{chem}[foss/2020a,fosscuda/2020a] Amber v20.11-AmberTools-20.15 w/ Python 3.8.2

easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020a-AmberTools-20.15-Python-3.8.2.eb

@@ -0,0 +1,60 @@
+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 = [
+    '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'),
+    ('CMake', '3.16.4'),
+    ('flex', '2.6.4'),
+    ('make', '4.3'),
+]
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('Boost', '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'),
+    ('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'

easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb

@@ -0,0 +1,61 @@
+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 = [
+    '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'),
+    ('CMake', '3.16.4'),
+    ('flex', '2.6.4'),
+    ('make', '4.3'),
+]
+
+dependencies = [
+    ('Python', '3.8.2'),
+    ('Boost', '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'),
+    ('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'

easybuild/easyconfigs/a/Amber/AmberTools-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}")
+

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.")