Commit graph

8191 commits

Author SHA1 Message Date
Dan Lipsa
83c7959580 Fix condition to enable mpi4py. (#11707)
* Fix condition to enable mpi4py.

* flake8

* Catalyst as paraview for mpi4py.

* Catalyst needs numpy and mpi4py.

* Remove leftover enable python.
2019-06-17 09:30:29 -04:00
Axel Huebl
b57ba6289c
openPMD-api: pybind11>=2.3.0 (#11744)
Update the dependency on pybind11 to the latest version
(constexpr signature support for all C++11 compilers + fixes).
2019-06-16 17:47:55 +02:00
Todd Gamblin
ce3a3507a4
cowsay: new package (#11743)
- A program that generates ASCII pictures of a cow with a message.

- This is used by the ISC19 Singularity tutorial, so we should probably
  have it in Spack.
2019-06-16 17:29:25 +02:00
Adam J. Stewart
3192318f36 Add py-geopandas 0.5.0 (#11737) 2019-06-16 08:57:13 +02:00
Adam J. Stewart
4965e9be53 Add libtiff 4.0.10 (#11732) 2019-06-16 08:52:16 +02:00
Adam J. Stewart
830964c2fb Add nasm 2.14.02 (#11729) 2019-06-16 08:50:05 +02:00
Adam J. Stewart
e259932a1e Add openjpeg 2.3.1 (#11728) 2019-06-16 08:49:36 +02:00
Adam J. Stewart
76490dcdbc Add py-cligj 0.5.0 (#11727) 2019-06-16 08:48:42 +02:00
Adam J. Stewart
69a746e941 Add py-numpy 1.16.4 (#11726) 2019-06-16 08:47:38 +02:00
Adam J. Stewart
7bb44f4620 Add libjpeg-turbo 2.0.2 (#11725) 2019-06-16 08:47:14 +02:00
Adam J. Stewart
92ab46b9ed Update URL for older version of jackcess (#11724) 2019-06-16 08:46:13 +02:00
Adam J. Stewart
53a4ea43c8 Add HDF 4.2.14 (#11723) 2019-06-16 08:45:23 +02:00
Adam J. Stewart
ffb7e83e65 Add new package py-boto3 (#11722) 2019-06-16 08:44:41 +02:00
Adam J. Stewart
0de9d15a49 Add new package py-s3transfer (#11721) 2019-06-16 08:43:41 +02:00
Adam J. Stewart
9a400d13a9 Add new package py-botocore (#11720) 2019-06-16 08:43:06 +02:00
Adam J. Stewart
2a15ab42fe Add new package py-jmespath (#11719) 2019-06-16 08:42:35 +02:00
Adam J. Stewart
07a90b214b Add new package py-freezegun (#11718) 2019-06-16 08:41:27 +02:00
Adam J. Stewart
639cb17322 Rename py-dateutil -> py-python-dateutil (#11717) 2019-06-16 08:40:56 +02:00
Adam J. Stewart
954a36c499 Add py-aenum package (#11716) 2019-06-16 08:39:54 +02:00
Kevin Manalo
91ef079511 intel: add version 19.0.4 (#11741) 2019-06-15 23:19:58 -05:00
Adam J. Stewart
3bad45fedf
Updates to poppler to get pdf2svg working (#11681) 2019-06-15 17:32:39 -05:00
Glenn Johnson
6592b4d46d Fix latest HPL for MKL use (#11712)
The 2.3 version of HPL needs LDFLAGS set for use of MKL libraries.
2019-06-15 15:46:59 -05:00
Axel Huebl
bccfb622e5 pybind11: v2.3.0 (#11713)
Add the latest 2.3.0 release and me as package maintainer.
2019-06-15 10:30:04 -05:00
brietzke
ef55319a9c new package: mutationpp (#11705)
* new package: mutationpp

* Update package.py

* flake8: correct package.py for flake8-python-style

* Update package.py

* modifications as requested by reviewer for #11705
2019-06-15 10:29:36 -05:00
Gabriel Rockefeller
537fa81c5d r3d: add version 2019-04-24 (#11710) 2019-06-15 14:27:03 +02:00
Justin S
9d6f37dc15 montage: new package at 6.0 (#11696) 2019-06-14 16:40:50 -05:00
Matthias Diener
f3eab78b80 scons: add version 3.0.5 (#11709) 2019-06-14 16:39:58 -05:00
Satish Balay
030f0951d4
dtk@develop now requires 'submodules=True' flag (#11694) 2019-06-14 11:04:48 -05:00
Justin M Wozniak
8afae13369 swift-t: New release packages for 1.4.3 (#11684) 2019-06-14 09:49:51 -05:00
Jordan Ogas
e275ddc169 add charliecloud-0.9.10 (#11471)
* add charliecloud-0.9.10; remove obsolete version

* revert older version changes; add version function

* fix space issue

* remove url declaration

* revert url removal

* remove self reference

* fix url; removed preferred tag; use newer package url
2019-06-13 16:50:55 -05:00
Mark W. Krentel
aca1bfdb6a intel-xed and hpcviewer: adapt to new resource placement (#11676)
Change 'destination' to 'placement' in the use of resource() for
intel-xed and hpcviewer.  Recent commits (1842873f and eb584d89)
changed the directory path for a resource and thus broke the build
for these packages.
2019-06-13 09:53:30 +02:00
marvinbernhardt
4f2144a68e added jpeg,png,ffmpeg variants to lammps (#10404) 2019-06-12 21:02:20 -06:00
Tamara Dahlgren
16530f84be Update remaining packages to use Stage.source_path (#11662)
#11528 updated Stage to always store a Package's source in a fixed
directory accessible via `Stage.source_path` This left behind a
number of packages which were expecting to access the source code
via `Stage.path`. This Updates those packages to use
`Stage.source_path` instead.

This also updates the name of the fixed directory: The original name
of the fixed directory was "src", so if an expanded archive created a
"src" directory, then users inspecting the directory structure could
see paths like "src/src" (which wasn't wrong but could be confusing).
Therefore this also updates the name of the fixed directory to
"spack-src".
2019-06-12 17:07:47 -07:00
Dave
fe8297da74 warpx: only allow master branch, and fix build on darwin (#11667)
* warpx: only allow master branch, and fix build on darwin

* warpx: Added CXXFLAGS=-std=c++11 for clang

* warpx: further clean up of openmp and c++11 flags

* warpx: Get around the problem with resources

The update uses placement instead of destination
2019-06-12 23:57:20 +02:00
Robert Pavel
a32382e787 Fixed Flecsi Backend Dependencies (#11679)
Fixed logic behind flecsi backends to not require legion for an mpi
build and to better support required combinations.
Also made graphviz support and tutorial building optional
2019-06-12 15:46:14 -06:00
Sinan
6ae5f38f26 new python package/py-typesentry (#11657)
* new python package/py-typesentry

* add proper version
2019-06-11 14:33:43 -04:00
Dan Lipsa
667e2f20fe Add support for using python3 in new verison of VTK. (#11673)
* Add support for python3 in new versions of VTK.
2019-06-11 12:50:22 -04:00
psakievich
a998fa25b0 Paraview: Add motionfx Intel workaround (#11608)
* Paraview/VTK: Fix failure on intel builds

Paraview@5.6.0 fails to build with intel compilers on certain platforms.
Error messages have been traced to the optional MotionFX lib.
(see https://discourse.paraview.org/t/error-build-5-6-0-rc1/572)
Turning off motionfx allows for succesful builds on these platforms.
2019-06-11 08:15:41 -04:00
Daniel Topa
35b1b81129 Add latest releases for pFUnit (#11642)
* Add latest releases for pFUnit
  - 3.2.10, 3.3.0, 3.3.1, 3.3.2, 3.3.3
  - 3.2.9 now with sha256
  - 4.0.0 is added, but commented out (build fails, see errors)

Verification builds

Darwin x86_64:
dantopa@cn100:pr-pfunit-darwin-general.spack $ spack find pfunit
==> 5 installed packages
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
pfunit@3.2.9  pfunit@3.2.10  pfunit@3.3.0  pfunit@3.3.1  pfunit@3.3.2  pfunit@3.3.3

Darwin Power9:
-- linux-rhel7-ppc64le / gcc@4.8.5 ------------------------------
pfunit@3.2.9  pfunit@3.2.10  pfunit@3.3.0  pfunit@3.3.1  pfunit@3.3.2  pfunit@3.3.3

Darwin ARM:
dantopa@cn805:pr-pfunit-darwin-arm.spack $ spack find pfunit
==> 5 installed packages
-- linux-rhel7-aarch64 / gcc@4.8.5 ------------------------------
pfunit@3.2.9  pfunit@3.2.10  pfunit@3.3.0  pfunit@3.3.1  pfunit@3.3.2  pfunit@3.3.3

2019-05-05

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* answer @citibeth comments

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* shortened offending comment to comply with flake8; suppressed error message on entry for v4.0.0

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* removed tailing space qt 20:55

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-06-10 18:19:52 -04:00
Geoffrey Oxberry
a52ed34fa4 ninja{-fortran}: make pkgs nonvirtual (fix #11628) (#11629) 2019-06-10 12:53:30 -04:00
Dan Lipsa
c98190a6ec ParaView and Catalyst use python3. (#11485)
Use python3 for latest paraview and catalyst versions.
2019-06-10 12:48:49 -04:00
Chuck Atkins
0953cd3a2e
Remove gnutls dependency and disable openssl when appropriate (#11646) 2019-06-10 11:19:26 -04:00
t-karatsu
7178ee3b63 Define LDFLAGS when using fujitsu compiler (#11669) 2019-06-10 11:01:32 -04:00
Quinn
58b797632e dateutils: new package (#11623)
* Adding the dateutils package
* Removing superfluous dependencies
2019-06-08 13:32:57 -07:00
Omar Padron
bdf831469a
fix qt build on gcc8.3 (#11633)
* fix qt build on gcc8.3

* source patches from upstream

* remove old code adding the same patch
2019-06-08 13:09:16 -04:00
Francois Budin
163ff9f1b6 Add ADIOS2 option to Trilinos (#11609)
ADIOS2 is the latest implementation of the ADaptable Input Output System,
ADIOS. This brand new architecture was designed to continue supporting the
performance legacy of ADIOS, and extend its current capabilities to address
current and future input/output (IO) challenges in the scientific data
lifecycle through effective research and development (R&D) activities.

ADIOS2 was recently added as a Third Party Library of Trilinos when it
was integrated to IOSS, a library inside the SEACAS package.
2019-06-08 16:34:34 +02:00
Jeffrey Salmond
9c1c50fb76 add openmp variant to lammps (#11643)
* add openmp variant to lammps

* add conflict for %gcc@9: and +openmp
2019-06-07 06:43:13 -06:00
Gregory Lee
7c8e9ab406 added tix package and python variant for tix (#11599)
* added tix package and python variant for tix

* addressing tix review requests

* python +tix requires +tkinter
2019-06-06 17:19:24 -04:00
Todd Gamblin
89b891d264
bugfix: lua-luafilesystem package should use stage.source_path (#11648) 2019-06-06 14:07:46 -07:00
Justin S
8c173da4b7 nettle: fix broken build (#11611)
* nettle: force C99 build

* nettle: update to use c99_flag

from @alalazo

Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2019-06-05 19:09:01 -05:00
Christoph Junghans
8fd64dfa08 lammps: added v20190605 (#11638) 2019-06-05 19:07:33 -05:00
Patrick Gartung
3c0b746f44
libxpm: revert change made in unrelated PR (#11634) 2019-06-05 15:13:19 -05:00
Gregory Lee
cfcf3996d8
set GUILE env var when building gnutls, fixes issue #11601 (#11607) 2019-06-05 10:14:06 -07:00
Andrew Gaspar
b3379a8890 Add Google Benchmark version 1.5.0 (#11626) 2019-06-04 22:53:07 -05:00
Patrick Gartung
efa45125fb
Revert "Git: patch to make git relocatable with buildcache. (#11596)" (#11625)
This reverts commit 30ec13f375.
2019-06-04 21:09:05 -05:00
Patrick Gartung
964a1d5997
Buildcache relocate.py error fix (#11616)
* Add a trailing / if file --mime does not return a mimetype with a / in it

* Flake8
2019-06-04 14:39:04 -05:00
Justin S
a7776972ad hotspot: new package at 6.0 (#11610) 2019-06-04 09:35:54 +02:00
Chuck Atkins
e4f0726927
mesa: Revert updated meson build and restore autotools build (#11595)
Due to the large number of issues this migration has caused, this rolls back
to the older autotools build.  However, it still keeps the updates wrt
variants and virtual packages.
2019-06-03 10:55:36 -04:00
Patrick Gartung
30ec13f375
Git: patch to make git relocatable with buildcache. (#11596)
* Apply patch to git to make it search for config files from its current location instead of the locations hard coded at install.

* Add provenance info for patch

* Pass needed flags to make

* Environment variables need because of relocation
2019-05-31 15:38:40 -05:00
sameershende
f5a2d7698d Package/tau/tau 2.28.1 update (#11591)
* Updating the TAU package with 2.28 and public repo

* Cleaning up TAU package and fixing binutils to install extras
The extras variant will install the extra ELF headers needed
by the TAU package.  The TAU package has been cleaned up and
extended.

* Adding some comments to the changes in binutils

* Adding correct python support, finding include and lib paths.

* Added PDT 3.25.1.

* Added TAU v2.28.1 with libdwarf and libelf.

* When +libdwarf is activated, +libelf is not automatically activated. It checks separately for libelf.
2019-05-31 10:01:19 -05:00
Justin S
a441fcbe69 alan: new package at 2.1.1 (#11593) 2019-05-30 17:50:14 -05:00
Valentin Reis
0b5ccd22da Adds the aml memory management library. (#11590)
AML is a collection of building blocks for explicit memory management on
complex architectures.

https://xgitlab.cels.anl.gov/argo/aml
https://argo-aml.readthedocs.io/en/latest/
2019-05-30 16:01:28 -05:00
Justin S
f089b9b053 r-randomglm: new package at 1.02-1 (#11589) 2019-05-30 13:35:01 -05:00
Nick Booher
786b59633d Revbayes update (#11559)
* revbayes: new version

* revbayes: pep8
2019-05-30 13:23:32 -04:00
Justin S
9b88f1b851 mathematica: new package at 12.0.0 (#11509)
* mathematica: new package at 12.0.0

* mathematica: add missing os import

* mathematica: fix url format
2019-05-30 13:21:16 -04:00
Frédéric Simonis
8b81f82156 precice: add version 1.5.0 (#11577) 2019-05-29 15:41:48 -05:00
Patrick Gartung
deab45e7c8 Xrootd: set PYTHON_EXECUTABLE with +python variant (#11581)
* Xrootd: set PYTHON_EXECUTABLE with +python variant

When building with python3 PYTHON_EXECUTABLE needs to be set for deprecated FindPythonInterp to work as expected.

* Add comment

* Flake8

* More flake8

* Update package.py

* typo
2019-05-29 15:41:30 -05:00
Patrick Gartung
7438bb7f45 ROOT: set PYTHON_EXECUTABLE (#11583)
Per @adamjstewart  use spec['python'].command.path
2019-05-29 15:41:13 -05:00
Justin S
ca05c2cbd8 py-flye: new package at 2.4.2 (#11584)
* py-flye: new package at 2.4.2

* py-flye: better python version constraint
2019-05-29 15:37:52 -05:00
Justin Too
a49ce3fc32 ROSE: add version 0.9.10.0, update to Autotools, add variants (#9484)
* Also add versions 0.9.9.104, 0.9.9.52, 0.9.9.0, and 'develop'
* Replace version 0.9.7 with 0.9.7.0
* Update Rose to be an Autotools package
* Update boost dependency to 1.60.0 or later (previously 1.47.0)
* Add EDG binary identifiers for ROSE versions installing from
  archives (rather than git)
* Add variants for mvapich2 backend, c++11, debug symbols,
  optimization, and ROSE-based projects (codethorn, autopar, and
  polyopt)
* Remove patch add_spack_compiler_recognition
2019-05-29 12:00:50 -07:00
Hadrien G
ca71f8b044 New versions and bugfixes for the ACTS package (#11578)
* Improve C++ standard computation in ACTS package

* Use a more clever strategy for aligning ACTS cxxstd with ROOT cxxstd

* Add new ACTS releases

* ACTS is not compatible with the new Boost CMake build system yet

* Explain why Boost 1.70 does not work currently
2019-05-29 13:45:09 -05:00
Dustin Wheeler
8804fbd891 Add LSF dependency for OpenMPI (#11532)
* Add LSF package, which cannot be installed by Spack and must be
  system-installed. The package install will fail if no external
  LSF is registered in packages.yaml (LSF may not be installed in a
  well-known location and the external entry helps Spack locate it
  for dependents).
* Add LSF dependency to OpenMPI when schedulers=lsf is chosen
2019-05-29 10:38:55 -07:00
Patrick Gartung
58a4959b1a
Add newer Google Benchmark version (#11580) 2019-05-29 12:02:41 -05:00
Patrick Gartung
3a20a93bfa
ROOT: Set PYTHON_EXECUTABLE with +python variant (#11579)
* ROOT: Set PYTHON_EXECUTABLE with +python variant

After cmake v3.12 FindPythonInterp used by llvm subsystem is deprecated. Setting -DPYTHON_EXECUTABLE=path_to_python fixes this error:

1 error found in build log:
     118    -- Doxygen disabled.
     119    -- Go bindings disabled.
     120    -- LLVM host triple: x86_64-unknown-linux-gnu
     121    -- LLVM default target triple: x86_64-unknown-linux-gnu
     122    -- Building with -fPIC
     123    -- Found PythonInterp: /usr/bin/python2.7
  >> 124    CMake Error at interpreter/llvm/src/CMakeLists.txt:613 (if):
     125      if given arguments:
     126    
     127        "VERSION_LESS" "2.7"
     128    
     129      Unknown arguments specified
     130

* Flake8

* Update var/spack/repos/builtin/packages/root/package.py

Co-Authored-By: Javier Cervantes <javiercvilla@gmail.com>
2019-05-29 12:02:21 -05:00
Kenneth Moreland
a7ffccfc97 vtkm: fix the directory cmake looks for the source code (#11576)
Previously, the vtkm package was adding a "../" option to the
cmake command line. I suppose this was supposed to be pointing
to the source code, but did not. Rather, Spack correctly adds
the source directory as the first argument to cmake. However,
because ../ was added, it used that as the source directory
instead.

Simply remove this argument to make CMake work correctly.
2019-05-29 11:10:12 -04:00
Axel Huebl
643e7806e0 Catch: 2.8.0 (#11570)
Add the latest Catch2 release.
2019-05-28 15:24:18 -05:00
mathsen
9c9a39538e GnuTLS by default depends on Guile, added a guile variant. Updated GnuTLS to 3.6.8 (#11571) 2019-05-28 15:23:59 -05:00
Satish Balay
0b57c3b8e5 petsc: add version 3.11.2 (#11572) 2019-05-28 15:23:00 -05:00
Denis Davydov
e094e19224 dealii: add 9.1.1 (#11573) 2019-05-28 15:22:39 -05:00
Daryl W. Grunau
6698d1dddb Add support for new unittest-cpp package (#11575)
* bump eospac version

* Revert "bump eospac version"

This reverts commit 835b1f822d8c083f6ab9eb17222c00409e8eb3da.

* Add support for new package: unittest-cpp
2019-05-28 15:21:24 -05:00
Levi Baber
36fda22ed9 r-geomorph: new version (#11556) 2019-05-26 23:34:17 -05:00
健美猞猁
47538a21ec Add a new version for gnutls. (#11546)
* Update URL and add a new version.

* Fix flake8 issues.

* Remove newly-added duplicate url_for_version.
2019-05-26 20:45:16 -05:00
Levi Baber
1efaaad344 py-markdown: new version (#11548) 2019-05-26 20:45:01 -05:00
健美猞猁
7433f9d2cc Add new versions for intel-mkl-dnn. (#11549)
* Add new versions for intel-mkl-dnn.

* Remove the last trailing line.

* Update url and set 0.19 as preferred.
2019-05-26 20:44:34 -05:00
Levi Baber
829bbd7884 r-emmli: new package (#11557) 2019-05-26 20:43:22 -05:00
Olaf Mersmann
af2de9eb2a Update GnuPG and associated packages (#11564)
* libassuan: Update to v2.5.3

* gnupg: Update to v2.2.15

* libgpg-error: Update to v1.36

* libgcrypt: Update to v1.8.4
2019-05-26 20:41:37 -05:00
Axel Huebl
86b2156921 New Package: sl (#11565)
Add the sl program.
2019-05-26 20:40:55 -05:00
Satish Balay
727089c4ef
xsdk@0.4.0: update dealii defaults wrt changes in a973ab475 (#11562)
wrt xsdk@develop - ginkgo requires openmp - so disable until we can add openmp dependencies consistantly
2019-05-26 10:43:06 -05:00
Mark W. Krentel
7c32a4c399 mbedtls: add pic variant (#11558)
Add variant 'pic' for including in shared libraries.

Add build dependency on perl.  Compiling mbedtls runs several perl
scripts.

Add versions 2.7.10 and 2.16.1, the heads of the two main stable
branches.
2019-05-24 21:50:13 -05:00
Stephen Hudson
bb09bdedc6 Update libensemble to v0.5.0 (#11544) 2019-05-24 15:11:56 -05:00
健美猞猁
137cad2915 Add nettle@3.4.1 (#11547) 2019-05-24 15:08:02 -05:00
Massimiliano Culpo
c291866b9a build env: simplify handling of parallel jobs (#11524)
This PR implements several refactors requested in #11373, specifically:

- Config scopes are used to handle builtin defaults, command line overrides 
  and package overrides (`parallel=False`)
- `Package.make_jobs` attribute has been removed; `make_jobs` remains
  as a module-scope variable in the build environment.
- The use of the argument `-j` has been rationalized across commands
  - move '-j'/'--jobs' argument into `spack.cmd.common.arguments`
- Add unit tests to check that setting parallel jobs works as expected
  - add new test to ensure that build job setting is isolated to each build
- Fix packages that used `Package.make_jobs` (i.e. `bazel`)
2019-05-24 11:45:22 -07:00
Massimiliano Culpo
1bd4521f72 Updated lmod (to version 8.1.5) and associated dependencies (#11552)
Lmod version 8.1.5
Lua version 5.3.5
Lua Filesystem 1.7.0.2

Turned tcl to a link dependency so that Lmod's configure can find it.
2019-05-24 12:45:52 -05:00
Adam J. Stewart
6212e0d9b2
Add latest version of py-cython (#11494)
* Add latest version of py-cython

* Fix cython unit tests
2019-05-23 20:01:45 -05:00
Hans Pabst
d6cf3b6718 LIBXSMM 1.12.1 (#11538) 2019-05-23 10:16:32 -05:00
Jon Rood
4c465d2602 Add cppcheck version 1.87. (#11536) 2019-05-22 18:52:48 -05:00
Jon Rood
e57edebb50 Add CMake 3.14.3 and 3.14.4. (#11534) 2019-05-22 15:46:52 -05:00
Omar Padron
a37efefd3d
package vtk - improve gl handling (#11530)
* package vtk - improve gl handling

* package vtk - minor cleanup
2019-05-22 12:04:29 -04:00
Dustin Wheeler
c2e087c411 Fix typo in openmpi@2.1.6 libmpi.so comment. (#11529) 2019-05-22 10:37:33 -05:00
Denis Davydov
a973ab4751 dealii: add 9.1.0 (#11527) 2019-05-21 16:23:03 -05:00