From 3edfa390f7abc902cbb1a2c66423f5228cd7b467 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Mon, 15 Aug 2016 11:19:40 +0100 Subject: [PATCH 01/12] Basic package file for plumed and boilerplate for external intel mpi --- etc/spack/packages.yaml | 5 + .../builtin/packages/intelmpi/package.py | 17 +++ .../repos/builtin/packages/plumed/package.py | 100 +++++------------- 3 files changed, 46 insertions(+), 76 deletions(-) create mode 100644 etc/spack/packages.yaml create mode 100644 var/spack/repos/builtin/packages/intelmpi/package.py diff --git a/etc/spack/packages.yaml b/etc/spack/packages.yaml new file mode 100644 index 0000000000..41d8c5f9f6 --- /dev/null +++ b/etc/spack/packages.yaml @@ -0,0 +1,5 @@ +packages: + intelmpi: + paths: + intelmpi@4.1.0%gcc@4.4.7 arch=linux-x86_64: /software/compilers/intel/13.0/impi/4.1.0.024 + buildable: False diff --git a/var/spack/repos/builtin/packages/intelmpi/package.py b/var/spack/repos/builtin/packages/intelmpi/package.py new file mode 100644 index 0000000000..16cfbab260 --- /dev/null +++ b/var/spack/repos/builtin/packages/intelmpi/package.py @@ -0,0 +1,17 @@ +from spack import * + +class Intelmpi(Package): + """Intel MPI""" + + homepage = "http://www.example.com" + url = "https://software.intel.com/en-us/intel-mpi-library" + + version('4.1.0') + + # Provides a virtual dependency 'mpi' + provides('mpi') + +# def install(self, spec, prefix): +# configure("--prefix=%s" % prefix) +# make() +# make("install") diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index b670b4c2b8..b179076b7f 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -22,91 +22,39 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -import subprocess - +# +# This is a template package file for Spack. We've put "FIXME" +# next to all the things you'll want to change. Once you've handled +# them, you can save this file and test your package like this: +# +# spack install plumed +# +# You can edit this file again by typing: +# +# spack edit plumed +# +# See the Spack documentation for more information on packaging. +# If you submit this package back to Spack as a pull request, +# please first remove this boilerplate and all FIXME comments. +# from spack import * class Plumed(Package): """PLUMED is an open source library for free energy calculations in - molecular systems which works together with some of the most popular - molecular dynamics engines. + molecular systems which works together with some of the most popular + molecular dynamics engines.""" - Free energy calculations can be performed as a function of many order - parameters with a particular focus on biological problems, using state - of the art methods such as metadynamics, umbrella sampling and - Jarzynski-equation based steered MD. + # FIXME: Add a proper url for your package's homepage here. + homepage = "http://www.plumed.org/home" + url = "https://github.com/plumed/plumed2" - The software, written in C++, can be easily interfaced with both fortran - and C/C++ codes. - """ - homepage = 'http://www.plumed.org/' - url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz' + version('2.2.3', git="https://github.com/plumed/plumed2.git", tag='v2.2.3') - version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8') - - variant('shared', default=True, description='Builds shared libraries') - variant('mpi', default=True, description='Activates MPI support') - variant('gsl', default=True, description='Activates GSL support') - - depends_on('zlib') - depends_on('blas') - depends_on('lapack') - - depends_on('mpi', when='+mpi') - depends_on('gsl', when='+gsl') - - # Dictionary mapping PLUMED versions to the patches it provides - # interactively - plumed_patches = { - '2.2.3': { - 'amber-14': '1', - 'gromacs-4.5.7': '2', - 'gromacs-4.6.7': '3', - 'gromacs-5.0.7': '4', - 'gromacs-5.1.2': '5', - 'lammps-6Apr13': '6', - 'namd-2.8': '7', - 'namd-2.9': '8', - 'espresso-5.0.2': '9' - } - } - - def apply_patch(self, other): - plumed = subprocess.Popen( - [join_path(self.spec.prefix.bin, 'plumed'), 'patch', '-p'], - stdin=subprocess.PIPE - ) - opts = Plumed.plumed_patches[str(self.version)] - search = '{0.name}-{0.version}'.format(other) - choice = opts[search] + '\n' - plumed.stdin.write(choice) - plumed.wait() - - def setup_dependent_package(self, module, ext_spec): - # Make plumed visible from dependent packages - module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed')) + # FIXME: Add additional dependencies if required. + depends_on('intelmpi') def install(self, spec, prefix): - # From plumed docs : - # Also consider that this is different with respect to what some other - # configure script does in that variables such as MPICXX are - # completely ignored here. In case you work on a machine where CXX is - # set to a serial compiler and MPICXX to a MPI compiler, to compile - # with MPI you should use: - # - # > ./configure CXX="$MPICXX" - configure_opts = [ - 'CXX={0}'.format(spec['mpi'].mpicxx) - ] if '+mpi' in self.spec else [] - - configure_opts.extend([ - '--prefix={0}'.format(prefix), - '--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'), - '--enable-mpi={0}'.format('yes' if '+mpi' in spec else 'no'), - '--enable-gsl={0}'.format('yes' if '+gsl' in spec else 'no') - ]) - - configure(*configure_opts) + # FIXME: Unknown build system make() make('install') From 27793d97dc18d235d4548d3f58176b60c70a2e40 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Mon, 15 Aug 2016 16:16:00 +0100 Subject: [PATCH 02/12] temp commit in current state --- var/spack/repos/builtin/packages/intelmpi/package.py | 6 ++++++ var/spack/repos/builtin/packages/plumed/package.py | 7 ++++--- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/intelmpi/package.py b/var/spack/repos/builtin/packages/intelmpi/package.py index 16cfbab260..7fec2a5832 100644 --- a/var/spack/repos/builtin/packages/intelmpi/package.py +++ b/var/spack/repos/builtin/packages/intelmpi/package.py @@ -11,6 +11,12 @@ class Intelmpi(Package): # Provides a virtual dependency 'mpi' provides('mpi') + def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) + spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) + spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) + spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + # def install(self, spec, prefix): # configure("--prefix=%s" % prefix) # make() diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index b179076b7f..58b3ba17c4 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -52,9 +52,10 @@ class Plumed(Package): version('2.2.3', git="https://github.com/plumed/plumed2.git", tag='v2.2.3') # FIXME: Add additional dependencies if required. - depends_on('intelmpi') + depends_on('mpi') def install(self, spec, prefix): - # FIXME: Unknown build system + configure("--prefix=" + prefix, + "--enable-mpi", + "-enable-modules=crystallization") make() - make('install') From b99e945e6da8f3e38090fe8e30f21bf105449240 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Wed, 17 Aug 2016 15:43:59 +0100 Subject: [PATCH 03/12] Added variants and dependencies to plumed but I'm getting an error when trying to resolve mpi to a valid virtual package --- etc/spack/packages.yaml | 5 +- .../builtin/packages/intelmpi/package.py | 31 ++++++++++ .../repos/builtin/packages/plumed/package.py | 61 +++++++++++++------ 3 files changed, 76 insertions(+), 21 deletions(-) diff --git a/etc/spack/packages.yaml b/etc/spack/packages.yaml index 41d8c5f9f6..e89562e8d2 100644 --- a/etc/spack/packages.yaml +++ b/etc/spack/packages.yaml @@ -1,5 +1,8 @@ packages: intelmpi: paths: - intelmpi@4.1.0%gcc@4.4.7 arch=linux-x86_64: /software/compilers/intel/13.0/impi/4.1.0.024 + intelmpi@4.1.0%gcc@4.4.7 arch=linux-x86_64: /software/compilers/intel/13.0/impi/4.1.0.024/intel64 buildable: False + all: + providers: + mpi: [intelmpi, openmpi] diff --git a/var/spack/repos/builtin/packages/intelmpi/package.py b/var/spack/repos/builtin/packages/intelmpi/package.py index 7fec2a5832..6750ee695a 100644 --- a/var/spack/repos/builtin/packages/intelmpi/package.py +++ b/var/spack/repos/builtin/packages/intelmpi/package.py @@ -1,3 +1,27 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## from spack import * class Intelmpi(Package): @@ -17,6 +41,13 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec): spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + def setup_dependent_package(self, module, dep_spec): + self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') + self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') + self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') + self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') + self.spec.cppflags = '-DMPICH_IGNORE_CXX_SEEK' + # def install(self, spec, prefix): # configure("--prefix=%s" % prefix) # make() diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index 58b3ba17c4..023de82b9b 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -22,21 +22,6 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -# -# This is a template package file for Spack. We've put "FIXME" -# next to all the things you'll want to change. Once you've handled -# them, you can save this file and test your package like this: -# -# spack install plumed -# -# You can edit this file again by typing: -# -# spack edit plumed -# -# See the Spack documentation for more information on packaging. -# If you submit this package back to Spack as a pull request, -# please first remove this boilerplate and all FIXME comments. -# from spack import * @@ -51,11 +36,47 @@ class Plumed(Package): version('2.2.3', git="https://github.com/plumed/plumed2.git", tag='v2.2.3') - # FIXME: Add additional dependencies if required. - depends_on('mpi') + # Variants + variant('crystallization', default=False, + description='Build support for optional crystallization module.') + variant('imd', default=False, + description='Build support for optional imd module.') + variant('manyrestraints', default=False, + description='Build support for optional manyrestraints module.') + variant('mpi', default=False, + description='Enable MPI support.') + + # Dependencies + depends_on("mpi", when="+mpi") + depends_on("netlib-lapack") + depends_on("openblas") def install(self, spec, prefix): - configure("--prefix=" + prefix, - "--enable-mpi", - "-enable-modules=crystallization") + configure("--prefix=" + prefix) +# "--enable-mpi", +# "-enable-modules=crystallization") + + # Construct list of optional modules + module_opts=[] + module_opts.extend([ + '+crystallization' if '+crystallization' in spec else '-crystallization', + '+imd' if '+imd' in spec else '-imd', + '+manyrestraints' if '+manyrestraints' in spec else '-manyrestraints' + ]) + + # Add optional arguments based on specs and variants +# config_args.extend([ + # Modules +# "--enable-modules=%s" % "".join(module_opts) if module_opts is not None, +# "--enable-mpi" if '+mpi' in spec +# ]) + + if modules_opts: + config_args.extend(["--enable-modules=%s" % "".join(module_opts)]) + + config_args.extend([ + "--enable-mpi" if '+mpi' in spec else "--disable-mpi" + ]) + make() + make("install") From 6641f424177ca3565a99c493827582f5511b100a Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Thu, 18 Aug 2016 13:19:36 +0100 Subject: [PATCH 04/12] Not compiling due to mpi error. Also getting this error from the command line so could be separate issue. Otherwise package definition first draft complete. --- etc/spack/packages.yaml | 6 +-- .../builtin/packages/intelmpi/package.py | 9 ++-- .../repos/builtin/packages/plumed/package.py | 44 ++++++++++++------- 3 files changed, 36 insertions(+), 23 deletions(-) diff --git a/etc/spack/packages.yaml b/etc/spack/packages.yaml index e89562e8d2..abdd888351 100644 --- a/etc/spack/packages.yaml +++ b/etc/spack/packages.yaml @@ -3,6 +3,6 @@ packages: paths: intelmpi@4.1.0%gcc@4.4.7 arch=linux-x86_64: /software/compilers/intel/13.0/impi/4.1.0.024/intel64 buildable: False - all: - providers: - mpi: [intelmpi, openmpi] +# all: +# providers: +# mpi: [intelmpi] diff --git a/var/spack/repos/builtin/packages/intelmpi/package.py b/var/spack/repos/builtin/packages/intelmpi/package.py index 6750ee695a..5a9cdcdbf1 100644 --- a/var/spack/repos/builtin/packages/intelmpi/package.py +++ b/var/spack/repos/builtin/packages/intelmpi/package.py @@ -37,16 +37,19 @@ class Intelmpi(Package): def setup_dependent_environment(self, spack_env, run_env, dependent_spec): spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++')) + spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx')) spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) + # NOTE: Need to find a better way of setting this compiler argument + # which is only required when building packages with intelmpi. + spack_env.set('CXXFLAGS', '-DMPICH_IGNORE_CXX_SEEK') def setup_dependent_package(self, module, dep_spec): self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') - self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++') + self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx') self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') - self.spec.cppflags = '-DMPICH_IGNORE_CXX_SEEK' +# self.spec.cxxflags = '-DMPICH_IGNORE_CXX_SEEK' # def install(self, spec, prefix): # configure("--prefix=%s" % prefix) diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index 023de82b9b..b1e74c5827 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -30,13 +30,15 @@ class Plumed(Package): molecular systems which works together with some of the most popular molecular dynamics engines.""" - # FIXME: Add a proper url for your package's homepage here. + # PLUMED homepage. The source is available on github. homepage = "http://www.plumed.org/home" url = "https://github.com/plumed/plumed2" version('2.2.3', git="https://github.com/plumed/plumed2.git", tag='v2.2.3') - # Variants + # Variants. PLUMED by default builds a number of optional modules. + # The ones listed here are not built by default for various reasons, + # such as stability, lack of testing, or lack of demand. variant('crystallization', default=False, description='Build support for optional crystallization module.') variant('imd', default=False, @@ -46,15 +48,14 @@ class Plumed(Package): variant('mpi', default=False, description='Enable MPI support.') - # Dependencies + # Dependencies. LAPACK and BLAS are recommended but not essential. depends_on("mpi", when="+mpi") depends_on("netlib-lapack") depends_on("openblas") def install(self, spec, prefix): - configure("--prefix=" + prefix) -# "--enable-mpi", -# "-enable-modules=crystallization") + # Prefix is the only compulsory argument. + config_args = ["--prefix=" + prefix] # Construct list of optional modules module_opts=[] @@ -64,19 +65,28 @@ def install(self, spec, prefix): '+manyrestraints' if '+manyrestraints' in spec else '-manyrestraints' ]) - # Add optional arguments based on specs and variants -# config_args.extend([ - # Modules -# "--enable-modules=%s" % "".join(module_opts) if module_opts is not None, -# "--enable-mpi" if '+mpi' in spec -# ]) - - if modules_opts: + # If we have specified any optional modules then add the argument ro + # enable or disable them. + if module_opts: config_args.extend(["--enable-modules=%s" % "".join(module_opts)]) - config_args.extend([ - "--enable-mpi" if '+mpi' in spec else "--disable-mpi" - ]) + # If using MPI then ensure the correct compiler wrapper is used. + if '+mpi' in spec: + config_args.extend([ + "--enable-mpi", + "CC=%s" % self.spec['mpi'].mpicc, + "CXX=%s" % self.spec['mpi'].mpicxx, + "FC=%s" % self.spec['mpi'].mpifc, + "F77=%s" % self.spec['mpi'].mpif77 + ]) + + # Add remaining variant flags. +# config_args.extend([ +# "--enable-mpi" if '+mpi' in spec else "--disable-mpi" +# ]) + + # Configure + configure(*config_args) make() make("install") From 13f636ec6879c992b3a73e0e4f8d6843b1de3397 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Fri, 19 Aug 2016 15:00:21 +0100 Subject: [PATCH 05/12] Added required arguments to get plumed to build with intelmpi --- .../repos/builtin/packages/plumed/package.py | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index b1e74c5827..95f32fc42c 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -60,12 +60,14 @@ def install(self, spec, prefix): # Construct list of optional modules module_opts=[] module_opts.extend([ - '+crystallization' if '+crystallization' in spec else '-crystallization', + '+crystallization' if ( + '+crystallization' in spec) else '-crystallization', '+imd' if '+imd' in spec else '-imd', - '+manyrestraints' if '+manyrestraints' in spec else '-manyrestraints' + '+manyrestraints' if ( + '+manyrestraints' in spec) else '-manyrestraints' ]) - # If we have specified any optional modules then add the argument ro + # If we have specified any optional modules then add the argument to # enable or disable them. if module_opts: config_args.extend(["--enable-modules=%s" % "".join(module_opts)]) @@ -80,10 +82,13 @@ def install(self, spec, prefix): "F77=%s" % self.spec['mpi'].mpif77 ]) - # Add remaining variant flags. -# config_args.extend([ -# "--enable-mpi" if '+mpi' in spec else "--disable-mpi" -# ]) + # If the MPI dependency is provided by the intelmpi package then + # the following additional argument is required to allow it to + # build. + if spec.satisfies('^intelmpi'): + config_args.extend([ + "STATIC_LIBS=-mt_mpi" + ]) # Configure configure(*config_args) From 90e5ccd98c8cc5ecbd57c95b22905f6a7060ebf4 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Fri, 19 Aug 2016 15:01:46 +0100 Subject: [PATCH 06/12] Cleaned up commented out code in intelmpi package --- var/spack/repos/builtin/packages/intelmpi/package.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/var/spack/repos/builtin/packages/intelmpi/package.py b/var/spack/repos/builtin/packages/intelmpi/package.py index 5a9cdcdbf1..5a0382a392 100644 --- a/var/spack/repos/builtin/packages/intelmpi/package.py +++ b/var/spack/repos/builtin/packages/intelmpi/package.py @@ -49,9 +49,3 @@ def setup_dependent_package(self, module, dep_spec): self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx') self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') -# self.spec.cxxflags = '-DMPICH_IGNORE_CXX_SEEK' - -# def install(self, spec, prefix): -# configure("--prefix=%s" % prefix) -# make() -# make("install") From 0c8462723b955fe4b650fb7331a8df3769284a57 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Mon, 22 Aug 2016 11:24:03 +0100 Subject: [PATCH 07/12] Found upstream plumed package and modified this one to match --- .../repos/builtin/packages/plumed/package.py | 125 +++++++++++++----- 1 file changed, 89 insertions(+), 36 deletions(-) diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index 95f32fc42c..c261e90fd8 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -22,17 +22,26 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## +import subprocess + from spack import * class Plumed(Package): """PLUMED is an open source library for free energy calculations in - molecular systems which works together with some of the most popular - molecular dynamics engines.""" + molecular systems which works together with some of the most popular + molecular dynamics engines. - # PLUMED homepage. The source is available on github. - homepage = "http://www.plumed.org/home" - url = "https://github.com/plumed/plumed2" + Free energy calculations can be performed as a function of many order + parameters with a particular focus on biological problems, using state + of the art methods such as metadynamics, umbrella sampling and + Jarzynski-equation based steered MD. + + The software, written in C++, can be easily interfaced with both fortran + and C/C++ codes. + """ + homepage = 'http://www.plumed.org/' + url = 'https://github.com/plumed/plumed2' version('2.2.3', git="https://github.com/plumed/plumed2.git", tag='v2.2.3') @@ -45,17 +54,80 @@ class Plumed(Package): description='Build support for optional imd module.') variant('manyrestraints', default=False, description='Build support for optional manyrestraints module.') - variant('mpi', default=False, - description='Enable MPI support.') + variant('shared', default=True, description='Builds shared libraries') + variant('mpi', default=True, description='Activates MPI support') + variant('gsl', default=True, description='Activates GSL support') - # Dependencies. LAPACK and BLAS are recommended but not essential. - depends_on("mpi", when="+mpi") - depends_on("netlib-lapack") - depends_on("openblas") + # Dependencies. LAPACK and BLAS are recommended but not essentia + depends_on('zlib') + depends_on('blas') + depends_on('lapack') + + depends_on('mpi', when='+mpi') + depends_on('gsl', when='+gsl') + + # Dictionary mapping PLUMED versions to the patches it provides + # interactively + plumed_patches = { + '2.2.3': { + 'amber-14': '1', + 'gromacs-4.5.7': '2', + 'gromacs-4.6.7': '3', + 'gromacs-5.0.7': '4', + 'gromacs-5.1.2': '5', + 'lammps-6Apr13': '6', + 'namd-2.8': '7', + 'namd-2.9': '8', + 'espresso-5.0.2': '9' + } + } + + def apply_patch(self, other): + plumed = subprocess.Popen( + [join_path(self.spec.prefix.bin, 'plumed'), 'patch', '-p'], + stdin=subprocess.PIPE + ) + opts = Plumed.plumed_patches[str(self.version)] + search = '{0.name}-{0.version}'.format(other) + choice = opts[search] + '\n' + plumed.stdin.write(choice) + plumed.wait() + + def setup_dependent_package(self, module, ext_spec): + # Make plumed visible from dependent packages + module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed')) def install(self, spec, prefix): - # Prefix is the only compulsory argument. - config_args = ["--prefix=" + prefix] + # From plumed docs : + # Also consider that this is different with respect to what some other + # configure script does in that variables such as MPICXX are + # completely ignored here. In case you work on a machine where CXX is + # set to a serial compiler and MPICXX to a MPI compiler, to compile + # with MPI you should use: + # + # > ./configure CXX="$MPICXX" + configure_opts = ["--prefix=" + prefix] + + # If using MPI then ensure the correct compiler wrapper is used. + if '+mpi' in spec: + configure_opts.extend([ + '--enable-mpi', + 'CXX={0}'.format(spec['mpi'].mpicxx) + ]) + + # If the MPI dependency is provided by the intelmpi package then + # the following additional argument is required to allow it to + # build. + if spec.satisfies('^intelmpi'): + configure_opts.extend([ + 'STATIC_LIBS=-mt_mpi' + ]) + + # Additional arguments + configure_opts.extend([ + '--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'), + '--enable-gsl={0}'.format('yes' if '+gsl' in spec else 'no') + ]) # Construct list of optional modules module_opts=[] @@ -70,28 +142,9 @@ def install(self, spec, prefix): # If we have specified any optional modules then add the argument to # enable or disable them. if module_opts: - config_args.extend(["--enable-modules=%s" % "".join(module_opts)]) - - # If using MPI then ensure the correct compiler wrapper is used. - if '+mpi' in spec: - config_args.extend([ - "--enable-mpi", - "CC=%s" % self.spec['mpi'].mpicc, - "CXX=%s" % self.spec['mpi'].mpicxx, - "FC=%s" % self.spec['mpi'].mpifc, - "F77=%s" % self.spec['mpi'].mpif77 - ]) - - # If the MPI dependency is provided by the intelmpi package then - # the following additional argument is required to allow it to - # build. - if spec.satisfies('^intelmpi'): - config_args.extend([ - "STATIC_LIBS=-mt_mpi" - ]) - - # Configure - configure(*config_args) + configure_opts.extend([ + '--enable-modules={0}'.format("".join(module_opts))]) + configure(*configure_opts) make() - make("install") + make('install') From 5661afa315f6401b39c5ea354697d80170c6c8f7 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Mon, 22 Aug 2016 12:03:47 +0100 Subject: [PATCH 08/12] Passed flake8 tests --- var/spack/repos/builtin/packages/plumed/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index c261e90fd8..3d9e8222ba 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -121,7 +121,7 @@ def install(self, spec, prefix): if spec.satisfies('^intelmpi'): configure_opts.extend([ 'STATIC_LIBS=-mt_mpi' - ]) + ]) # Additional arguments configure_opts.extend([ @@ -130,7 +130,7 @@ def install(self, spec, prefix): ]) # Construct list of optional modules - module_opts=[] + module_opts = [] module_opts.extend([ '+crystallization' if ( '+crystallization' in spec) else '-crystallization', From 226d4f04f3b931755124f6b56741cd89099a3fec Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Mon, 22 Aug 2016 12:09:50 +0100 Subject: [PATCH 09/12] Spelling tweaks and consistent quoting --- var/spack/repos/builtin/packages/plumed/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index 3d9e8222ba..8a0e631463 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -58,7 +58,7 @@ class Plumed(Package): variant('mpi', default=True, description='Activates MPI support') variant('gsl', default=True, description='Activates GSL support') - # Dependencies. LAPACK and BLAS are recommended but not essentia + # Dependencies. LAPACK and BLAS are recommended but not essential. depends_on('zlib') depends_on('blas') depends_on('lapack') @@ -106,7 +106,7 @@ def install(self, spec, prefix): # with MPI you should use: # # > ./configure CXX="$MPICXX" - configure_opts = ["--prefix=" + prefix] + configure_opts = ['--prefix=' + prefix] # If using MPI then ensure the correct compiler wrapper is used. if '+mpi' in spec: From 87d15212eb468348bf6de114a70e9d3ffbc85fe1 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Mon, 22 Aug 2016 12:30:17 +0100 Subject: [PATCH 10/12] Cleaned branch to only include plumed package --- etc/spack/packages.yaml | 8 --- .../builtin/packages/intelmpi/package.py | 51 ------------------- 2 files changed, 59 deletions(-) delete mode 100644 etc/spack/packages.yaml delete mode 100644 var/spack/repos/builtin/packages/intelmpi/package.py diff --git a/etc/spack/packages.yaml b/etc/spack/packages.yaml deleted file mode 100644 index abdd888351..0000000000 --- a/etc/spack/packages.yaml +++ /dev/null @@ -1,8 +0,0 @@ -packages: - intelmpi: - paths: - intelmpi@4.1.0%gcc@4.4.7 arch=linux-x86_64: /software/compilers/intel/13.0/impi/4.1.0.024/intel64 - buildable: False -# all: -# providers: -# mpi: [intelmpi] diff --git a/var/spack/repos/builtin/packages/intelmpi/package.py b/var/spack/repos/builtin/packages/intelmpi/package.py deleted file mode 100644 index 5a0382a392..0000000000 --- a/var/spack/repos/builtin/packages/intelmpi/package.py +++ /dev/null @@ -1,51 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. -# -# This file is part of Spack. -# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. -# LLNL-CODE-647188 -# -# For details, see https://github.com/llnl/spack -# Please also see the LICENSE file for our notice and the LGPL. -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU Lesser General Public License (as -# published by the Free Software Foundation) version 2.1, February 1999. -# -# This program is distributed in the hope that it will be useful, but -# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and -# conditions of the GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this program; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -############################################################################## -from spack import * - -class Intelmpi(Package): - """Intel MPI""" - - homepage = "http://www.example.com" - url = "https://software.intel.com/en-us/intel-mpi-library" - - version('4.1.0') - - # Provides a virtual dependency 'mpi' - provides('mpi') - - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): - spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc')) - spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpicxx')) - spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpif77')) - spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpif90')) - # NOTE: Need to find a better way of setting this compiler argument - # which is only required when building packages with intelmpi. - spack_env.set('CXXFLAGS', '-DMPICH_IGNORE_CXX_SEEK') - - def setup_dependent_package(self, module, dep_spec): - self.spec.mpicc = join_path(self.prefix.bin, 'mpicc') - self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx') - self.spec.mpifc = join_path(self.prefix.bin, 'mpif90') - self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77') From 65abd279cda184303922bb610f518009f2e6f6d0 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Mon, 22 Aug 2016 13:44:21 +0100 Subject: [PATCH 11/12] Renamed intelmpi as suggested --- var/spack/repos/builtin/packages/plumed/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index 8a0e631463..02d9852add 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -115,10 +115,10 @@ def install(self, spec, prefix): 'CXX={0}'.format(spec['mpi'].mpicxx) ]) - # If the MPI dependency is provided by the intelmpi package then + # If the MPI dependency is provided by the intel-mpi package then # the following additional argument is required to allow it to # build. - if spec.satisfies('^intelmpi'): + if spec.satisfies('^intel-mpi'): configure_opts.extend([ 'STATIC_LIBS=-mt_mpi' ]) From 07e0da24c5614533a93c392cf2b6f03c8b00b949 Mon Sep 17 00:00:00 2001 From: Andrew Williams Date: Thu, 25 Aug 2016 10:21:56 +0100 Subject: [PATCH 12/12] Reverted url to point to tarball rather than git tag --- var/spack/repos/builtin/packages/plumed/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py index 02d9852add..79632abf38 100644 --- a/var/spack/repos/builtin/packages/plumed/package.py +++ b/var/spack/repos/builtin/packages/plumed/package.py @@ -41,9 +41,9 @@ class Plumed(Package): and C/C++ codes. """ homepage = 'http://www.plumed.org/' - url = 'https://github.com/plumed/plumed2' + url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz' - version('2.2.3', git="https://github.com/plumed/plumed2.git", tag='v2.2.3') + version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8') # Variants. PLUMED by default builds a number of optional modules. # The ones listed here are not built by default for various reasons,