Merge pull request #14386 from fwautele/20211119151842_new_pr_AmberTo…

…ols21 {chem}[foss/2021a] AmberTools v21 w/ Python 3.9.5
easybuilders · Aug 25, 2022 · 1e945a8 · 1e945a8
2 parents bb64ec7 + 1be7a03
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diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb
@@ -0,0 +1,49 @@
+easyblock = 'EB_Amber'
+
+name = 'AmberTools'
+version = '21'
+
+homepage = 'https://ambermd.org/'
+description = """AmberTools consists of several independently developed packages that work well by themselves,
+ and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations,
+ with either explicit water or generalized Born solvent models."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+toolchainopts = {'usempi': True}
+
+sources = [SOURCE_TAR_BZ2]
+patches = [
+    'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
+    'AmberTools-20_cmake-locate-netcdf.patch',
+    'AmberTools-21_CMake-FlexiBLAS.patch',
+]
+checksums = [
+    'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd',  # AmberTools-21.tar.bz2
+    # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch
+    '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc',
+    '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0',  # AmberTools-20_cmake-locate-netcdf.patch
+    '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36',  # AmberTools-21_CMake-FlexiBLAS.patch
+]
+
+builddependencies = [
+    ('Bison', '3.7.6'),
+    ('pkg-config', '0.29.2'),
+    ('CMake', '3.20.1'),
+    ('flex', '2.6.4'),
+    ('make', '4.3'),
+]
+
+dependencies = [
+    ('Python', '3.9.5'),
+    ('matplotlib', '3.4.2'),
+    ('netCDF', '4.8.0'),
+    ('netCDF-Fortran', '4.5.3'),
+    ('FFTW', '3.3.9'),
+    ('Boost', '1.76.0'),
+    ('arpack-ng', '3.8.0'),
+    ('PnetCDF', '1.12.2'),
+]
+
+runtest = False
+
+moduleclass = 'chem'
diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_CMake-FlexiBLAS.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_CMake-FlexiBLAS.patch
@@ -0,0 +1,91 @@
+make CMake scripts that picks BLAS/LAPACK library aware of FlexiBLAS
+author: Kenneth Hoste (HPC-UGent)
+--- cmake/patched-cmake-modules/FindBLASFixed.cmake.orig	2022-05-04 18:53:42.410384491 +0200
++++ cmake/patched-cmake-modules/FindBLASFixed.cmake	2022-05-04 18:54:39.034612008 +0200
+@@ -36,7 +36,7 @@
+ #   BLA_F95     if set on tries to find the f95 interfaces for BLAS/LAPACK
+ #
+ # ######### ## List of vendors (BLA_VENDOR) valid in this module #
+-# Goto,OpenBLAS,ATLAS PhiPACK,CXML,DXML,SunPerf,SCSL,SGIMATH,IBMESSL,
++# Goto,OpenBLAS,FlexiBLAS ATLAS PhiPACK,CXML,DXML,SunPerf,SCSL,SGIMATH,IBMESSL,
+ # ACML,ACML_MP,ACML_GPU,Apple, NAS, Generic
+
+ include(CMakePushCheckState)
+@@ -49,8 +49,8 @@
+ 	set(BLA_VENDOR_DEFAULT "All")
+ endif ()
+
+-set(BLA_VENDOR ${BLA_VENDOR_DEFAULT} CACHE STRING "BLAS vendor to use for BLAS and Lapack.  Valid values: All, Goto, OpenBLAS, ATLAS, PhiPACK, CXML, DXML, SunPerf, SCSL, SGIMATH, IBMESSL, ACML, ACML_MP, ACML_GPU, Apple, NAS, Generic")
+-validate_configuration_enum(BLA_VENDOR  All Goto OpenBLAS ATLAS PhiPACK CXML DXML SunPerf SCSL SGIMATH IBMESSL ACML ACML_MP ACML_GPU Apple NAS Generic)
++set(BLA_VENDOR ${BLA_VENDOR_DEFAULT} CACHE STRING "BLAS vendor to use for BLAS and Lapack.  Valid values: All, Goto, OpenBLAS, FlexiBLAS, ATLAS, PhiPACK, CXML, DXML, SunPerf, SCSL, SGIMATH, IBMESSL, ACML, ACML_MP, ACML_GPU, Apple, NAS, Generic")
++validate_configuration_enum(BLA_VENDOR  All Goto OpenBLAS FlexiBLAS ATLAS PhiPACK CXML DXML SunPerf SCSL SGIMATH IBMESSL ACML ACML_MP ACML_GPU Apple NAS Generic)
+
+ if(DEFINED BLAS_FIND_QUIETLY)
+ 	set(CMAKE_REQUIRED_QUIET ${BLAS_FIND_QUIETLY})
+@@ -159,6 +159,20 @@
+  endif()
+ endif ()
+
++if (BLA_VENDOR STREQUAL "FlexiBLAS" OR BLA_VENDOR STREQUAL "All")
++ if(NOT BLAS_LIBRARIES)
++	 # FlexiBLAS (https://github.com/mpimd-csc/flexiblas)
++	check_fortran_libraries(
++	BLAS_LIBRARIES
++	BLAS
++	sgemm
++	""
++	"flexiblas"
++	""
++	)
++ endif()
++endif ()
++
+ if (BLA_VENDOR STREQUAL "OpenBLAS" OR BLA_VENDOR STREQUAL "All")
+  if(NOT BLAS_LIBRARIES)
+ 	# OpenBLAS (http://www.openblas.net)
+@@ -524,4 +538,4 @@
+ endif()
+
+ cmake_pop_check_state()
+-set(CMAKE_FIND_LIBRARY_SUFFIXES ${_blas_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})
+\ No newline at end of file
++set(CMAKE_FIND_LIBRARY_SUFFIXES ${_blas_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})
+--- cmake/patched-cmake-modules/FindLAPACKFixed.cmake.orig	2022-05-04 18:56:14.315407989 +0200
++++ cmake/patched-cmake-modules/FindLAPACKFixed.cmake	2022-05-04 18:56:39.930772703 +0200
+@@ -36,7 +36,7 @@
+ #   BLA_F95     if set on tries to find the f95 interfaces for BLAS/LAPACK
+ #
+ # ## List of vendors (BLA_VENDOR) valid in this module:
+-# OpenBLAS, ACML,Apple, NAS, Generic
++# OpenBLAS, FlexiBLAS, ACML,Apple, NAS, Generic
+
+ set(_lapack_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES})
+
+@@ -173,6 +173,20 @@
+ 		endif()
+ 	endif ()
+
++	if(BLA_VENDOR STREQUAL "FlexiBLAS" OR BLA_VENDOR STREQUAL "All")
++		if(NOT LAPACK_LIBRARIES)
++			check_lapack_libraries(
++			LAPACK_LIBRARIES
++			LAPACK
++			cheev
++			""
++			"flexiblas"
++			"${BLAS_LIBRARIES}"
++			""
++			)
++		endif()
++	endif()
++	
+ 	if(BLA_VENDOR STREQUAL "OpenBLAS" OR BLA_VENDOR STREQUAL "All")
+ 		if(NOT LAPACK_LIBRARIES)
+ 			check_lapack_libraries(
+@@ -289,4 +303,4 @@
+ endif()
+
+ cmake_pop_check_state()
+-set(CMAKE_FIND_LIBRARY_SUFFIXES ${_lapack_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})
+\ No newline at end of file
++set(CMAKE_FIND_LIBRARY_SUFFIXES ${_lapack_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES})