From e74c2c2f3f6889dfb2488e077766aff8414241d3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 29 May 2021 09:43:14 +0100 Subject: [PATCH 01/11] adding easyconfigs: Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb, Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb and patches: Amber-20_cmake-locate-netcdf.patch --- ...mberTools-20.15-foss-2020a-Python-3.8.2.eb | 55 ++++++++++++++++++ ...Tools-20.15-fosscuda-2020a-Python-3.8.2.eb | 56 +++++++++++++++++++ .../Amber/Amber-20_cmake-locate-netcdf.patch | 13 +++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-20_cmake-locate-netcdf.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb new file mode 100644 index 000000000000..a789d3f4b584 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,55 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 20 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (15, 11) # (AmberTools, Amber) +version = '%s.%s-AmberTools-%s.%s' % (local_amber_ver, patchlevels[1], local_ambertools_ver, patchlevels[0]) +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +# Amber CMake fails when 'usempi': True is set and we add '-DMPI=TRUE' +toolchainopts = {'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, +] + +builddependencies = [ + ('Bison', '3.5.3'), + ('CMake', '3.16.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('Boost.Python', '1.72.0'), + ('bzip2', '1.0.8'), + ('libreadline', '8.0'), + ('matplotlib', '3.2.1', '-Python-%(pyver)s'), + ('netCDF-Fortran', '4.5.2'), + ('netCDF', '4.7.4'), + ('Perl', '5.30.2'), + ('PnetCDF', '1.12.1'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA + ('Tkinter', '3.8.2'), + ('X11', '20200222'), + ('zlib', '1.2.11'), +] + +# Different tests pass and fail when using different numbers of processes. +# The manual makes it clear that this is expected. +runtest = False + +ambermpi = True +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb new file mode 100644 index 000000000000..030f5a17ab97 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb @@ -0,0 +1,56 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 20 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (15, 11) # (AmberTools, Amber) +version = '%s.%s-AmberTools-%s.%s' % (local_amber_ver, patchlevels[1], local_ambertools_ver, patchlevels[0]) +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'fosscuda', 'version': '2020a'} +# Building with MPI causes the 'MPI=TRUE' Amber CMake option to fail +toolchainopts = {'usempi': False, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, +] + +builddependencies = [ + ('Bison', '3.5.3'), + ('CMake', '3.16.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('Boost.Python', '1.72.0'), + ('bzip2', '1.0.8'), + ('libreadline', '8.0'), + ('matplotlib', '3.2.1', '-Python-%(pyver)s'), + ('NCCL', '2.7.8', '-CUDA-11.0.2', True), # fosscuda only + ('netCDF-Fortran', '4.5.2'), + ('netCDF', '4.7.4'), + ('Perl', '5.30.2'), + ('PnetCDF', '1.12.1'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA + ('Tkinter', '3.8.2'), + ('X11', '20200222'), + ('zlib', '1.2.11'), +] + +# Different tests pass and fail when using different numbers of processes. +# The manual makes it clear that this is expected. +runtest = False + +ambermpi = True +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-20_cmake-locate-netcdf.patch b/easybuild/easyconfigs/a/Amber/Amber-20_cmake-locate-netcdf.patch new file mode 100644 index 000000000000..3ece09e84c10 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20_cmake-locate-netcdf.patch @@ -0,0 +1,13 @@ +Ensure that CMake recurses available paths if the Fortran libs aren't available in the netCDF module + +James Carpenter 2021-01-23 +--- amber20_src/cmake/jedbrown/FindNetCDF.cmake.orig 2020-04-28 02:19:51.000000000 +0100 ++++ amber20_src/cmake/jedbrown/FindNetCDF.cmake 2021-01-25 11:41:47.005657000 +0000 +@@ -52,6 +52,7 @@ + + macro (NetCDF_check_interface lang header libs) + find_path (NetCDF_INCLUDES_${lang} NAMES ${header} HINTS "${NetCDF_INCLUDES}" NO_DEFAULT_PATH) ++ find_path (NetCDF_INCLUDES_${lang} NAMES ${header} HINTS "${NetCDF_INCLUDES}") + + find_library (NetCDF_LIBRARIES_${lang} NAMES ${libs} HINTS "${NetCDF_lib_dirs}") + From 4ce698fe9373a6fae65989cdc71de463631cf740 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 29 May 2021 11:45:31 +0100 Subject: [PATCH 02/11] run the tests --- .../Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb | 4 ---- ...er-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb | 6 +----- 2 files changed, 1 insertion(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb index a789d3f4b584..c087ac6d9b7b 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb @@ -45,10 +45,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -# Different tests pass and fail when using different numbers of processes. -# The manual makes it clear that this is expected. -runtest = False - ambermpi = True static = False diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb index 030f5a17ab97..659c65be59c6 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb @@ -34,7 +34,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('libreadline', '8.0'), ('matplotlib', '3.2.1', '-Python-%(pyver)s'), - ('NCCL', '2.7.8', '-CUDA-11.0.2', True), # fosscuda only + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), ('netCDF-Fortran', '4.5.2'), ('netCDF', '4.7.4'), ('Perl', '5.30.2'), @@ -46,10 +46,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -# Different tests pass and fail when using different numbers of processes. -# The manual makes it clear that this is expected. -runtest = False - ambermpi = True static = False From 873f8fb1195d615ebd00ce2dc0100c609445cf57 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 29 May 2021 12:30:29 +0100 Subject: [PATCH 03/11] disable tests --- .../Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb | 3 +++ ...Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb index c087ac6d9b7b..e4b073670530 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb @@ -45,6 +45,9 @@ dependencies = [ ('zlib', '1.2.11'), ] +# Tests are flaky +runtest = False + ambermpi = True static = False diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb index 659c65be59c6..f6529ea0d150 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb @@ -46,6 +46,9 @@ dependencies = [ ('zlib', '1.2.11'), ] +# Tests are flaky +runtest = False + ambermpi = True static = False From 4d9cd8b4152cd8a35517c58a5b099b99b270d7ed Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 11 Jun 2021 18:01:15 +0100 Subject: [PATCH 04/11] change name / version / versionsuffix; switch to usempi=True --- ...oss-2020a-AmberTools-20.15-Python-3.8.2.eb | 52 ++++++++++++++++++ ...uda-2020a-AmberTools-20.15-Python-3.8.2.eb | 53 +++++++++++++++++++ 2 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb new file mode 100644 index 000000000000..dd80dc1f90be --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -0,0 +1,52 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 20 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (15, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s-Python-%%(pyver)s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, +] + +builddependencies = [ + ('Bison', '3.5.3'), + ('CMake', '3.16.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('Boost.Python', '1.72.0'), + ('bzip2', '1.0.8'), + ('libreadline', '8.0'), + ('matplotlib', '3.2.1', '-Python-%(pyver)s'), + ('netCDF-Fortran', '4.5.2'), + ('netCDF', '4.7.4'), + ('Perl', '5.30.2'), + ('PnetCDF', '1.12.1'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA + ('Tkinter', '3.8.2'), + ('X11', '20200222'), + ('zlib', '1.2.11'), +] + +# Tests are flaky +runtest = False + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb new file mode 100644 index 000000000000..35bb11acd45c --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -0,0 +1,53 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 20 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (15, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s-Python-%%(pyver)s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'fosscuda', 'version': '2020a'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, +] + +builddependencies = [ + ('Bison', '3.5.3'), + ('CMake', '3.16.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('Boost.Python', '1.72.0'), + ('bzip2', '1.0.8'), + ('libreadline', '8.0'), + ('matplotlib', '3.2.1', '-Python-%(pyver)s'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('netCDF-Fortran', '4.5.2'), + ('netCDF', '4.7.4'), + ('Perl', '5.30.2'), + ('PnetCDF', '1.12.1'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA + ('Tkinter', '3.8.2'), + ('X11', '20200222'), + ('zlib', '1.2.11'), +] + +# Tests are flaky +runtest = False + +static = False + +moduleclass = 'chem' From 9d0526314d8e00405c5e524a2ea53cb4a54094ef Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 11 Jun 2021 18:02:14 +0100 Subject: [PATCH 05/11] delete old versions of files --- ...mberTools-20.15-foss-2020a-Python-3.8.2.eb | 54 ------------------ ...Tools-20.15-fosscuda-2020a-Python-3.8.2.eb | 55 ------------------- 2 files changed, 109 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb delete mode 100644 easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index e4b073670530..000000000000 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,54 +0,0 @@ -name = 'Amber' -local_amber_ver = 20 -local_ambertools_ver = 20 -# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php -patchlevels = (15, 11) # (AmberTools, Amber) -version = '%s.%s-AmberTools-%s.%s' % (local_amber_ver, patchlevels[1], local_ambertools_ver, patchlevels[0]) -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://ambermd.org/amber.html' -description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing - molecular dynamics and structure prediction.""" - -toolchain = {'name': 'foss', 'version': '2020a'} -# Amber CMake fails when 'usempi': True is set and we add '-DMPI=TRUE' -toolchainopts = {'openmp': True} - -sources = [ - '%%(name)s%s.tar.bz2' % local_amber_ver, - 'AmberTools%s.tar.bz2' % local_ambertools_ver, -] -patches = [ - '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, -] - -builddependencies = [ - ('Bison', '3.5.3'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), - ('make', '4.3'), -] - -dependencies = [ - ('Boost.Python', '1.72.0'), - ('bzip2', '1.0.8'), - ('libreadline', '8.0'), - ('matplotlib', '3.2.1', '-Python-%(pyver)s'), - ('netCDF-Fortran', '4.5.2'), - ('netCDF', '4.7.4'), - ('Perl', '5.30.2'), - ('PnetCDF', '1.12.1'), - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA - ('Tkinter', '3.8.2'), - ('X11', '20200222'), - ('zlib', '1.2.11'), -] - -# Tests are flaky -runtest = False - -ambermpi = True -static = False - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb deleted file mode 100644 index f6529ea0d150..000000000000 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-AmberTools-20.15-fosscuda-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,55 +0,0 @@ -name = 'Amber' -local_amber_ver = 20 -local_ambertools_ver = 20 -# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php -patchlevels = (15, 11) # (AmberTools, Amber) -version = '%s.%s-AmberTools-%s.%s' % (local_amber_ver, patchlevels[1], local_ambertools_ver, patchlevels[0]) -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://ambermd.org/amber.html' -description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing - molecular dynamics and structure prediction.""" - -toolchain = {'name': 'fosscuda', 'version': '2020a'} -# Building with MPI causes the 'MPI=TRUE' Amber CMake option to fail -toolchainopts = {'usempi': False, 'openmp': True} - -sources = [ - '%%(name)s%s.tar.bz2' % local_amber_ver, - 'AmberTools%s.tar.bz2' % local_ambertools_ver, -] -patches = [ - '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, -] - -builddependencies = [ - ('Bison', '3.5.3'), - ('CMake', '3.16.4'), - ('flex', '2.6.4'), - ('make', '4.3'), -] - -dependencies = [ - ('Boost.Python', '1.72.0'), - ('bzip2', '1.0.8'), - ('libreadline', '8.0'), - ('matplotlib', '3.2.1', '-Python-%(pyver)s'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), - ('netCDF-Fortran', '4.5.2'), - ('netCDF', '4.7.4'), - ('Perl', '5.30.2'), - ('PnetCDF', '1.12.1'), - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA - ('Tkinter', '3.8.2'), - ('X11', '20200222'), - ('zlib', '1.2.11'), -] - -# Tests are flaky -runtest = False - -ambermpi = True -static = False - -moduleclass = 'chem' From dda4a1ead3c1208c8f6316954be61609979cf259 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Jun 2021 13:51:08 +0200 Subject: [PATCH 06/11] AmberTools/20: Fix problems with CMake and usempi. When using usempi CMake doesn't define MPI_xxx_LIBRARIES causing AmberTools import_libraries to error out. --- ...oss-2020a-AmberTools-20.15-Python-3.8.2.eb | 1 + ...uda-2020a-AmberTools-20.15-Python-3.8.2.eb | 1 + ...ols-20_fix_missing_MPI_LIBRARY_error.patch | 21 +++++++++++++++++++ 3 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb index dd80dc1f90be..d691711a2e6d 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -19,6 +19,7 @@ sources = [ ] patches = [ '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, + 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, ] builddependencies = [ diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb index 35bb11acd45c..707ae7a4dd8f 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -19,6 +19,7 @@ sources = [ ] patches = [ '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, + 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, ] builddependencies = [ diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch new file mode 100644 index 000000000000..8d96ce176c0e --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch @@ -0,0 +1,21 @@ +When using "usempi" there will be no MPI_xxx_LIBRARIES set and that causes +import_libraries to error out. We know it is correct so comment out that +FATAL_ERROR. + +Åke Sandgren, 2021-06-16 +diff -ru amber20_src.orig/cmake/LibraryTracking.cmake amber20_src/cmake/LibraryTracking.cmake +--- amber20_src.orig/cmake/LibraryTracking.cmake 2021-04-25 02:51:44.000000000 +0200 ++++ amber20_src/cmake/LibraryTracking.cmake 2021-06-16 13:30:26.568317368 +0200 +@@ -170,9 +170,9 @@ + + cmake_parse_arguments(IMP_LIBS "" "" "LIBRARIES;INCLUDES" ${ARGN}) + +- if("${IMP_LIBS_LIBRARIES}" STREQUAL "") +- message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") +- endif() ++ #if("${IMP_LIBS_LIBRARIES}" STREQUAL "") ++ # message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") ++ #endif() + + if(NOT "${IMP_LIBS_UNPARSED_ARGUMENTS}" STREQUAL "") + message(FATAL_ERROR "Incorrect usage. Extra arguments provided.") From a755491d2fde5c7878ed2822f4e6e75becd44627 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Jun 2021 13:05:33 +0100 Subject: [PATCH 07/11] switch patch name to be AmberTools and move Python to start of deps --- .../Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb index d691711a2e6d..62b0ec9d47a8 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -18,7 +18,7 @@ sources = [ 'AmberTools%s.tar.bz2' % local_ambertools_ver, ] patches = [ - '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, + 'AmberTools-%s_cmake-locate-netcdf.patch' % local_amber_ver, 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, ] @@ -30,6 +30,7 @@ builddependencies = [ ] dependencies = [ + ('Python', '3.8.2'), ('Boost.Python', '1.72.0'), ('bzip2', '1.0.8'), ('libreadline', '8.0'), @@ -38,7 +39,6 @@ dependencies = [ ('netCDF', '4.7.4'), ('Perl', '5.30.2'), ('PnetCDF', '1.12.1'), - ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA ('Tkinter', '3.8.2'), ('X11', '20200222'), From e1e025d287172a006e88dd88815a426cba0b183f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Jun 2021 13:05:58 +0100 Subject: [PATCH 08/11] switch patch name to be AmberTools and move Python to start of deps --- ...mber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb index 707ae7a4dd8f..b393d5755e33 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -18,7 +18,7 @@ sources = [ 'AmberTools%s.tar.bz2' % local_ambertools_ver, ] patches = [ - '%%(name)s-%s_cmake-locate-netcdf.patch' % local_amber_ver, + 'AmberTools-%s_cmake-locate-netcdf.patch' % local_amber_ver, 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, ] @@ -30,6 +30,7 @@ builddependencies = [ ] dependencies = [ + ('Python', '3.8.2'), ('Boost.Python', '1.72.0'), ('bzip2', '1.0.8'), ('libreadline', '8.0'), @@ -39,7 +40,6 @@ dependencies = [ ('netCDF', '4.7.4'), ('Perl', '5.30.2'), ('PnetCDF', '1.12.1'), - ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), # mpi4py required for MMPBSA ('Tkinter', '3.8.2'), ('X11', '20200222'), From 3b9e3aa28c5dc30177813f024063d18e066d9ae4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Jun 2021 13:06:41 +0100 Subject: [PATCH 09/11] rename patch --- ...ocate-netcdf.patch => AmberTools-20_cmake-locate-netcdf.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/Amber/{Amber-20_cmake-locate-netcdf.patch => AmberTools-20_cmake-locate-netcdf.patch} (100%) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20_cmake-locate-netcdf.patch b/easybuild/easyconfigs/a/Amber/AmberTools-20_cmake-locate-netcdf.patch similarity index 100% rename from easybuild/easyconfigs/a/Amber/Amber-20_cmake-locate-netcdf.patch rename to easybuild/easyconfigs/a/Amber/AmberTools-20_cmake-locate-netcdf.patch From ee9762f2323340260eee7716af92c72d50f41569 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 16 Jun 2021 13:13:46 +0100 Subject: [PATCH 10/11] local_ambertools_ver in patch name and add checksums --- ...ber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb | 9 ++++++++- ...20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb | 9 ++++++++- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb index 62b0ec9d47a8..e504690c753d 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -18,9 +18,16 @@ sources = [ 'AmberTools%s.tar.bz2' % local_ambertools_ver, ] patches = [ - 'AmberTools-%s_cmake-locate-netcdf.patch' % local_amber_ver, + 'AmberTools-%s_cmake-locate-netcdf.patch' % local_ambertools_ver, 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, ] +checksums = [ + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 + 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools20.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', +] builddependencies = [ ('Bison', '3.5.3'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb index b393d5755e33..2a12ffd6d832 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -18,9 +18,16 @@ sources = [ 'AmberTools%s.tar.bz2' % local_ambertools_ver, ] patches = [ - 'AmberTools-%s_cmake-locate-netcdf.patch' % local_amber_ver, + 'AmberTools-%s_cmake-locate-netcdf.patch' % local_ambertools_ver, 'AmberTools-%s_fix_missing_MPI_LIBRARY_error.patch' % local_ambertools_ver, ] +checksums = [ + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 + 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools20.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', +] builddependencies = [ ('Bison', '3.5.3'), From 99766b9fe6a28a97b2302d333f6e7b1731aefab2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 16 Jun 2021 13:48:42 +0100 Subject: [PATCH 11/11] only needs Boost, not Boost.Python --- .../Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb | 2 +- .../Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb index e504690c753d..2cc15a50cb39 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -38,7 +38,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.2'), - ('Boost.Python', '1.72.0'), + ('Boost', '1.72.0'), ('bzip2', '1.0.8'), ('libreadline', '8.0'), ('matplotlib', '3.2.1', '-Python-%(pyver)s'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb index 2a12ffd6d832..5a8159af3bb1 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -38,7 +38,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.2'), - ('Boost.Python', '1.72.0'), + ('Boost', '1.72.0'), ('bzip2', '1.0.8'), ('libreadline', '8.0'), ('matplotlib', '3.2.1', '-Python-%(pyver)s'),