", sha256="2ef3a49a6d54c4248ef2541efc3c860824fc8295a7226760f24f0bb2c5dd41f2")
depends_on("python@2.6:")
depends_on("py-argparse", when="^python@:2.6,3.0:3.1")
depends_on("git")
# Package copies a Python script and bash-completion files, so

51
var/spack/repos/builtin/packages/gpdb/package.py
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@ -1,51 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Gpdb(AutotoolsPackage):
"""
Greenplum Database (GPDB) is an advanced, fully featured, open source
data warehouse, based on PostgreSQL. It provides powerful and rapid
analytics on petabyte scale data volumes. Uniquely geared toward big
data analytics, Greenplum Database is powered by the world's most
advanced cost-based query optimizer delivering high analytical query
performance on large data volumes.
"""
homepage = "https://github.com/greenplum-db/gpdb"
url = "https://github.com/greenplum-db/gpdb/archive/6.2.1.tar.gz"
version("6.2.1", sha256="60c81d71665d623ea98a0e9bd8e6df7fecf6b30eb60a5881ccef781ff5214438")
version("6.1.0", sha256="81fa854b0ac5fe4e0de5fdee9a7b7c2514e1ea1feefa4e4d10518538a5c5b2a8")
version("6.0.1", sha256="8902f5d64386447f61c25686f283a785858760e0dcf9a049266db058d3597156")
version("6.0.0", sha256="8514140bee9db514d18a769034562e7f3464f74828595903a64dbf3d175ab71a")
version("5.24.0", sha256="4ea5cfcc20f149669bb3713378158e15b5c5949b367351a0f497ba1602d61fc1")
version("5.23.0", sha256="b06a797eb941362d5473b84d5def349b5ce12ce87ab116bea7c74ad193738ae9")
depends_on("zstd")
depends_on("py-setuptools@:44")
depends_on("apr")
depends_on("libevent")
depends_on("curl")
depends_on("xerces-c")
depends_on("bison", type="build")
depends_on("libxml2")
depends_on("flex")
depends_on("readline")
depends_on("py-subprocess32", type=("build", "run"))
depends_on("python@:2.8.0", type=("build", "run"))
depends_on("py-lockfile", type=("build", "run"))
depends_on("py-psutil", type=("build", "run"))
depends_on("py-utils@:1.0.0", type=("build", "run"))
def configure_args(self):
args = ["--with-python", "--disable-orca", "--enable-depend", "--with-libxml"]
return args
def setup_run_environment(self, env):
env.append_path("GPHOME", self.prefix)
env.append_path("PYTHONPATH", self.prefix.lib.python)

2
var/spack/repos/builtin/packages/gplates/package.py
View file

@ -21,7 +21,6 @@ class Gplates(CMakePackage):
manual_download = True
version("2.3.0", sha256="7d4be9d524d1fcbb6a81de29bd1d4b13133082db23f0808965c5efe30e9538ab")
version("2.1.0", sha256="5a52242520d7e243c541e164c8417b23f4e17fcd79ed81f865b2c13628bb0e07")
depends_on("cmake@3.5:", when="@2.3:", type="build")
depends_on("cmake@2.8.8:", when="@2.1", type="build")
@ -31,7 +30,6 @@ class Gplates(CMakePackage):
depends_on("glu")
depends_on("glew")
depends_on("python@2:3", when="@2.3:")
depends_on("python@2", when="@:2.1")
depends_on("boost@1.35:1.75+program_options+python+system+thread", when="@2.3:")
# Boost's Python library has a different name starting with 1.67.
depends_on("boost@1.34:1.66+program_options+python+system+thread", when="@2.1")

8
var/spack/repos/builtin/packages/grass/package.py
View file

@ -25,12 +25,6 @@ class Grass(AutotoolsPackage):
version("7.8.2", sha256="33576f7078f805b39ca20c2fa416ac79c64260c0581072a6dc7d813f53aa9abb")
version("7.8.1", sha256="6ae578fd67afcce7abec4ba4505dcc55b3d2dfe0ca46b99d966cb148c654abb3")
version("7.8.0", sha256="4b1192294e959ffd962282344e4ff325c4472f73abe605e246a1da3beda7ccfa")
version("7.6.1", sha256="9e25c99cafd16ed8f5e2dca75b5a10dc2af0568dbedf3fc39f1c5a0a9c840b0b")
version("7.4.4", sha256="96a39e273103f7375a670eba94fa3e5dad2819c5c5664c9aee8f145882a94e8c")
version("7.4.3", sha256="004e65693ee97fd4d5dc7ad244e3286a115dccd88964d04be61c07db6574b399")
version("7.4.2", sha256="18eb19bc0aa4cd7be3f30f79ac83f9d0a29c63657f4c1b05bf4c5d5d57a8f46d")
version("7.4.1", sha256="560b8669caaafa9e8dbd4bbf2b4b4bbab7dca1cc46ee828eaf26c744fe0635fc")
version("7.4.0", sha256="cb6fa188e030a3a447fc5451fbe0ecbeb4069ee2fd1bf52ed8e40e9b89e293cc")
variant("cxx", default=True, description="Support C++ functionality")
variant("tiff", default=False, description="Support TIFF functionality")
@ -67,7 +61,6 @@ class Grass(AutotoolsPackage):
depends_on("flex", type="build")
depends_on("bison", type="build")
depends_on("proj")
depends_on("proj@:4", when="@:7.5")
# GRASS 7.8.0 was supposed to support PROJ 6, but it still checks for
# share/proj/epsg, which was removed in PROJ 6
depends_on("proj@:5", when="@:7.8.0")
@ -75,7 +68,6 @@ class Grass(AutotoolsPackage):
# https://courses.neteler.org/grass-gis-7-8-1-released-with-proj-6-and-gdal-3-support/
depends_on("proj@6:", when="@7.8.1:")
depends_on("python@2.7:", type=("build", "run"))
depends_on("python@2.7:2.8", when="@:7.6", type=("build", "run"))
depends_on("py-six", when="@7.8:", type=("build", "run"))
# Optional packages

12
var/spack/repos/builtin/packages/grib-api/disable_numpy.patch
View file

@ -1,12 +0,0 @@
--- a/python/CMakeLists.txt
+++ b/python/CMakeLists.txt
@@ -6,7 +6,8 @@ if( HAVE_PYTHON )
#endif()
# check for Numpy
- find_package( NumPy )
+ # find_package( NumPy )
+ set(NUMPY_FOUND FALSE)
###############################################################################
# swig python interface

17
var/spack/repos/builtin/packages/grib-api/package.py
View file

@ -55,8 +55,6 @@ class GribApi(CMakePackage):
)
variant("pthreads", default=False, description="Enable POSIX threads")
variant("openmp", default=False, description="Enable OpenMP threads")
variant("python", default=False, description="Enable the Python interface")
variant("numpy", default=False, description="Enable numpy support in the Python interface")
variant("fortran", default=False, description="Enable the Fortran support")
variant(
"examples", default=True, description="Build the examples (part of the full test suite)"
@ -78,24 +76,13 @@ class GribApi(CMakePackage):
depends_on("jasper", when="jp2k=jasper")
depends_on("libpng", when="+png")
depends_on("libaec", when="+aec")
depends_on("python@2.5:2", when="+python", type=("build", "link", "run"))
depends_on("py-numpy", when="+python+numpy", type=("build", "run"))
extends("python", when="+python")
conflicts("+openmp", when="+pthreads", msg="Cannot enable both POSIX threads and OMP")
conflicts(
"+numpy",
when="~python",
msg="Numpy variant is valid only when the Python interface is " "enabled",
)
# The following enforces linking against the specified JPEG2000 backend.
patch("enable_only_openjpeg.patch", when="jp2k=openjpeg")
patch("enable_only_jasper.patch", when="jp2k=jasper")
# Disable NumPy even if it's available.
patch("disable_numpy.patch", when="+python~numpy")
# CMAKE_INSTALL_RPATH must be a semicolon-separated list.
patch("cmake_install_rpath.patch")
@ -108,7 +95,6 @@ def cmake_args(self):
var_opt_list = [
("+pthreads", "GRIB_THREADS"),
("+openmp", "GRIB_OMP_THREADS"),
("+python", "PYTHON"),
("+fortran", "FORTRAN"),
("+examples", "EXAMPLES"),
("+test", "TESTS"),
@ -159,7 +145,4 @@ def cmake_args(self):
else:
args.append("-DENABLE_AEC=OFF")
if "^python" in self.spec:
args.append("-DPYTHON_EXECUTABLE:FILEPATH=" + python.path)
return args

29
var/spack/repos/builtin/packages/halc/package.py
View file

@ -1,29 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Halc(MakefilePackage):
"""HALC is software that makes error correction for long reads with
high throughput."""
homepage = "https://github.com/lanl001/halc"
url = "https://github.com/lanl001/halc/archive/v1.1.tar.gz"
version("1.1", sha256="79675c3d6c40f567c2e1a5b5e7ec4fb150036582054f6ad079e06b73bd71c1ad")
depends_on("blasr", type="run")
depends_on("lordec", type="run")
depends_on("dos2unix", type="build")
depends_on("python", type="run")
parallel = False
def install(self, spec, prefix):
install_tree("bin", prefix.bin)
install("runHALC.py", prefix.bin)
dos2unix = which("dos2unix")
dos2unix(join_path(self.prefix.bin, "runHALC.py"))

4
var/spack/repos/builtin/packages/herwig3/package.py
View file

@ -36,7 +36,6 @@ class Herwig3(AutotoolsPackage):
depends_on("vbfnlo@3:")
depends_on("madgraph5amc")
depends_on("njet")
depends_on("py-gosam", when="^python@2.7.0:2.7")
depends_on("gosam-contrib")
depends_on("openloops")
@ -60,9 +59,6 @@ def configure_args(self):
"--with-evtgen=" + self.spec["evtgen"].prefix,
]
if self.spec.satisfies("^python@2.7.0:2.7"):
args.append("--with-gosam=" + self.spec["gosam"].prefix)
return args
def flag_handler(self, name, flags):

56
var/spack/repos/builtin/packages/hic-pro/package.py
View file

@ -1,56 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class HicPro(MakefilePackage):
"""HiC-Pro is a package designed to process Hi-C data,
from raw fastq files (paired-end Illumina data)
to the normalized contact maps"""
homepage = "https://github.com/nservant/HiC-Pro"
url = "https://github.com/nservant/HiC-Pro/archive/v2.10.0.tar.gz"
version("2.10.0", sha256="df181ea5c57247caf6b25fd15dfbb03df597ff8c4f57599d88607648bb61f1b7")
depends_on("bowtie2")
depends_on("samtools")
depends_on("python+ucs4@2.7:2.8")
depends_on("r")
depends_on("py-numpy", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-pysam", type=("build", "run"))
depends_on("py-bx-python", type=("build", "run"))
depends_on("r-rcolorbrewer", type=("build", "run"))
depends_on("r-ggplot2", type=("build", "run"))
def edit(self, spec, prefix):
config = FileFilter("config-install.txt")
config.filter("PREFIX =.*", "PREFIX = {0}".format(prefix))
config.filter("BOWTIE2 PATH =.*", "BOWTIE2_PATH = {0}".format(spec["bowtie2"].prefix))
config.filter("SAMTOOLS_PATH =.*", "SAMTOOLS_PATH = {0}".format(spec["samtools"].prefix))
config.filter("R_PATH =.*", "R_RPTH ={0}".format(spec["r"].prefix))
config.filter("PYTHON_PATH =.*", "PYTHON_RPTH ={0}".format(spec["python"].prefix))
def build(self, spec, preifx):
make("-f", "./scripts/install/Makefile", "CONFIG_SYS=./config-install.txt")
make("mapbuilder")
make("readstrimming")
make("iced")
def install(self, spec, prefix):
# Patch INSTALLPATH in config-system.txt
config = FileFilter("config-system.txt")
config.filter("/HiC-Pro_%s" % self.version, "")
# Install
install("config-hicpro.txt", prefix)
install("config-install.txt", prefix)
install("config-system.txt", prefix)
install_tree("bin", prefix.bin)
install_tree("annotation", prefix.annotation)
install_tree("doc", prefix.doc)
install_tree("scripts", prefix.scripts)
install_tree("test-op", join_path(prefix, "test-op"))

2
var/spack/repos/builtin/packages/hicops/package.py
View file

@ -81,11 +81,9 @@ class Hicops(CMakePackage):
depends_on("py-setuptools")
depends_on("py-bottleneck")
depends_on("py-pyparsing")
depends_on("py-subprocess32")
depends_on("py-six")
depends_on("py-setuptools-scm")
depends_on("py-et-xmlfile")
depends_on("py-argparse")
depends_on("py-cython")
depends_on("py-cycler")
depends_on("py-pytz")

1
var/spack/repos/builtin/packages/httpie/package.py
View file

@ -35,4 +35,3 @@ class Httpie(PythonPackage):
depends_on("py-requests@2.11:", type=("build", "run"))
depends_on("py-requests@2.22:+socks", when="@2.5:", type=("build", "run"))
depends_on("py-requests-toolbelt@0.9.1:", when="@2.5:", type=("build", "run"))
depends_on("py-argparse@1.2.1:", type=("build", "run"), when="^python@:2.6,3.0:3.1")

1
var/spack/repos/builtin/packages/isescan/package.py
View file

@ -21,7 +21,6 @@ class Isescan(Package):
depends_on("py-scipy@0.13.1:", type="run")
depends_on("py-biopython@1.62:", type="run")
depends_on("py-fastcluster", type="run")
depends_on("py-argparse", when="^python@:2.6,3.0:3.1", type="run")
depends_on("blast-plus@2.2.31:", type="run")
depends_on("fraggenescan@:1.30", type="run")
depends_on("hmmer@3.1b2:", type="run")

5
var/spack/repos/builtin/packages/itstool/package.py
View file

@ -17,10 +17,5 @@ class Itstool(AutotoolsPackage):
maintainers = ["agoodLANL"]
version("2.0.7", sha256="6b9a7cd29a12bb95598f5750e8763cee78836a1a207f85b74d8b3275b27e87ca")
version("2.0.2", sha256="bf909fb59b11a646681a8534d5700fec99be83bb2c57badf8c1844512227033a")
version("2.0.1", sha256="ec6b1b32403cbe338b6ac63c61ab1ecd361f539a6e41ef50eae56a4f577234d1")
version("2.0.0", sha256="14708111b11b4a70e240e3b404d7a58941e61dbb5caf7e18833294d654c09169")
version("1.2.0", sha256="46fed63fb89c72dbfc03097b4477084ff05ad6f171212d8f1f1546ea543978aa")
depends_on("libxml2+python", type=("build", "run"))
depends_on("python@2.0:2", when="@:2.0.2")

1
var/spack/repos/builtin/packages/lbann/package.py
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@ -243,7 +243,6 @@ class Lbann(CMakePackage, CudaPackage, ROCmPackage):
depends_on("python@3: +shared", type=("build", "run"), when="@:0.90,0.99: +pfe")
extends("python", when="+pfe")
depends_on("py-setuptools", type="build", when="+pfe")
depends_on("py-argparse", type="run", when="@:0.90,0.99: +pfe ^python@:2.6,3.0:3.1")
depends_on("py-protobuf+cpp@3.10.0:", type=("build", "run"), when="@:0.90,0.99: +pfe")
depends_on("protobuf+shared@3.10.0:", when="@:0.90,0.99:")

11
var/spack/repos/builtin/packages/lhapdf5/package.py
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@ -27,17 +27,8 @@ class Lhapdf5(AutotoolsPackage):
version("5.8.0", sha256="8381ea5f785dde95772a2b6d5890f1cb72012e223e6861823fd81b09eedaa7a3")
version("5.7.1", sha256="40529629351598317fbf7b5905661e51b23778019d50451eee78d7b1118e2559")
variant("python2", default=False, description="Enable Python2 extension")
depends_on("python@2.3:2.7", when="+python2")
def setup_build_environment(self, env):
env.append_flags("FFLAGS", "-std=legacy")
if self.spec.satisfies("+python2"):
env.append_flags("PYTHON", join_path(self.spec["python"].prefix.bin, "python"))
def configure_args(self):
args = []
if self.spec.satisfies("-python2"):
args.append("--disable-pyext")
return args
return ["--disable-pyext"]

3
var/spack/repos/builtin/packages/libproxy/package.py
View file

@ -20,12 +20,11 @@ class Libproxy(CMakePackage):
version("0.4.13", sha256="d610bc0ef81a18ba418d759c5f4f87bf7102229a9153fb397d7d490987330ffd")
variant("perl", default=False, description="Enable Perl bindings")
variant("python", default=True, description="Enable Python bindings")
variant("python", default=True, description="Enable Python bindings", when="@0.4.16:")
depends_on("zlib")
depends_on("perl", type=("build", "run"), when="+perl")
depends_on("python", type=("build", "run"), when="+python")
depends_on("python@:3.6", type=("build", "run"), when="@:0.4.15 +python")
def cmake_args(self):
return [

112
var/spack/repos/builtin/packages/llvm/llvm4-lld-ELF-Symbols.patch
View file

@ -1,112 +0,0 @@
--- a/lldb/include/lldb/Utility/TaskPool.h
+++ b/lldb/include/lldb/Utility/TaskPool.h
@@ -33,6 +33,7 @@
#include <queue>
#include <thread>
#include <vector>
+#include <functional>
// Global TaskPool class for running tasks in parallel on a set of worker thread
// created the first
# Fix lld templates: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=230463
--- a/lld/ELF/LTO.cpp
+++ b/lld/ELF/LTO.cpp
@@ -158,7 +158,7 @@
return Ret;
}
-template void BitcodeCompiler::template add<ELF32LE>(BitcodeFile &);
-template void BitcodeCompiler::template add<ELF32BE>(BitcodeFile &);
-template void BitcodeCompiler::template add<ELF64LE>(BitcodeFile &);
-template void BitcodeCompiler::template add<ELF64BE>(BitcodeFile &);
+template void BitcodeCompiler::add<ELF32LE>(BitcodeFile &);
+template void BitcodeCompiler::add<ELF32BE>(BitcodeFile &);
+template void BitcodeCompiler::add<ELF64LE>(BitcodeFile &);
+template void BitcodeCompiler::add<ELF64BE>(BitcodeFile &);
--- a/lld/ELF/Symbols.cpp
+++ b/lld/ELF/Symbols.cpp
@@ -343,45 +343,45 @@
template bool SymbolBody::hasThunk<ELF64LE>() const;
template bool SymbolBody::hasThunk<ELF64BE>() const;
-template uint32_t SymbolBody::template getVA<ELF32LE>(uint32_t) const;
-template uint32_t SymbolBody::template getVA<ELF32BE>(uint32_t) const;
-template uint64_t SymbolBody::template getVA<ELF64LE>(uint64_t) const;
-template uint64_t SymbolBody::template getVA<ELF64BE>(uint64_t) const;
-
-template uint32_t SymbolBody::template getGotVA<ELF32LE>() const;
-template uint32_t SymbolBody::template getGotVA<ELF32BE>() const;
-template uint64_t SymbolBody::template getGotVA<ELF64LE>() const;
-template uint64_t SymbolBody::template getGotVA<ELF64BE>() const;
-
-template uint32_t SymbolBody::template getGotOffset<ELF32LE>() const;
-template uint32_t SymbolBody::template getGotOffset<ELF32BE>() const;
-template uint64_t SymbolBody::template getGotOffset<ELF64LE>() const;
-template uint64_t SymbolBody::template getGotOffset<ELF64BE>() const;
-
-template uint32_t SymbolBody::template getGotPltVA<ELF32LE>() const;
-template uint32_t SymbolBody::template getGotPltVA<ELF32BE>() const;
-template uint64_t SymbolBody::template getGotPltVA<ELF64LE>() const;
-template uint64_t SymbolBody::template getGotPltVA<ELF64BE>() const;
-
-template uint32_t SymbolBody::template getThunkVA<ELF32LE>() const;
-template uint32_t SymbolBody::template getThunkVA<ELF32BE>() const;
-template uint64_t SymbolBody::template getThunkVA<ELF64LE>() const;
-template uint64_t SymbolBody::template getThunkVA<ELF64BE>() const;
-
-template uint32_t SymbolBody::template getGotPltOffset<ELF32LE>() const;
-template uint32_t SymbolBody::template getGotPltOffset<ELF32BE>() const;
-template uint64_t SymbolBody::template getGotPltOffset<ELF64LE>() const;
-template uint64_t SymbolBody::template getGotPltOffset<ELF64BE>() const;
-
-template uint32_t SymbolBody::template getPltVA<ELF32LE>() const;
-template uint32_t SymbolBody::template getPltVA<ELF32BE>() const;
-template uint64_t SymbolBody::template getPltVA<ELF64LE>() const;
-template uint64_t SymbolBody::template getPltVA<ELF64BE>() const;
-
-template uint32_t SymbolBody::template getSize<ELF32LE>() const;
-template uint32_t SymbolBody::template getSize<ELF32BE>() const;
-template uint64_t SymbolBody::template getSize<ELF64LE>() const;
-template uint64_t SymbolBody::template getSize<ELF64BE>() const;
+template uint32_t SymbolBody::getVA<ELF32LE>(uint32_t) const;
+template uint32_t SymbolBody::getVA<ELF32BE>(uint32_t) const;
+template uint64_t SymbolBody::getVA<ELF64LE>(uint64_t) const;
+template uint64_t SymbolBody::getVA<ELF64BE>(uint64_t) const;
+
+template uint32_t SymbolBody::getGotVA<ELF32LE>() const;
+template uint32_t SymbolBody::getGotVA<ELF32BE>() const;
+template uint64_t SymbolBody::getGotVA<ELF64LE>() const;
+template uint64_t SymbolBody::getGotVA<ELF64BE>() const;
+
+template uint32_t SymbolBody::getGotOffset<ELF32LE>() const;
+template uint32_t SymbolBody::getGotOffset<ELF32BE>() const;
+template uint64_t SymbolBody::getGotOffset<ELF64LE>() const;
+template uint64_t SymbolBody::getGotOffset<ELF64BE>() const;
+
+template uint32_t SymbolBody::getGotPltVA<ELF32LE>() const;
+template uint32_t SymbolBody::getGotPltVA<ELF32BE>() const;
+template uint64_t SymbolBody::getGotPltVA<ELF64LE>() const;
+template uint64_t SymbolBody::getGotPltVA<ELF64BE>() const;
+
+template uint32_t SymbolBody::getThunkVA<ELF32LE>() const;
+template uint32_t SymbolBody::getThunkVA<ELF32BE>() const;
+template uint64_t SymbolBody::getThunkVA<ELF64LE>() const;
+template uint64_t SymbolBody::getThunkVA<ELF64BE>() const;
+
+template uint32_t SymbolBody::getGotPltOffset<ELF32LE>() const;
+template uint32_t SymbolBody::getGotPltOffset<ELF32BE>() const;
+template uint64_t SymbolBody::getGotPltOffset<ELF64LE>() const;
+template uint64_t SymbolBody::getGotPltOffset<ELF64BE>() const;
+
+template uint32_t SymbolBody::getPltVA<ELF32LE>() const;
+template uint32_t SymbolBody::getPltVA<ELF32BE>() const;
+template uint64_t SymbolBody::getPltVA<ELF64LE>() const;
+template uint64_t SymbolBody::getPltVA<ELF64BE>() const;
+
+template uint32_t SymbolBody::getSize<ELF32LE>() const;
+template uint32_t SymbolBody::getSize<ELF32BE>() const;
+template uint64_t SymbolBody::getSize<ELF64LE>() const;
+template uint64_t SymbolBody::getSize<ELF64BE>() const;
template class elf::Undefined<ELF32LE>;
template class elf::Undefined<ELF32BE>;

10
var/spack/repos/builtin/packages/llvm/llvm_gcc7.patch
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@ -1,10 +0,0 @@
--- a/lldb/include/lldb/Utility/TaskPool.h 2016-09-06 16:57:50.000000000 -0400
+++ b/lldb/include/lldb/Utility/TaskPool.h 2017-08-29 16:29:41.448584015 -0400
@@ -28,6 +28,7 @@
#include <cassert>
#include <cstdint>
+#include <functional>
#include <future>
#include <list>
#include <queue>

38
var/spack/repos/builtin/packages/llvm/package.py
View file

@ -34,7 +34,6 @@ class Llvm(CMakePackage, CudaPackage):
family = "compiler" # Used by lmod
# fmt: off
version("main", branch="main")
version("15.0.4", sha256="e24b4d3bf7821dcb1c901d1e09096c1f88fb00095c5a6ef893baab4836975e52")
version("15.0.3", sha256="8ac8e4c0982bf236526d737d385db5e1e66543ab217a9355d54159659eae3774")
@ -68,17 +67,6 @@ class Llvm(CMakePackage, CudaPackage):
version("5.0.2", sha256="fe87aa11558c08856739bfd9bd971263a28657663cb0c3a0af01b94f03b0b795")
version("5.0.1", sha256="84ca454abf262579814a2a2b846569f6e0cb3e16dc33ca3642b4f1dff6fbafd3")
version("5.0.0", sha256="1f1843315657a4371d8ca37f01265fa9aae17dbcf46d2d0a95c1fdb3c6a4bab6")
version("4.0.1", sha256="cd664fb3eec3208c08fb61189c00c9118c290b3be5adb3215a97b24255618be5")
version("4.0.0", sha256="28ca4b2fc434cb1f558e8865386c233c2a6134437249b8b3765ae745ffa56a34")
version("3.9.1", sha256="f5b6922a5c65f9232f83d89831191f2c3ccf4f41fdd8c63e6645bbf578c4ab92")
version("3.9.0", sha256="9c6563a72c8b5b79941c773937d997dd2b1b5b3f640136d02719ec19f35e0333")
version("3.8.1", sha256="69360f0648fde0dc3d3c4b339624613f3bc2a89c4858933bc3871a250ad02826")
version("3.8.0", sha256="b5cc5974cc2fd4e9e49e1bbd0700f872501a8678bd9694fa2b36c65c026df1d1")
version("3.7.1", sha256="d2cb0eb9b8eb21e07605bfe5e7a5c6c5f5f8c2efdac01ec1da6ffacaabe4195a")
version("3.7.0", sha256="dc00bc230be2006fb87b84f6fe4800ca28bc98e6692811a98195da53c9cb28c6")
version("3.6.2", sha256="f75d703a388ba01d607f9cf96180863a5e4a106827ade17b221d43e6db20778a")
version("3.5.1", sha256="5d739684170d5b2b304e4fb521532d5c8281492f71e1a8568187bfa38eb5909d")
# fmt: on
# NOTE: The debug version of LLVM is an order of magnitude larger than
# the release version, and may take up 20-30 GB of space. If you want
@ -234,13 +222,11 @@ class Llvm(CMakePackage, CudaPackage):
depends_on("cmake@3.4.3:", type="build")
depends_on("cmake@3.13.4:", type="build", when="@12:")
depends_on("ninja", type="build")
depends_on("python@2.7:2.8", when="@:4 ~python", type="build")
depends_on("python", when="@5: ~python", type="build")
depends_on("python", when="~python", type="build")
depends_on("pkgconfig", type="build")
# Universal dependency
depends_on("python@2.7:2.8", when="@:4+python")
depends_on("python", when="@5:+python")
depends_on("python", when="+python")
# clang and clang-tools dependencies
depends_on("z3@4.7.1:", when="+z3")
@ -261,20 +247,14 @@ class Llvm(CMakePackage, CudaPackage):
depends_on("swig@3:", when="@12:")
depends_on("libedit", when="+lldb")
depends_on("ncurses", when="+lldb")
depends_on("py-six", when="@5.0.0: +lldb +python")
depends_on("py-six", when="+lldb+python")
# gold support, required for some features
depends_on("binutils+gold+ld+plugins", when="+gold")
# polly plugin
depends_on("gmp", when="@:3.6 +polly")
depends_on("isl", when="@:3.6 +polly")
# Older LLVM do not build with newer compilers, and vice versa
conflicts("%gcc@8:", when="@:5")
conflicts("%gcc@:5.0", when="@8:")
# clang/lib: a lambda parameter cannot shadow an explicitly captured entity
conflicts("%clang@8:", when="@:4")
# Internal compiler error on gcc 8.4 on aarch64 https://bugzilla.redhat.com/show_bug.cgi?id=1958295
conflicts("%gcc@8.4:8.4.9", when="@12: target=aarch64:")
@ -290,14 +270,6 @@ class Llvm(CMakePackage, CudaPackage):
conflicts("%clang@:10", when="@13:+libcxx")
conflicts("%apple-clang@:11", when="@13:+libcxx")
# libcxx-4 and compiler-rt-4 fail to build with "newer" clang and gcc versions:
conflicts("%gcc@7:", when="@:4+libcxx")
conflicts("%clang@6:", when="@:4+libcxx")
conflicts("%apple-clang@6:", when="@:4+libcxx")
conflicts("%gcc@7:", when="@:4+compiler-rt")
conflicts("%clang@6:", when="@:4+compiler-rt")
conflicts("%apple-clang@6:", when="@:4+compiler-rt")
# cuda_arch value must be specified
conflicts("cuda_arch=none", when="+cuda", msg="A value for cuda_arch must be specified.")
@ -306,14 +278,10 @@ class Llvm(CMakePackage, CudaPackage):
# Fixed in upstream versions of both
conflicts("^cmake@3.19.0", when="@6:11.0.0")
# Github issue #4986
patch("llvm_gcc7.patch", when="@4.0.0:4.0.1+lldb %gcc@7.0:")
# sys/ustat.h has been removed in favour of statfs from glibc-2.28. Use fixed sizes:
patch("llvm5-sanitizer-ustat.patch", when="@4:6.0.0+compiler-rt")
# Fix lld templates: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=230463
patch("llvm4-lld-ELF-Symbols.patch", when="@4+lld%clang@6:")
patch("llvm5-lld-ELF-Symbols.patch", when="@5+lld%clang@7:")
# Fix missing std:size_t in 'llvm@4:5' when built with '%clang@7:'

6
var/spack/repos/builtin/packages/madgraph5amc/package.py
View file

@ -32,11 +32,6 @@ class Madgraph5amc(MakefilePackage):
url="https://launchpad.net/mg5amcnlo/2.0/2.8.x/+download/MG5_aMC_v2.8.0.tar.gz",
)
version("2.7.3.py3", sha256="400c26f9b15b07baaad9bd62091ceea785c2d3a59618fdc27cad213816bc7225")
version(
"2.7.3.py2",
sha256="0b665356f4d9359e6e382e0f408dc11db594734567c6b2f0ec0e0697f2dbe099",
url="https://launchpad.net/mg5amcnlo/2.0/2.7.x/+download/MG5_aMC_v2.7.3.tar.gz",
)
variant(
"atlas",
@ -55,7 +50,6 @@ class Madgraph5amc(MakefilePackage):
depends_on("fastjet")
depends_on("py-six", when="@2.7.3.py3,2.8.0:", type=("build", "run"))
depends_on("python@2.7.0:2.8.0", when="@2.7.3.py2", type=("build", "run"))
depends_on("python@3.7:", when="@2.7.3.py3", type=("build", "run"))
depends_on("python@2.7.0:2.8.0,3.7:", when="@2.8.0:", type=("build", "run"))
depends_on("libtirpc")

44
var/spack/repos/builtin/packages/magics/package.py
View file

@ -28,22 +28,9 @@ class Magics(CMakePackage):
version("4.2.6", sha256="9b34a375d9125ab6e8a715b970da2e479f96370bac6a5bb8a015a079ed9e027c")
version("4.2.4", sha256="920c7dbb1aaabe65a31c6c18010829210f8b2f8d614b6c405dc5a4530e346f07")
version("4.1.0", sha256="da626c31f53716990754dd72ab7b2f3902a8ad924b23ef3309bd14900d170541")
version("2.34.3", sha256="38487562e83c0470f94d9c7fb9418cbadf92f1e643033237baba2abdc77e6238")
version("2.34.1", sha256="8df27f8f262ebc32a61f8696df15a7b4a6e4203b2a8e53fe7aa13caa1c4e3fa4")
version("2.33.0", sha256="32d3079749f89988715a8c3df01b712d9b989b7fd242828ec09563e47c5a3e82")
version("2.32.0", sha256="233b046c93b84be60ac8011212668de35c2693d89fffcaad333b42b8c4ffad06")
version("2.31.0", sha256="13c314661bb154499a87db9063238d6ecebad0d4fec37b0f3d90fe34aa37eec6")
version("2.29.6", sha256="88cfa5e2bd823c4669a3d2fe0349f14545e810333c1b4d031ce74a7a5218a2db")
version("2.29.4", sha256="82bdb4f7e38776776d2155a82d0acaa017402365a043731708345ac4ac00198f")
version("2.29.0", sha256="4c5067c4630e831bf81d15454476ff0d050c488b768f6a10272aad62ce8d0f92")
conflicts("%gcc@11:", when="@:4.4", msg="missing #include <limits>")
# The patch reorders includes and adds namespaces where necessary to
# resolve ambiguity of invocations of isnan and isinf functions. The
# patch is not needed since the version 2.29.1
patch("resolve_isnan_ambiguity.patch", when="@2.29.0")
variant(
"grib",
default="eccodes",
@ -52,7 +39,6 @@ class Magics(CMakePackage):
)
variant("netcdf", default=False, description="Enable NetCDF support")
variant("cairo", default=False, description="Enable cairo support[png/jpeg]")
variant("python", default=False, description="Enable Python interface")
variant("fortran", default=False, description="Enable Fortran interface")
variant("metview", default=False, description="Enable metview support")
variant("qt", default=False, description="Enable metview support with qt")
@ -69,7 +55,6 @@ class Magics(CMakePackage):
depends_on("cmake@2.8.11:", type="build")
depends_on("pkgconfig", type="build")
depends_on("python", type="build")
depends_on("python@:2", type="build", when="@:3")
depends_on("perl", type="build")
depends_on("perl-xml-parser", type="build")
@ -108,27 +93,8 @@ class Magics(CMakePackage):
depends_on("libemos grib=grib-api", when="+bufr grib=grib-api")
depends_on("qt", when="+metview+qt")
extends("python", when="+python")
# Python 2 is required for running the building scripts. Since we can't
# have two different versions of Python at the same time, we haven't even
# tested if the Python interface supports Python 3.
depends_on("python", when="+python", type=("link", "run"))
depends_on("py-numpy", when="+python", type=("build", "run"))
depends_on("swig", when="+python", type="build")
# Versions @4: supports python 2.7 and 3.x, and require python
# and py-jinja2 for build (even though does not build python interface)
depends_on("python", when="@4.0.0:", type=("build"))
depends_on("py-jinja2", when="@4.0.0:", type=("build"))
conflicts("grib=eccodes", when="@:2.29.0", msg="Eccodes is supported starting version 2.29.1")
conflicts(
"+python", when="@:2.28", msg="Python interface is supported starting version 2.29.0"
)
conflicts(
"+python",
when="@4:",
msg="Python interface is separate from the library " "starting with 4.0.0",
)
depends_on("python", type=("build"))
depends_on("py-jinja2", type=("build"))
# Replace system python and perl by spack versions:
def patch(self):
@ -162,12 +128,6 @@ def cmake_args(self):
else:
args.append("-DENABLE_CAIRO=OFF")
if "+python" in self.spec:
args.append("-DENABLE_PYTHON=ON")
else:
if self.spec.satisfies("@2.29.0:"):
args.append("-DENABLE_PYTHON=OFF")
if "+fortran" in self.spec:
args.append("-DENABLE_FORTRAN=ON")
else:

73
var/spack/repos/builtin/packages/magics/resolve_isnan_ambiguity.patch
View file

@ -1,73 +0,0 @@
--- a/src/common/Polyline.cc 2016-04-28 14:38:09.000000000 +0200
+++ b/src/common/Polyline.cc 2016-09-14 13:31:35.784617803 +0200
@@ -31,2 +30,0 @@
-#include "TeCoord2D.h"
-#include "TeGeometryAlgorithms.h"
--- a/src/decoders/GribRegularInterpretor.cc 2016-04-28 14:38:09.000000000 +0200
+++ b/src/decoders/GribRegularInterpretor.cc 2016-09-14 13:43:41.673614590 +0200
@@ -2083,2 +2083,2 @@
- if (isnan(val1)) {
- if (isnan(val2)) {
+ if (std::isnan(val1)) {
+ if (std::isnan(val2)) {
@@ -2090 +2090 @@
- if (isnan(val2)) {
+ if (std::isnan(val2)) {
@@ -2101 +2101 @@
- if (isnan(val) || isinf(val) || isinf(-val)) {
+ if (std::isnan(val) || std::isinf(val) || std::isinf(-val)) {
@@ -2105 +2105 @@
- if (isnan(val))
+ if (std::isnan(val))
--- a/src/decoders/GribSatelliteInterpretor.cc 2016-04-28 14:38:09.000000000 +0200
+++ b/src/decoders/GribSatelliteInterpretor.cc 2016-09-14 13:48:55.243699910 +0200
@@ -33,5 +32,0 @@
-#include "TeProjection.h"
-#include "TeDataTypes.h"
-#include "TeRasterParams.h"
-#include "TeDecoderMemory.h"
-#include "TeRasterRemap.h"
--- a/src/decoders/NetcdfGeoMatrixInterpretor.cc 2016-04-28 14:38:09.000000000 +0200
+++ b/src/decoders/NetcdfGeoMatrixInterpretor.cc 2016-09-14 13:52:37.481201085 +0200
@@ -93 +93 @@
- if ( !isnan(*d) ) {
+ if ( !std::isnan(*d) ) {
--- a/src/decoders/NetcdfOrcaInterpretor.cc 2016-04-28 14:38:09.000000000 +0200
+++ b/src/decoders/NetcdfOrcaInterpretor.cc 2016-09-14 13:51:16.248650570 +0200
@@ -210,2 +210,2 @@
- if ( isnan(val1) ) {
- if ( isnan(val2) ) {
+ if ( std::isnan(val1) ) {
+ if ( std::isnan(val2) ) {
@@ -218 +218 @@
- if ( isnan(val2) ) {
+ if ( std::isnan(val2) ) {
@@ -226 +226 @@
- if (isnan(val) || isinf(val) || isinf(-val) ) {
+ if (std::isnan(val) || std::isinf(val) || std::isinf(-val) ) {
@@ -230 +230 @@
- if (isnan(val) ) val = missing;
+ if (std::isnan(val) ) val = missing;
@@ -296 +296 @@
- if (isnan(value) )
+ if (std::isnan(value) )
--- a/src/terralib/kernel/TeCentroid.cpp 2016-04-28 14:38:09.000000000 +0200
+++ b/src/terralib/kernel/TeCentroid.cpp 2016-09-14 14:17:31.675996554 +0200
@@ -23,0 +24,2 @@
+#include "TeGeometryAlgorithms.h"
+
@@ -30 +31,0 @@
-#include "TeGeometryAlgorithms.h"
--- a/src/terralib/kernel/TeDatabase.h 2014-11-07 17:39:24.000000000 +0100
+++ b/src/terralib/kernel/TeDatabase.h 2016-09-14 14:20:01.041100590 +0200
@@ -33,0 +34 @@
+#include "TeGeometry.h"
@@ -38 +38,0 @@
-#include "TeGeometry.h"
--- a/src/terralib/kernel/TeOverlayUtils.h 2014-11-07 17:39:24.000000000 +0100
+++ b/src/terralib/kernel/TeOverlayUtils.h 2016-09-14 14:21:51.649920405 +0200
@@ -37,0 +38,2 @@
+#include "TeGeometry.h"
+
@@ -44 +45,0 @@
-#include "TeGeometry.h"

11
var/spack/repos/builtin/packages/manta/for_aarch64.patch
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@ -1,11 +0,0 @@
--- spack-src/src/cmake/boost.cmake.bak 2019-06-29 07:04:47.000000000 +0900
+++ spack-src/src/cmake/boost.cmake 2021-03-30 11:36:39.000000000 +0900
@@ -168,6 +168,8 @@
message (FATAL_ERROR "Failed to unpack boost library ${THIS_BOOST_VERSION}")
endif ()
execute_process(
+ COMMAND "sed" -i "s/-m64//g" ${BOOST_BUILD_DIR}/boost_1_58_0/tools/build/src/tools/gcc.jam)
+ execute_process(
COMMAND ${CMAKE_COMMAND} -E touch "${BOOST_BUILD_DIR}/boost_unpack_complete")
endif ()

26
var/spack/repos/builtin/packages/manta/package.py
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@ -1,26 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Manta(CMakePackage):
"""Structural variant and indel caller for mapped sequencing data"""
homepage = "https://github.com/Illumina/manta"
url = "https://github.com/Illumina/manta/releases/download/v1.3.2/manta-1.3.2.release_src.tar.bz2"
version("1.6.0", sha256="c846d61b02483265c09d58bd85dacf5326a94f38179b5ae4f70694be96e1368f")
version("1.5.0", sha256="9aa1a59c9cb8d2dd33724a42959c9398aff7840c5bf3c895d2483a8093b3d2dc")
version("1.4.0", sha256="4f8f827485e3ad9a12318bfcbf62fa622263378767514eb938bc02ad5ad74f10")
version("1.3.2", sha256="eb346d1a44aff1180732dcd03864b89efc1245652e1993107fb60da4ad739f79")
version("1.3.1", sha256="9ba943623088e552a4b45bccea48125a0553905f4cc7ea86a9de567e155a5888")
version("1.3.0", sha256="3db4b5475c33e3aeeb5435969c74364af9d2d77dd3bcf8dc70bf44a851e450dd")
depends_on("cmake@2.8.12:", type="build")
depends_on("python@2.7.0:2.7", type=("build", "run"))
depends_on("zlib")
patch("for_aarch64.patch", when="target=aarch64:")

1
var/spack/repos/builtin/packages/mbedtls/package.py
View file

@ -93,7 +93,6 @@ class Mbedtls(MakefilePackage):
depends_on("perl", type="test")
depends_on("python@3:", type="test", when="@3:")
depends_on("python@:2", type="test", when="@:2")
# See https://github.com/Mbed-TLS/mbedtls/issues/4917
# Only 2.16.12, 2.28.0 and 3.1.0 support clang 12.

10
var/spack/repos/builtin/packages/mercurial/package.py
View file

@ -23,16 +23,8 @@ class Mercurial(PythonPackage):
version("5.1.1", sha256="35fc8ba5e0379c1b3affa2757e83fb0509e8ac314cbd9f1fd133cf265d16e49f")
version("4.9.1", sha256="1bdd21bb87d1e05fb5cd395d488d0e0cc2f2f90ce0fd248e31a03595da5ccb47")
version("4.4.1", sha256="8f2a5512d6cc2ffb08988aef639330a2f0378e4ac3ee0e1fbbdb64d9fff56246")
version("4.1.2", sha256="09415253fb409a77e19b9951532a3c22c4e07e74bab80652527064617daab194")
version("3.9.1", sha256="625e4fc7e85ec2278c2828bdc547fce74091b3bbe4d9eeeba2d61af51195df74")
version("3.9", sha256="834f25dcff44994198fb8a7ba161a6e24204dbd63c8e6270577e06e6cedbdabc")
version("3.8.4", sha256="4b2e3ef19d34fa1d781cb7425506a05d4b6b1172bab69d6ea78874175fdf3da6")
version("3.8.3", sha256="f84556cdf9a331984261549d9d08143ab9da33d7c03f0aa323b0ee52d0782a4c")
version("3.8.2", sha256="cb78b16956140625266a8a6d1fadc7c868969d994086e1ec60279a66bf20bffd")
version("3.8.1", sha256="face1f058de5530b56b0dfd3b4d0b23d89590c588605c06f3d18b79e8c30d594")
depends_on("python+bz2+ssl+zlib@2.6:2.8", when="@:4.2", type=("build", "run"))
depends_on("python+bz2+ssl+zlib@2.7:2.8,3.5.3:3.5,3.6.2:", when="@4.3:", type=("build", "run"))
depends_on("python+bz2+ssl+zlib@2.7:2.8,3.5.3:3.5,3.6.2:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-docutils", type="build")
depends_on("py-pygments", type=("build", "run"))

1
var/spack/repos/builtin/packages/mlperf-deepcam/package.py
View file

@ -28,7 +28,6 @@ class MlperfDeepcam(Package, CudaPackage):
depends_on("py-pillow", type=("build", "run"))
depends_on("py-numpy", type=("build", "run"))
depends_on("py-pillow", type=("build", "run"))
depends_on("py-argparse", when="^python@:2.6,3.0:3.1", type=("build", "run"))
depends_on("py-pandas", type=("build", "run"))
depends_on("py-apex", type=("build", "run"))
depends_on("py-wandb", type=("build", "run"))

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@ -1,100 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
from spack.pkg.builtin.boost import Boost
class MofemCephas(CMakePackage):
"""MoFEM is finite element core library"""
homepage = "http://mofem.eng.gla.ac.uk"
git = "https://bitbucket.org/likask/mofem-cephas.git"
maintainers = ["likask"]
version("develop", branch="develop")
version("0.8.17", tag="v0.8.17")
version("0.8.16", tag="v0.8.16")
version("0.8.15", tag="v0.8.15")
version("0.8.14", tag="v0.8.14")
version("0.8.13", tag="v0.8.13")
version("0.8.12", tag="v0.8.12")
version("0.8.11", tag="v0.8.11")
version("0.8.10", tag="v0.8.10")
version("0.8.9", tag="v0.8.9")
version("0.8.8", tag="v0.8.8")
version("0.8.7", tag="v0.8.7")
# This option can be only used for development of core lib
variant(
"copy_user_modules",
default=True,
description="Copy user modules directory " "instead of linking to source",
)
variant("adol-c", default=True, description="Compile with ADOL-C")
variant("tetgen", default=True, description="Compile with Tetgen")
variant("med", default=True, description="Compile with Med")
variant("slepc", default=False, description="Compile with Slepc")
depends_on("mpi")
depends_on("boost@:1.68")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
depends_on("parmetis")
# Fixed version of hdf5, to remove some problems with dependent
# packages, f.e. MED format
depends_on("hdf5@:1.8.19+hl+mpi+fortran")
depends_on("petsc@:3.9.3+mumps+mpi")
depends_on("slepc", when="+slepc")
depends_on("moab")
# Upper bound set to ADOL-C until issues with memory leaks
# for versions 2.6: fully resolved
depends_on("adol-c@2.5.2~examples", when="+adol-c")
depends_on("tetgen", when="+tetgen")
depends_on("med", when="+med")
extendable = True
root_cmakelists_dir = "mofem"
def cmake_args(self):
spec = self.spec
options = []
# obligatory options
options.extend(
[
"-DWITH_SPACK=YES",
"-DPETSC_DIR=%s" % spec["petsc"].prefix,
"-DPETSC_ARCH=",
"-DMOAB_DIR=%s" % spec["moab"].prefix,
"-DBOOST_DIR=%s" % spec["boost"].prefix,
]
)
# build tests
options.append(self.define("MOFEM_BUILD_TESTS", self.run_tests))
# variant packages
if "+adol-c" in spec:
options.append("-DADOL-C_DIR=%s" % spec["adol-c"].prefix)
if "+tetgen" in spec:
options.append("-DTETGEN_DIR=%s" % spec["tetgen"].prefix)
if "+med" in spec:
options.append("-DMED_DIR=%s" % spec["med"].prefix)
if "+slepc" in spec:
options.append("-DSLEPC_DIR=%s" % spec["slepc"].prefix)
# copy users modules, i.e. stand alone vs linked users modules
options.append(self.define_from_variant("STAND_ALLONE_USERS_MODULES", "copy_user_modules"))
return options

102
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@ -1,102 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class MofemFractureModule(CMakePackage):
"""mofem fracture module"""
homepage = "http://mofem.eng.gla.ac.uk"
git = "https://bitbucket.org/likask/mofem_um_fracture_mechanics.git"
maintainers = ["likask"]
version("develop", branch="develop")
version("0.9.50", tag="v0.9.50")
version("0.9.49", tag="v0.9.49")
version("0.9.48", tag="v0.9.48")
version("0.9.47", tag="v0.9.47")
version("0.9.46", tag="v0.9.46")
version("0.9.45", tag="v0.9.45")
version("0.9.44", tag="v0.9.44")
version("0.9.42", tag="v0.9.42")
variant(
"copy_user_modules",
default=True,
description="Copy user modules directory instead linking",
)
extends("mofem-cephas")
depends_on("mofem-users-modules@0.8.17", when="@0.9.50")
depends_on("mofem-users-modules@0.8.16", when="@0.9.49")
depends_on("mofem-users-modules@0.8.15", when="@0.9.48")
depends_on("mofem-users-modules", type=("build", "link", "run"))
# The CMakeLists.txt installed with mofem-cephas package set cmake
# environment to install extension from extension repository. It searches
# for modules in user provides paths, for example in Spack source path.Also
# it finds all cmake exported targets installed in lib directory, which are
# built with dependent extensions, f.e.mofem - users - modules or others if
# needed.
@property
def root_cmakelists_dir(self):
"""The relative path to the directory containing CMakeLists.txt
This path is relative to the root of the extracted tarball,
not to the ``build_directory``. Defaults to the current directory.
:return: directory containing CMakeLists.txt
"""
spec = self.spec
return spec["mofem-users-modules"].prefix.users_modules
def cmake_args(self):
spec = self.spec
# obligatory options
options = [
self.define("WITH_SPACK", True),
self.define("EXTERNAL_MODULES_BUILD", True),
self.define("UM_INSTALL_BREFIX", spec["mofem-users-modules"].prefix),
self.define("EXTERNAL_MODULE_SOURCE_DIRS", self.stage.source_path),
self.define_from_variant("STAND_ALLONE_USERS_MODULES", "copy_user_modules"),
]
# Set module version
if self.spec.version == Version("develop"):
options.extend(
[
"-DFM_VERSION_MAJOR=%s" % 0,
"-DFM_VERSION_MINOR=%s" % 0,
"-DFM_VERSION_BUILD=%s" % 0,
]
)
else:
options.extend(
[
"-DFM_VERSION_MAJOR=%s" % self.spec.version[0],
"-DFM_VERSION_MINOR=%s" % self.spec.version[1],
"-DFM_VERSION_BUILD=%s" % self.spec.version[2],
]
)
# build tests
options.append(self.define("MOFEM_UM_BUILD_TESTS", self.run_tests))
return options
# This function is not needed to run code installed by extension, nor in
# the install process. However, for users like to have access to source
# code to play, change and make it. Having source code at hand one can
# compile in own build directory it in package view when the extension is
# activated.
@run_after("install")
def copy_source_code(self):
source = self.stage.source_path
prefix = self.prefix
install_tree(source, prefix.ext_users_modules.fracture_mechanics)

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var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py
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@ -1,81 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class MofemMinimalSurfaceEquation(CMakePackage):
"""mofem minimal surface equation"""
homepage = "http://mofem.eng.gla.ac.uk"
git = "https://bitbucket.org/likask/mofem_um_minimal_surface_equation.git"
maintainers = ["likask"]
version("develop", branch="develop")
version("0.3.10", tag="v0.3.10")
version("0.3.9", tag="v0.3.9")
variant(
"copy_user_modules",
default=True,
description="Copy user modules directory instead linking",
)
extends("mofem-cephas")
depends_on("mofem-users-modules", type=("build", "link", "run"))
# The CMakeLists.txt installed with mofem - cephas package set cmake
# environment to install extension from extension repository.It searches
# for modules in user provides paths, for example in Spack source path.Also
# it finds all cmake exported targets installed in lib directory, which are
# built with dependent extensions, f.e.mofem - users - modules or others if
# needed.
@property
def root_cmakelists_dir(self):
"""The relative path to the directory containing CMakeLists.txt
This path is relative to the root of the extracted tarball,
not to the ``build_directory``. Defaults to the current directory.
:return: directory containing CMakeLists.txt
"""
spec = self.spec
return spec["mofem-users-modules"].prefix.users_modules
def cmake_args(self):
spec = self.spec
from_variant = self.define_from_variant
source = self.stage.source_path
options = []
# obligatory options
options.extend(
[
"-DWITH_SPACK=YES",
"-DEXTERNAL_MODULES_BUILD=YES",
"-DUM_INSTALL_BREFIX=%s" % spec["mofem-users-modules"].prefix,
"-DEXTERNAL_MODULE_SOURCE_DIRS=%s" % source,
from_variant("STAND_ALLONE_USERS_MODULES", "copy_user_modules"),
]
)
# build tests
options.append(self.define("MOFEM_UM_BUILD_TESTS", self.run_tests))
return options
# This function is not needed to run code installed by extension, nor in
# the install process. However, for users like to have access to source
# code to play, change and make it. Having source code at hand one can
# compile in own build directory it in package view when the extension is
# activated.
@run_after("install")
def copy_source_code(self):
source = self.stage.source_path
prefix = self.prefix
install_tree(source, prefix.ext_users_modules.minimal_surface_equation)

80
var/spack/repos/builtin/packages/mofem-users-modules/package.py
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@ -1,80 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class MofemUsersModules(CMakePackage):
"""MofemUsersModules creates installation environment for user-provided
modules and extends of mofem-cephas package. For more information how to
work with Spack and MoFEM see
http://mofem.eng.gla.ac.uk/mofem/html/install_spack.html"""
homepage = "http://mofem.eng.gla.ac.uk"
git = "https://likask@bitbucket.org/mofem/users-modules-cephas.git"
version("develop", branch="develop")
version("0.8.17", commit="60b2341f1635f595d571096dd8c70a7cf7538aeb")
version("0.8.16", commit="f6af51ad7db5b5dbc9d9acc6e753277a857c9f24")
version("0.8.15", commit="4843b2d92ec21ad100a8d637698f56b3a2e14af3")
version("0.8.14", commit="cfaa32133c574a31beaeb36202d033280521ddff")
version("0.8.12", commit="7b2ce5595a95d1b919f50103513c44bb2bc9e6d2")
version("0.8.11", commit="329b06d758137f1ec830f157d383b5ea415963de")
version("0.8.10", commit="ca03a8222b20f9c8ff93a2d6f4c3babbcfde2058")
version("0.8.8", commit="eb40f3c218badcd528ab08ee952835fb2ff07fd3")
version("0.8.7", commit="a83b236f26f258f4d6bafc379ddcb9503088df56")
maintainers = ["likask"]
variant(
"copy_user_modules",
default=True,
description="Copy user modules directory instead linking",
)
extends("mofem-cephas")
depends_on("mofem-cephas@0.8.17", when="@0.8.17")
depends_on("mofem-cephas@0.8.16", when="@0.8.16")
depends_on("mofem-cephas@0.8.15", when="@0.8.15")
depends_on("mofem-cephas@0.8.14", when="@0.8.14")
depends_on("mofem-cephas@0.8.12:0.8.13", when="@0.8.12")
depends_on("mofem-cephas@0.8.11", when="@0.8.11")
depends_on("mofem-cephas@0.8.10", when="@0.8.10")
depends_on("mofem-cephas@0.8.8:0.8.9", when="@0.8.8")
depends_on("mofem-cephas@0.8.7", when="@0.8.7")
depends_on("mofem-cephas@develop", when="@develop")
def cmake_args(self):
spec = self.spec
from_variant = self.define_from_variant
options = []
# obligatory options
options.extend(
[
"-DMOFEM_DIR=%s" % spec["mofem-cephas"].prefix.users_module,
"-DWITH_SPACK=YES",
from_variant("STAND_ALLONE_USERS_MODULES", "copy_user_modules"),
]
)
# build tests
options.append(self.define("MOFEM_UM_BUILD_TESTS", self.run_tests))
return options
# This function is not needed to run code installed by extension, nor in
# the install process. However, the source code of users modules is
# necessary to compile other sub-modules. Also, for users like to have
# access to source code to play, change and make it. Having source code at
# hand one can compile in own build directory it in package view when the
# extension is activated.
@run_after("install")
def copy_source_code(self):
source = self.stage.source_path
prefix = self.prefix
install_tree(source, prefix.users_modules)

20
var/spack/repos/builtin/packages/mozjs/Bug-638056-Avoid-The-cacheFlush-support-is-missing-o.patch
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@ -1,20 +0,0 @@
From: Mike Hommey <mh@glandium.org>
Date: Fri, 18 Mar 2011 09:25:57 +0100
Subject: Bug 638056 - Avoid "The cacheFlush support is missing on this
platform" error on exotic platforms
---
js/src/Makefile.in | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
--- a/js/src/Makefile.in
+++ b/js/src/Makefile.in
@@ -382,7 +382,7 @@ CPPSRCS += checks.cc \
# END enclude sources for V8 dtoa
#############################################
-ifeq (,$(filter-out powerpc sparc,$(TARGET_CPU)))
+ifeq (,$(filter arm %86 x86_64,$(TARGET_CPU)))
VPATH += $(srcdir)/assembler \
$(srcdir)/assembler/wtf \

153
var/spack/repos/builtin/packages/mozjs/fix-811665.patch
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@ -1,153 +0,0 @@
Description: Fix FTBFS with gcc6
Most fixes are returning NULL instead of false and a narrowing issues.
Author: Tobias Frost <tobi@debian.org>
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811665
Last-Update: 2016-09-25
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/js/src/ctypes/CTypes.cpp
+++ b/js/src/ctypes/CTypes.cpp
@@ -4753,7 +4753,7 @@ NewFunctionInfo(JSContext* cx,
for (JSUint32 i = 0; i < argLength; ++i) {
bool isEllipsis;
if (!IsEllipsis(cx, argTypes[i], &isEllipsis))
- return false;
+ return NULL;
if (isEllipsis) {
fninfo->mIsVariadic = true;
if (i < 1) {
--- a/js/src/jsapi.cpp
+++ b/js/src/jsapi.cpp
@@ -3985,7 +3985,7 @@ JS_Enumerate(JSContext *cx, JSObject *ob
AutoIdVector props(cx);
JSIdArray *ida;
if (!GetPropertyNames(cx, obj, JSITER_OWNONLY, &props) || !VectorToIdArray(cx, props, &ida))
- return false;
+ return NULL;
for (size_t n = 0; n < size_t(ida->length); ++n)
JS_ASSERT(js_CheckForStringIndex(ida->vector[n]) == ida->vector[n]);
return ida;
--- a/js/src/jsfun.cpp
+++ b/js/src/jsfun.cpp
@@ -2051,7 +2051,7 @@ fun_toStringHelper(JSContext *cx, JSObje
JSString *str = JS_DecompileFunction(cx, fun, indent);
if (!str)
- return false;
+ return NULL;
if (!indent)
cx->compartment->toSourceCache.put(fun, str);
@@ -2657,7 +2657,7 @@ LookupInterpretedFunctionPrototype(JSCon
const Shape *shape = funobj->nativeLookup(id);
if (!shape) {
if (!ResolveInterpretedFunctionPrototype(cx, funobj))
- return false;
+ return NULL;
shape = funobj->nativeLookup(id);
}
JS_ASSERT(!shape->configurable());
--- a/js/src/jsiter.cpp
+++ b/js/src/jsiter.cpp
@@ -425,7 +425,7 @@ NewIteratorObject(JSContext *cx, uintN f
*/
JSObject *obj = js_NewGCObject(cx, FINALIZE_OBJECT0);
if (!obj)
- return false;
+ return NULL;
obj->init(cx, &js_IteratorClass, NULL, NULL, NULL, false);
obj->setMap(cx->compartment->emptyEnumeratorShape);
return obj;
--- a/js/src/jsparse.cpp
+++ b/js/src/jsparse.cpp
@@ -3352,7 +3352,7 @@ Parser::functionDef(JSAtom *funAtom, Fun
if (!outertc->inFunction() && bodyLevel && funAtom && !lambda && outertc->compiling()) {
JS_ASSERT(pn->pn_cookie.isFree());
if (!DefineGlobal(pn, outertc->asCodeGenerator(), funAtom))
- return false;
+ return NULL;
}
pn->pn_blockid = outertc->blockid();
--- a/js/src/jsstr.cpp
+++ b/js/src/jsstr.cpp
@@ -1734,7 +1734,7 @@ class RegExpGuard
if (flat) {
patstr = flattenPattern(cx, fm.patstr);
if (!patstr)
- return false;
+ return NULL;
} else {
patstr = fm.patstr;
}
@@ -3408,7 +3408,7 @@ js_InitStringClass(JSContext *cx, JSObje
UndefinedValue(), NULL, NULL,
JSPROP_READONLY | JSPROP_PERMANENT | JSPROP_SHARED, 0, 0,
NULL)) {
- return JS_FALSE;
+ return NULL;
}
return proto;
--- a/js/src/jstypedarray.cpp
+++ b/js/src/jstypedarray.cpp
@@ -1334,7 +1334,7 @@ class TypedArrayTemplate
if (size != 0 && count >= INT32_MAX / size) {
JS_ReportErrorNumber(cx, js_GetErrorMessage, NULL,
JSMSG_NEED_DIET, "size and count");
- return false;
+ return NULL;
}
int32 bytelen = size * count;
@@ -1668,7 +1668,7 @@ TypedArrayConstruct(JSContext *cx, jsint
default:
JS_NOT_REACHED("shouldn't have gotten here");
- return false;
+ return NULL;
}
}
--- a/js/src/jsxml.cpp
+++ b/js/src/jsxml.cpp
@@ -282,7 +282,7 @@ NewXMLNamespace(JSContext *cx, JSLinearS
obj = NewBuiltinClassInstanceXML(cx, &js_NamespaceClass);
if (!obj)
- return JS_FALSE;
+ return NULL;
JS_ASSERT(JSVAL_IS_VOID(obj->getNamePrefixVal()));
JS_ASSERT(JSVAL_IS_VOID(obj->getNameURIVal()));
JS_ASSERT(JSVAL_IS_VOID(obj->getNamespaceDeclared()));
@@ -431,7 +431,7 @@ ConvertQNameToString(JSContext *cx, JSOb
size_t length = str->length();
jschar *chars = (jschar *) cx->malloc((length + 2) * sizeof(jschar));
if (!chars)
- return JS_FALSE;
+ return NULL;
*chars = '@';
const jschar *strChars = str->getChars(cx);
if (!strChars) {
--- a/js/src/methodjit/InvokeHelpers.cpp
+++ b/js/src/methodjit/InvokeHelpers.cpp
@@ -728,7 +728,7 @@ AtSafePoint(JSContext *cx)
{
JSStackFrame *fp = cx->fp();
if (fp->hasImacropc())
- return false;
+ return NULL;
JSScript *script = fp->script();
return script->maybeNativeCodeForPC(fp->isConstructing(), cx->regs->pc);
--- a/js/src/nanojit/NativeX64.cpp
+++ b/js/src/nanojit/NativeX64.cpp
@@ -1899,7 +1899,7 @@ namespace nanojit
}
}
- static const AVMPLUS_ALIGN16(int64_t) negateMask[] = {0x8000000000000000LL,0};
+ static const AVMPLUS_ALIGN16(int64_t) negateMask[] = {(int64_t) 0x8000000000000000ULL,0};
void Assembler::asm_fneg(LIns *ins) {
Register rr, ra;

74
var/spack/repos/builtin/packages/mozjs/package.py
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@ -1,74 +0,0 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Mozjs(AutotoolsPackage):
"""SpiderMonkey is Mozilla's JavaScript engine written in C/C++.
It is used in various Mozilla products, including Firefox, and is
available under the MPL2."""
homepage = "https://firefox-source-docs.mozilla.org/js/index.html"
version(
"24.2.0",
sha256="e62f3f331ddd90df1e238c09d61a505c516fe9fd8c5c95336611d191d18437d8",
url="https://ftp.mozilla.org/pub/js/mozjs-24.2.0.tar.bz2",
)
version(
"17.0.0",
sha256="321e964fe9386785d3bf80870640f2fa1c683e32fe988eeb201b04471c172fba",
url="https://ftp.mozilla.org/pub/js/mozjs17.0.0.tar.gz",
)
version(
"1.8.5",
sha256="5d12f7e1f5b4a99436685d97b9b7b75f094d33580227aa998c406bbae6f2a687",
url="https://ftp.mozilla.org/pub/js/js185-1.0.0.tar.gz",
)
depends_on("perl@5.6:", type="build")
depends_on("pkgconfig", type="build")
depends_on("python@2.7.3:2.8", type="build")
depends_on("zip", type="build")
depends_on("unzip", type="build")
depends_on("nspr", when="@:27")
depends_on("libffi@3.0.9:")
depends_on("readline", when="@17.0.0:")
depends_on("zlib@1.2.3")
configure_directory = "js/src"
build_directory = "js/src/spack-build"
patch("perl-bug.patch")
# Note: According to https://github.com/apache/couchdb-pkg/tree/master/js/rpm/SOURCES
# There is some patch for mozjs@1.8.5 to fix compile issue.
# Patches required to fix the issue:https://bugzilla.mozilla.org/show_bug.cgi?id=638056
patch(
"Bug-638056-Avoid-The-cacheFlush-support-is-missing-o.patch",
sha256="b1c869a65f5ebc10741d4631cc2e1e166c6ed53035cfa56bede55a4c19b7b118",
when="@1.8.5",
)
patch(
"fix-811665.patch",
sha256="2b298b8a693865b38e2b0d33277bb5ffe152c6ecf43648e85113fec586aa4752",
when="@1.8.5",
)
def configure_args(self):
spec = self.spec
config_args = [
"--enable-readline", # enables readline support in JS shell
"--enable-threadsafe", # enables support for multiple threads
"--enable-system-ffi",
"--with-system-zlib={0}".format(spec["zlib"].prefix),
"--with-system-nspr",
"--with-nspr-prefix={0}".format(spec["nspr"].prefix),
]
if spec.target.family == "aarch64":
config_args.append("--host=aarch64-linux-gnu")
if spec.satisfies("@1.8.5"):
config_args.append("--disable-readline")
return config_args

21
var/spack/repos/builtin/packages/mozjs/perl-bug.patch
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@ -1,21 +0,0 @@
Perl has deprecated the feature:
defined(@array)
In Perl 5.22+, this deprecation warning has been converted
to a fatal error. This results in the following error message:
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at milestone.pl line 58.
This patch takes the suggestion of omitting defined().
--- a/js/src/config/milestone.pl 2017-02-14 15:00:42.234275243 -0600
+++ b/js/src/config/milestone.pl 2017-02-14 15:01:19.453313360 -0600
@@ -55,7 +55,7 @@
#
my $milestone = Moz::Milestone::getOfficialMilestone($MILESTONE_FILE);
-if (defined(@TEMPLATE_FILE)) {
+if (@TEMPLATE_FILE) {
my $TFILE;
foreach $TFILE (@TEMPLATE_FILE) {

25
var/spack/repos/builtin/packages/mpip/package.py
View file

@ -17,7 +17,6 @@ class Mpip(AutotoolsPackage):
version("master", branch="master")
version("3.5", sha256="e366843d53fa016fb03903e51c8aac901aa5155edabe64698a8d6fa618a03bbd")
version("3.4.1", sha256="66a86dafde61546be80a130c46e4295f47fb764cf312ae62c70a6dc456a59dac")
variant("demangling", default=True, description="Build with demangling support")
@ -56,14 +55,12 @@ class Mpip(AutotoolsPackage):
conflicts("platform=darwin")
# make-wrappers.py wrapper generator script requires python
depends_on("python@2:", when="@3.5:", type="build")
depends_on("python@:2", when="@3.4.1", type="build")
depends_on("python@2:", type="build")
depends_on("mpi")
# '+setjmp' adds '--disable-libunwind' to the confiure args
depends_on("unwind", when="@3.5: +libunwind ~setjmp")
depends_on("unwind", when="+libunwind ~setjmp")
@when("@3.5:")
def configure_args(self):
spec = self.spec
@ -122,21 +119,3 @@ def build_targets(self):
targets.append("shared")
return targets
@when("@3.4.1")
def configure_args(self):
config_args = ["--without-f77"]
config_args.append("--with-cc=%s" % self.spec["mpi"].mpicc)
config_args.append("--with-cxx=%s" % self.spec["mpi"].mpicxx)
if "+demangling" in self.spec:
config_args.append("--enable-demangling")
else:
config_args.append("--disable-demangling")
if "+setjmp" in self.spec:
config_args.append("--enable-setjmp")
else:
config_args.append("--disable-setjmp")
return config_args

1
var/spack/repos/builtin/packages/mxnet/package.py
View file

@ -110,7 +110,6 @@ class Mxnet(CMakePackage, CudaPackage):
depends_on("python@3.6:", when="@2.0.0:+python", type=("build", "run"))
depends_on("py-pip", when="+python", type="build")
depends_on("py-wheel", when="+python", type="build")
depends_on("py-contextvars", when="@2.0.0:+python ^python@3.6.0:3.6", type=("build", "run"))
depends_on("py-setuptools", when="+python", type="build")
depends_on("py-cython", when="+python", type="build")
depends_on("py-numpy@1.17:", when="@2.0.0:+python", type=("build", "run"))

20
var/spack/repos/builtin/packages/node-js/package.py
View file

@ -38,13 +38,6 @@ class NodeJs(Package):
version("12.18.3", sha256="6ea85f80e01b007cc9b566b8836513bc5102667d833bad4c1092be60fa60c2d4")
version("12.16.0", sha256="ae2dfe74485d821d4fef7cf1802acd2322cd994c853a2327c4306952f4453441")
version("12.14.0", sha256="5c1939867228f3845c808ef84a89c8ee93cc35f857bf7587ecee1b5a6d9da67b")
version("11.1.0", sha256="3f53b5ac25b2d36ad538267083c0e603d9236867a936c22a9116d95fa10c60d5")
version("10.13.0", sha256="aa06825fff375ece7c0d881ae0de5d402a857e8cabff9b4a50f2f0b7b44906be")
version("8.11.4", sha256="459144e361d64ca7362c37cc9717c044ef909d348cb5aa3f2b62538560a6085a")
version("8.9.1", sha256="32491b7fcc4696b2cdead45c47e52ad16bbed8f78885d32e873952fee0f971e1")
version("7.1.0", sha256="595e7e2a37d1e0573044a90077bb12c0f750e5d8851899ffa74038238da9a983")
version("6.3.0", sha256="4ed7a99985f8afee337cc22d5fef61b495ab4238dfff3750ac9019e87fc6aae6")
version("6.2.2", sha256="b6baee57a0ede496c7c7765001f7495ad74c8dfe8c34f1a6fb2cd5d8d526ffce")
variant("debug", default=False, description="Include debugger support")
variant("doc", default=False, description="Compile with documentation")
@ -66,12 +59,10 @@ class NodeJs(Package):
depends_on("gmake@3.81:", type="build")
depends_on("libtool", type="build", when=sys.platform != "darwin")
depends_on("pkgconfig", type="build")
depends_on("python@2.7:2.8,3.5:", when="@12:", type="build")
depends_on("python@2.7:2.8", when="@:11", type="build")
depends_on("python@2.7:2.8,3.5:", type="build")
# depends_on('bash-completion', when="+bash-completion")
depends_on("icu4c", when="+icu4c")
depends_on("openssl@1.0.2d:1.0", when="@:9+openssl")
depends_on("openssl@1.1:", when="@10:+openssl")
depends_on("openssl@1.1:", when="+openssl")
depends_on("zlib", when="+zlib")
phases = ["configure", "build", "install"]
@ -79,7 +70,7 @@ class NodeJs(Package):
# https://github.com/spack/spack/issues/19310
conflicts(
"%gcc@:4.8",
msg="fails to build with gcc 4.8 " "(see https://github.com/spack/spack/issues/19310",
msg="fails to build with gcc 4.8 (see https://github.com/spack/spack/issues/19310",
)
def setup_build_environment(self, env):
@ -135,10 +126,7 @@ def configure_args(self):
return args
def configure(self, spec, prefix):
if self.version >= Version("10.11.0"):
python("configure.py", *self.configure_args())
else:
python("configure", *self.configure_args())
python("configure.py", *self.configure_args())
def build(self, spec, prefix):
make()

1
var/spack/repos/builtin/packages/nrm/package.py
View file

@ -20,7 +20,6 @@ class Nrm(PythonPackage):
depends_on("py-pyyaml", type=("build", "run"))
depends_on("py-tornado@5.1.1", type=("build", "run"))
depends_on("py-numpy", type=("build", "run"))
depends_on("py-argparse@1.2.1:", type=("build", "run"), when="^python@:2.6,3.0:3.1")
depends_on("py-jsonschema@2.6.0", type=("build", "run"))
depends_on("py-warlock", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))

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