Merge pull request #14028 from boegel/20210917202853_new_pr_AmberTools20

fix AmberTools v20 easyconfig using intel/2020a toolchain

easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb

@@ -19,26 +19,41 @@ sources = [{
     'download_filename': local_download_credentials,
     'filename': SOURCE_TAR_BZ2,
 }]
-patches = ['Amber-20_fix-hardcoding.patch']
+patches = [
+    'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
+    'AmberTools-20_cmake-locate-netcdf.patch',
+    'AmberTools-20_fix_xblas_missing_make_dependency.patch',
+]
 checksums = [
     'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9',  # AmberTools-20.tar.bz2
-    'a71f1bd70bac8d5e25386d6db90e95874ad300b956ed5b5afbc8848b7c1e00dc',  # Amber-20_fix-hardcoding.patch
+    # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch'
+    '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc',
+    '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0',  # AmberTools-20_cmake-locate-netcdf.patch
+    # AmberTools-20_fix_xblas_missing_make_dependency.patch
+    'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65'
 ]
 
 builddependencies = [
     ('Bison', '3.5.3'),
     ('pkg-config', '0.29.2'),
+    ('CMake', '3.16.4'),
+    ('flex', '2.6.4'),
+    ('make', '4.3'),
 ]
 dependencies = [
     ('Python', '3.8.2'),
+    ('SciPy-bundle', '2020.03', versionsuffix),
+    ('matplotlib', '3.2.1', versionsuffix),
     ('netCDF', '4.7.4'),
     ('netCDF-Fortran', '4.5.2'),
+    ('FFTW', '3.3.8'),
 ]
 
-# fix linking to netCDF library: also requires linking to HDF5 & cURL libs, which in turns require others,
-# all of which are indirect dependencies via netCDF
-local_netcdf_libs = "-lnetcdf -lhdf5 -lsz -ldl -liomp5 -lcurl -lssl -lcrypto -lz -lm -lpthread"
-preconfigopts = "sed -i'' 's/-lnetcdf/%s/g' AmberTools/src/cpptraj/configure && " % local_netcdf_libs
-configopts = "-nosanderapi"
+# pysander should link with icc and not gcc
+prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc -shared "/g' """
+prebuildopts += "%(builddir)s/AmberTools/src/pysander/setup.py && "
+
+# Tests use pmemd which is not part of AmberTools
+runtest = False
 
 moduleclass = 'chem'

easybuild/easyconfigs/a/AmberTools/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/AmberTools/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 AmberTools.orig/cmake/LibraryTracking.cmake AmberTools/cmake/LibraryTracking.cmake
+--- AmberTools.orig/cmake/LibraryTracking.cmake	2021-04-25 02:51:44.000000000 +0200
++++ AmberTools/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.")

easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_xblas_missing_make_dependency.patch

@@ -0,0 +1,19 @@
+Fix a missing dependency in xblas causing problems when building with large -j
+
+Åke Sandgren, 2021-07-01
+diff -ru amber20_src.orig/AmberTools/src/xblas/Makefile amber20_src/AmberTools/src/xblas/Makefile
+--- amber20_src.orig/AmberTools/src/xblas/Makefile	2020-01-02 18:26:09.000000000 +0100
++++ amber20_src/AmberTools/src/xblas/Makefile	2021-07-01 11:34:05.281580939 +0200
+@@ -97,10 +97,10 @@
+ 	grep 'FAIL/TOTAL' testall.result >testall.summary
+ 	cat testall.summary
+
+-common-lib:
++common-lib: header
+ 	cd $(SRC_DIR)/common && $(MAKE)
+
+-common-test-lib:
++common-test-lib: header
+ 	cd $(TEST_DIR)/common && $(MAKE)
+
+