{chem}[foss/2024a] AmberTools v25.2 by pavelToman · Pull Request #23582 · easybuilders/easybuild-easyconfigs

pavelToman · 2025-08-06T12:32:34Z

(created using eb --new-pr)
requires:

github-actions · 2025-08-06T12:33:01Z

Updated software `AmberTools-25.2-foss-2024a.eb`

Diff against AmberTools-23.6-foss-2023a.eb

easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb

diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2024a.eb
index ca7d8074aa..fafe6bc87a 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2024a.eb
@@ -1,9 +1,9 @@
 easyblock = 'EB_Amber'
 
 name = 'AmberTools'
-local_ambertools_ver = 23
+local_ambertools_ver = 25
 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
-patchlevels = (6, 0)  # (AmberTools, Amber)
+patchlevels = (2, 0)  # (AmberTools, Amber)
 version = '%s.%s' % (local_ambertools_ver, patchlevels[0])
 
 homepage = 'https://ambermd.org/'
@@ -11,7 +11,7 @@ description = """AmberTools consists of several independently developed packages
  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': '2023a'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'usempi': True}
 
 # download requires registration
@@ -27,14 +27,13 @@ patches = [
     'AmberTools-20_fix_xblas_missing_make_dependency.patch',
     'AmberTools-21_CMake-FlexiBLAS.patch',
     'AmberTools-21_fix_incorrect_dvout_call.patch',
-    'AmberTools-21_fix_more_blas_argument_problems.patch',
     'AmberTools-21_fix_potential_use_before_init.patch',
     'AmberTools-21_fix_rism_argument_mismatch.patch',
     'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch',
-    'AmberTools-22_fix_test_missing_cuda_dir.patch',
+    'AmberTools-25_fix_test_missing_dirs.patch',
 ]
 checksums = [
-    {'AmberTools23.tar.bz2': 'debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d'},
+    {'AmberTools25.tar.bz2': 'ac009b2adeb25ccd2191db28905b867df49240e038dc590f423edf0d84f8a13b'},
     {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'},
     {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch':
      '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'},
@@ -43,42 +42,53 @@ checksums = [
     {'AmberTools-21_CMake-FlexiBLAS.patch': '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36'},
     {'AmberTools-21_fix_incorrect_dvout_call.patch':
      '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b'},
-    {'AmberTools-21_fix_more_blas_argument_problems.patch':
-     'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c'},
     {'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'},
-    {'AmberTools-22_fix_test_missing_cuda_dir.patch':
-     'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737'},
+    {'AmberTools-25_fix_test_missing_dirs.patch': '1c4c44cb012b625933781e9811f1657d5ddfd14cfbf4894bb1f767995eadc3b6'},
 ]
 
 builddependencies = [
-    ('CMake', '3.26.3'),
-    ('pkgconf', '1.9.5'),
+    ('CMake', '3.29.3'),
+    ('pkgconf', '2.2.0'),
     ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
     ('make', '4.4.1'),
+    ('Cython', '3.0.10'),
 ]
 
 dependencies = [
-    ('zlib', '1.2.13'),
+    ('zlib', '1.3.1'),
     ('bzip2', '1.0.8'),
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('Perl', '5.36.1'),
-    ('Perl-bundle-CPAN', '5.36.1'),
-    ('Boost', '1.82.0'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('Perl', '5.38.2'),
+    ('Perl-bundle-CPAN', '5.38.2'),
+    ('Boost', '1.85.0'),
     ('libreadline', '8.2'),
-    ('matplotlib', '3.7.2'),
+    ('matplotlib', '3.9.2'),
     ('netCDF', '4.9.2'),
     ('netCDF-Fortran', '4.6.1'),
-    ('PnetCDF', '1.12.3'),
+    ('PnetCDF', '1.14.0'),
     ('Tkinter', '%(pyver)s'),
-    ('X11', '20230603'),
-    ('mpi4py', '3.1.4'),
+    ('X11', '20240607'),
+    ('mpi4py', '4.0.1'),
+    ('FFTW', '3.3.10'),
+    ('netcdf4-python', '1.7.1.post2'),
+    ('PyYAML', '6.0.2'),
+    ('RDKit', '2025.03.3'),
+    ('PLUMED', '2.9.3'),
+]
+
+_fe_toolkit_pkgs = ['edgembar', 'fetkutils', 'ndfes']
+
+sanity_check_commands = [
+    f"python -c 'import {', '.join(_fe_toolkit_pkgs)}'",
+    "pip check",
+    "python -c 'import parmed'",
 ]
 
 runtest = True

Diff against AmberTools-21.12-foss-2021b.eb

easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb

diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2024a.eb
index 5d584ac768..fafe6bc87a 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2024a.eb
@@ -1,9 +1,9 @@
 easyblock = 'EB_Amber'
 
 name = 'AmberTools'
-local_ambertools_ver = 21
+local_ambertools_ver = 25
 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
-patchlevels = (12, 0)  # (AmberTools, Amber)
+patchlevels = (2, 0)  # (AmberTools, Amber)
 version = '%s.%s' % (local_ambertools_ver, patchlevels[0])
 
 homepage = 'https://ambermd.org/'
@@ -11,10 +11,10 @@ description = """AmberTools consists of several independently developed packages
  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': '2021b'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'usempi': True}
 
-# download requires registration, see http://ambermd.org/AmberTools17-get.html
+# download requires registration
 local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium'
 source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % local_ambertools_ver]
 sources = [{
@@ -26,65 +26,69 @@ patches = [
     'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
     'AmberTools-20_fix_xblas_missing_make_dependency.patch',
     'AmberTools-21_CMake-FlexiBLAS.patch',
-    'AmberTools-21_fix_DGESVD_workspace_query.patch',
     'AmberTools-21_fix_incorrect_dvout_call.patch',
-    'AmberTools-21_fix_incorrect_mexit_calls.patch',
-    'AmberTools-21_fix_more_blas_argument_problems.patch',
-    'AmberTools-21_fix_multiple_definition.patch',
     'AmberTools-21_fix_potential_use_before_init.patch',
     'AmberTools-21_fix_rism_argument_mismatch.patch',
     'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch',
-    'AmberTools-22_fix_test_missing_cuda_dir.patch',
-    'AmberTools-21_dont_include_config.h_in_top_Makefile.patch',
+    'AmberTools-25_fix_test_missing_dirs.patch',
 ]
 checksums = [
-    'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd',  # AmberTools21.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-21_dont_include_config.h_in_top_Makefile.patch
-    'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9',
+    {'AmberTools25.tar.bz2': 'ac009b2adeb25ccd2191db28905b867df49240e038dc590f423edf0d84f8a13b'},
+    {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'},
+    {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch':
+     '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'},
+    {'AmberTools-20_fix_xblas_missing_make_dependency.patch':
+     'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65'},
+    {'AmberTools-21_CMake-FlexiBLAS.patch': '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36'},
+    {'AmberTools-21_fix_incorrect_dvout_call.patch':
+     '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b'},
+    {'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'},
+    {'AmberTools-25_fix_test_missing_dirs.patch': '1c4c44cb012b625933781e9811f1657d5ddfd14cfbf4894bb1f767995eadc3b6'},
 ]
 
 builddependencies = [
-    ('Bison', '3.7.6'),
-    ('pkg-config', '0.29.2'),
-    ('CMake', '3.21.1'),
+    ('CMake', '3.29.3'),
+    ('pkgconf', '2.2.0'),
+    ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
-    ('make', '4.3'),
+    ('make', '4.4.1'),
+    ('Cython', '3.0.10'),
 ]
 
 dependencies = [
-    ('zlib', '1.2.11'),
+    ('zlib', '1.3.1'),
     ('bzip2', '1.0.8'),
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),
-    ('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'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('Perl', '5.38.2'),
+    ('Perl-bundle-CPAN', '5.38.2'),
+    ('Boost', '1.85.0'),
+    ('libreadline', '8.2'),
+    ('matplotlib', '3.9.2'),
+    ('netCDF', '4.9.2'),
+    ('netCDF-Fortran', '4.6.1'),
+    ('PnetCDF', '1.14.0'),
     ('Tkinter', '%(pyver)s'),
-    ('X11', '20210802'),
+    ('X11', '20240607'),
+    ('mpi4py', '4.0.1'),
+    ('FFTW', '3.3.10'),
+    ('netcdf4-python', '1.7.1.post2'),
+    ('PyYAML', '6.0.2'),
+    ('RDKit', '2025.03.3'),
+    ('PLUMED', '2.9.3'),
+]
+
+_fe_toolkit_pkgs = ['edgembar', 'fetkutils', 'ndfes']
+
+sanity_check_commands = [
+    f"python -c 'import {', '.join(_fe_toolkit_pkgs)}'",
+    "pip check",
+    "python -c 'import parmed'",
 ]
 
 runtest = True

Diff against AmberTools-22.3-foss-2021b.eb

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

diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2024a.eb
index a7fbe6089c..fafe6bc87a 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2024a.eb
@@ -1,9 +1,9 @@
 easyblock = 'EB_Amber'
 
 name = 'AmberTools'
-local_ambertools_ver = 22
+local_ambertools_ver = 25
 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
-patchlevels = (3, 0)  # (AmberTools, Amber)
+patchlevels = (2, 0)  # (AmberTools, Amber)
 version = '%s.%s' % (local_ambertools_ver, patchlevels[0])
 
 homepage = 'https://ambermd.org/'
@@ -11,7 +11,7 @@ description = """AmberTools consists of several independently developed packages
  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': '2021b'}
+toolchain = {'name': 'foss', 'version': '2024a'}
 toolchainopts = {'usempi': True}
 
 # download requires registration
@@ -26,65 +26,69 @@ patches = [
     'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
     'AmberTools-20_fix_xblas_missing_make_dependency.patch',
     'AmberTools-21_CMake-FlexiBLAS.patch',
-    'AmberTools-21_fix_DGESVD_workspace_query.patch',
     'AmberTools-21_fix_incorrect_dvout_call.patch',
-    'AmberTools-21_fix_incorrect_mexit_calls.patch',
-    'AmberTools-21_fix_more_blas_argument_problems.patch',
-    'AmberTools-21_fix_multiple_definition.patch',
     'AmberTools-21_fix_potential_use_before_init.patch',
     'AmberTools-21_fix_rism_argument_mismatch.patch',
     'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch',
-    'AmberTools-22_fix_test_missing_cuda_dir.patch',
-    'AmberTools-22_fix_missing_error_check_on_test_run.patch',
+    'AmberTools-25_fix_test_missing_dirs.patch',
 ]
 checksums = [
-    '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',
+    {'AmberTools25.tar.bz2': 'ac009b2adeb25ccd2191db28905b867df49240e038dc590f423edf0d84f8a13b'},
+    {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'},
+    {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch':
+     '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'},
+    {'AmberTools-20_fix_xblas_missing_make_dependency.patch':
+     'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65'},
+    {'AmberTools-21_CMake-FlexiBLAS.patch': '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36'},
+    {'AmberTools-21_fix_incorrect_dvout_call.patch':
+     '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b'},
+    {'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'},
+    {'AmberTools-25_fix_test_missing_dirs.patch': '1c4c44cb012b625933781e9811f1657d5ddfd14cfbf4894bb1f767995eadc3b6'},
 ]
 
 builddependencies = [
-    ('CMake', '3.21.1'),
-    ('pkg-config', '0.29.2'),
-    ('Bison', '3.7.6'),
+    ('CMake', '3.29.3'),
+    ('pkgconf', '2.2.0'),
+    ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
-    ('make', '4.3'),
+    ('make', '4.4.1'),
+    ('Cython', '3.0.10'),
 ]
 
 dependencies = [
-    ('zlib', '1.2.11'),
+    ('zlib', '1.3.1'),
     ('bzip2', '1.0.8'),
-    ('Python', '3.9.6'),
-    ('SciPy-bundle', '2021.10'),
-    ('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'),
+    ('Python', '3.12.3'),
+    ('SciPy-bundle', '2024.05'),
+    ('Perl', '5.38.2'),
+    ('Perl-bundle-CPAN', '5.38.2'),
+    ('Boost', '1.85.0'),
+    ('libreadline', '8.2'),
+    ('matplotlib', '3.9.2'),
+    ('netCDF', '4.9.2'),
+    ('netCDF-Fortran', '4.6.1'),
+    ('PnetCDF', '1.14.0'),
     ('Tkinter', '%(pyver)s'),
-    ('X11', '20210802'),
+    ('X11', '20240607'),
+    ('mpi4py', '4.0.1'),
+    ('FFTW', '3.3.10'),
+    ('netcdf4-python', '1.7.1.post2'),
+    ('PyYAML', '6.0.2'),
+    ('RDKit', '2025.03.3'),
+    ('PLUMED', '2.9.3'),
+]
+
+_fe_toolkit_pkgs = ['edgembar', 'fetkutils', 'ndfes']
+
+sanity_check_commands = [
+    f"python -c 'import {', '.join(_fe_toolkit_pkgs)}'",
+    "pip check",
+    "python -c 'import parmed'",
 ]
 
 runtest = True

pavelToman · 2025-08-06T12:33:06Z

@boegelbot please test @ jsc-zen3 EB_ARGS="--include-easyblocks-from-pr 3868"

boegelbot · 2025-08-06T12:40:08Z

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=23582 EB_ARGS="--include-easyblocks-from-pr 3868" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23582 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7501

Test results coming soon (I hope)...

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- notification for comment with ID 3159980942 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2025-08-06T12:47:47Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3868
FAILED
Build succeeded for 1 out of 2 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/a1d8e54d9d7df21385eefe79af9a01be for a full test report.

pavelToman · 2025-08-06T12:53:22Z

Test report by @boegelbot Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3868 FAILED Build succeeded for 1 out of 2 (1 easyconfigs in total) jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21 See https://gist.github.com/boegelbot/a1d8e54d9d7df21385eefe79af9a01be for a full test report.

missing patch - add it for now, but it should be from anoither PR (2025a)

pavelToman · 2025-08-06T13:07:23Z

@boegelbot please test @ jsc-zen3 EB_ARGS="--include-easyblocks-from-pr 3868"

boegelbot · 2025-08-06T13:10:09Z

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=23582 EB_ARGS="--include-easyblocks-from-pr 3868" EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23582 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7502

Test results coming soon (I hope)...

Details

- notification for comment with ID 3160106291 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2025-08-06T14:43:49Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3868
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.6, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/4931b4998fd5c1e44c725813d5111a73 for a full test report.

pavelToman · 2025-08-12T13:37:05Z

Replaced by:

{chem}[foss/2024a] AmberTools v24.10 #23652

adding easyconfigs: AmberTools-25.2-foss-2024a.eb

219b590

pavelToman added the update label Aug 6, 2025

add patch

b91e820

Thyre added the 2024a issues & PRs related to 2024a common toolchains label Aug 7, 2025

pavelToman marked this pull request as draft August 12, 2025 08:41

pavelToman closed this Aug 12, 2025

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{chem}[foss/2024a] AmberTools v25.2#23582

{chem}[foss/2024a] AmberTools v25.2#23582
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Updated software AmberTools-25.2-foss-2024a.eb

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pavelToman commented Aug 6, 2025 •

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Updated software `AmberTools-25.2-foss-2024a.eb`