Merge pull request #16166 from akesandgren/20220831075433_new_pr_Ambe…

…r220

{chem}[foss/2021b] Amber v22.0 w/ Python 3.9.6

easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb

@@ -0,0 +1,96 @@
+name = 'Amber'
+local_amber_ver = 22
+local_ambertools_ver = 22
+# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php
+patchlevels = (3, 0)  # (AmberTools, Amber)
+version = '%s.%s' % (local_amber_ver, patchlevels[1])
+versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0])
+
+homepage = 'https://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': '2021b'}
+toolchainopts = {'usempi': True, 'openmp': True}
+
+sources = [
+    '%%(name)s%s.tar.bz2' % local_amber_ver,
+    {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'},
+]
+patches = [
+    {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'},
+    {'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'},
+    'Amber-22_reduce_precision_of_kmmd_test.patch',
+    'Amber-22_remove_undeclared_redundant_variable.patch',
+]
+checksums = [
+    '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16',  # Amber22.tar.bz2
+    '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121',  # AmberTools22.tar.bz2
+    '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0',  # AmberTools-20_cmake-locate-netcdf.patch
+    # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch
+    '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc',
+    # AmberTools-20_fix_xblas_missing_make_dependency.patch
+    'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65',
+    '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36',  # AmberTools-21_CMake-FlexiBLAS.patch
+    # AmberTools-21_fix_DGESVD_workspace_query.patch
+    '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd',
+    '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b',  # AmberTools-21_fix_incorrect_dvout_call.patch
+    'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f',  # AmberTools-21_fix_incorrect_mexit_calls.patch
+    # AmberTools-21_fix_more_blas_argument_problems.patch
+    'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c',
+    'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b',  # AmberTools-21_fix_multiple_definition.patch
+    # AmberTools-21_fix_potential_use_before_init.patch
+    '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139',
+    # AmberTools-21_fix_rism_argument_mismatch.patch
+    '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1',
+    # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch
+    '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f',
+    'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737',  # AmberTools-22_fix_test_missing_cuda_dir.patch
+    # AmberTools-22_fix_missing_error_check_on_test_run.patch
+    'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475',
+    'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e',  # Amber-22_reduce_precision_of_kmmd_test.patch
+    # Amber-22_remove_undeclared_redundant_variable.patch
+    'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb',
+]
+
+builddependencies = [
+    ('CMake', '3.21.1'),
+    ('Bison', '3.7.6'),
+    ('flex', '2.6.4'),
+    ('make', '4.3'),
+]
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('bzip2', '1.0.8'),
+    ('Python', '3.9.6'),
+    ('SciPy-bundle', '2021.10'),  # mpi4py required for MMPBSA
+    ('Perl', '5.34.0'),
+    ('Boost', '1.77.0'),
+    ('libreadline', '8.1'),
+    ('matplotlib', '3.4.3'),
+    ('netCDF', '4.8.1'),
+    ('netCDF-Fortran', '4.5.3'),
+    ('PnetCDF', '1.12.3'),
+    ('Tkinter', '3.9.6'),
+    ('X11', '20210802'),
+]
+
+# All tests are expected to pass or be skipped
+runtest = True
+
+static = False
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/Amber/Amber-22_reduce_precision_of_kmmd_test.patch

@@ -0,0 +1,29 @@
+Reduce the number of digits checked for kmmd_pmemd/kmmd_pmemd:gb tests.
+Partially ok:ed by Amber devs. They will investigate and come back with
+more info.
+
+Åke Sandgren, 2022-08-25
+diff -ru amber22_src.orig/test/kmmd/kmmd_pmemd/Run.kmmd amber22_src/test/kmmd/kmmd_pmemd/Run.kmmd
+--- amber22_src.orig/test/kmmd/kmmd_pmemd/Run.kmmd	2022-04-09 03:11:47.000000000 +0200
++++ amber22_src/test/kmmd/kmmd_pmemd/Run.kmmd	2022-08-25 10:52:13.397649018 +0200
+@@ -64,7 +64,7 @@
+ #cp $output            $output.save
+
+ ##diff the test and reference
+-../../dacdif -t 2  $output.save $output 
++../../dacdif -a 0.03  $output.save $output 
+
+ /bin/rm -f mdin mdinfo mdcrd mdfrc restrt logfile tidied*txt *.dat
+ exit(0)
+diff -ru amber22_src.orig/test/kmmd/kmmd_pmemd_gb/Run.kmmd amber22_src/test/kmmd/kmmd_pmemd_gb/Run.kmmd
+--- amber22_src.orig/test/kmmd/kmmd_pmemd_gb/Run.kmmd	2022-04-09 03:11:47.000000000 +0200
++++ amber22_src/test/kmmd/kmmd_pmemd_gb/Run.kmmd	2022-08-25 10:52:20.981592091 +0200
+@@ -64,7 +64,7 @@
+ #cp $output            $output.save
+
+ ##diff the test and reference
+-../../dacdif -t 2  $output.save $output 
++../../dacdif -a 0.01  $output.save $output 
+
+ /bin/rm -f mdin mdinfo mdcrd mdfrc restrt tidied*txt *.dat
+ exit(0)

easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch

@@ -0,0 +1,26 @@
+Remove the undeclared (and unused) variable i from the private clause
+in an OpenMP pragma, which otherwise results in an error:
+
+   93 |     !$omp parallel do private(ihkl,i,f,angle)
+      |                                    1
+Error: Symbol i at (1) has no IMPLICIT type
+
+Bob Dröge, University of Groningen, 2022-08-18
+--- amber22_src.orig/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90	2022-08-18 13:12:24.807724049 +0200
++++ amber22_src/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90	2022-08-18 13:12:42.039809811 +0200
+@@ -90,7 +90,7 @@
+     call check_precondition(size(frac, 2) == size(scatter_type_index))
+     call check_precondition(size(hkl, 2) == size(atomic_scatter_factor, 1))
+
+-    !$omp parallel do private(ihkl,i,f,angle)
++    !$omp parallel do private(ihkl,f,angle)
+     do ihkl = 1, size(hkl, 2)
+
+       ! Fhkl = SUM( fj * exp(2 * M_PI * i * (h * xj + k * yj + l * zj)) ),
+@@ -127,4 +127,4 @@
+   end subroutine calc_f_non_bulk
+
+
+-end module xray_non_bulk_impl_cpu_module
+\ No newline at end of file
++end module xray_non_bulk_impl_cpu_module

test/easyconfigs/easyconfigs.py

@@ -1336,21 +1336,29 @@ def template_easyconfig_test(self, spec):
 
     # make sure all patch files are available
     specdir = os.path.dirname(spec)
+    basedir = os.path.dirname(os.path.dirname(specdir))
     specfn = os.path.basename(spec)
     for idx, patch in enumerate(ec['patches']):
-        if isinstance(patch, (tuple, list)):
-            patch = patch[0]
+        patch_dir = specdir
+        if isinstance(patch, str):
+            patch_name = patch
+        elif isinstance(patch, (tuple, list)):
+            patch_name = patch[0]
+        elif isinstance(patch, dict):
+            patch_name = patch['name']
+            if patch['alt_location']:
+                patch_dir = os.path.join(basedir, letter_dir_for(patch['alt_location']), patch['alt_location'])
 
         # only check actual patch files, not other files being copied via the patch functionality
-        patch_full = os.path.join(specdir, patch)
-        if patch.endswith('.patch'):
+        patch_full = os.path.join(patch_dir, patch_name)
+        if patch_name.endswith('.patch'):
             msg = "Patch file %s is available for %s" % (patch_full, specfn)
             self.assertTrue(os.path.isfile(patch_full), msg)
 
         # verify checksum for each patch file
-        if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch.endswith('.patch')):
+        if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch_name.endswith('.patch')):
             checksum = patch_checksums[idx]
-            error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum)
+            error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch_name, ec_fn, checksum)
             res = verify_checksum(patch_full, checksum)
             self.assertTrue(res, error_msg)