{chem}[foss/2024a] AmberTools v24.10 by pavelToman · Pull Request #23652 · easybuilders/easybuild-easyconfigs

pavelToman · 2025-08-12T13:36:11Z

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

Update Amber easyblock for AmberTools >= 24.x easybuild-easyblocks#3868

…Tools-24_skip-tests.patch, AmberTools-24_fix_test_missing_dirs.patch

github-actions · 2025-08-12T13:37:27Z

Updated software `AmberTools-24.10-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-24.10-foss-2024a.eb
index ca7d8074aa..c8883d2bad 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-24.10-foss-2024a.eb
@@ -1,9 +1,9 @@
 easyblock = 'EB_Amber'
 
 name = 'AmberTools'
-local_ambertools_ver = 23
+local_ambertools_ver = 24
 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
-patchlevels = (6, 0)  # (AmberTools, Amber)
+patchlevels = (10, 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 +27,14 @@ 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-24_fix_test_missing_dirs.patch',
+    'AmberTools-24_skip-tests.patch',
 ]
 checksums = [
-    {'AmberTools23.tar.bz2': 'debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d'},
+    {'AmberTools24.tar.bz2': '52fb4fb3370a89b7ce738a2dc3e513c2fc1943fde4b4381846d9e75cc48d840f'},
     {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'},
     {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch':
      '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'},
@@ -43,42 +43,54 @@ 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-24_fix_test_missing_dirs.patch': '1c4c44cb012b625933781e9811f1657d5ddfd14cfbf4894bb1f767995eadc3b6'},
+    {'AmberTools-24_skip-tests.patch': '290bfd539991a1f7ddb60ff8e50e56bbc99b881047727653f82b9d6377f4baa2'},
 ]
 
 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', '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-24.10-foss-2024a.eb
index 5d584ac768..c8883d2bad 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-24.10-foss-2024a.eb
@@ -1,9 +1,9 @@
 easyblock = 'EB_Amber'
 
 name = 'AmberTools'
-local_ambertools_ver = 21
+local_ambertools_ver = 24
 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
-patchlevels = (12, 0)  # (AmberTools, Amber)
+patchlevels = (10, 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 +26,71 @@ 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-24_fix_test_missing_dirs.patch',
+    'AmberTools-24_skip-tests.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',
+    {'AmberTools24.tar.bz2': '52fb4fb3370a89b7ce738a2dc3e513c2fc1943fde4b4381846d9e75cc48d840f'},
+    {'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-24_fix_test_missing_dirs.patch': '1c4c44cb012b625933781e9811f1657d5ddfd14cfbf4894bb1f767995eadc3b6'},
+    {'AmberTools-24_skip-tests.patch': '290bfd539991a1f7ddb60ff8e50e56bbc99b881047727653f82b9d6377f4baa2'},
 ]
 
 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', '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-24.10-foss-2024a.eb
index a7fbe6089c..c8883d2bad 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-24.10-foss-2024a.eb
@@ -1,9 +1,9 @@
 easyblock = 'EB_Amber'
 
 name = 'AmberTools'
-local_ambertools_ver = 22
+local_ambertools_ver = 24
 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
-patchlevels = (3, 0)  # (AmberTools, Amber)
+patchlevels = (10, 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 +26,71 @@ 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-24_fix_test_missing_dirs.patch',
+    'AmberTools-24_skip-tests.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',
+    {'AmberTools24.tar.bz2': '52fb4fb3370a89b7ce738a2dc3e513c2fc1943fde4b4381846d9e75cc48d840f'},
+    {'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-24_fix_test_missing_dirs.patch': '1c4c44cb012b625933781e9811f1657d5ddfd14cfbf4894bb1f767995eadc3b6'},
+    {'AmberTools-24_skip-tests.patch': '290bfd539991a1f7ddb60ff8e50e56bbc99b881047727653f82b9d6377f4baa2'},
 ]
 
 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', 'ndfes']
+
+sanity_check_commands = [
+    f"python -c 'import {', '.join(_fe_toolkit_pkgs)}'",
+    "pip check",
+    "python -c 'import parmed'",
 ]
 
 runtest = True

pavelToman · 2025-08-12T13:38:05Z

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

boegelbot · 2025-08-12T13:40:11Z

@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=23652 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_23652 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7558

Test results coming soon (I hope)...

Details

- notification for comment with ID 3179381756 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 · 2025-08-12T15:28:53Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3868
SUCCESS
Build succeeded for 1 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/3cc937c4035f25de54398cf2ba86c2e6 for a full test report.

pavelToman · 2025-08-12T15:39:39Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4219.shinx.os - Linux RHEL 9.4, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/1b4bc7897e33dd20399f66cba929333c for a full test report.

smoors · 2025-08-16T19:24:18Z

Test report by @smoors
FAILED
Build succeeded for 2 out of 3 (1 easyconfigs in total)
node741.hydra.os - Linux Rocky Linux 9.5, x86_64, AMD EPYC 9535 64-Core Processor (zen5), Python 3.9.21
See https://gist.github.com/smoors/13b30d70b1299c02893692efa15a945e for a full test report.

smoors · 2025-08-17T15:45:38Z

Test report by @smoors
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in total)
node614.hydra.os - Linux Rocky Linux 9.5, x86_64, AMD EPYC 9384X 32-Core Processor (zen4), Python 3.9.21
See https://gist.github.com/smoors/e8a8e4195bc036cc7cadba2317838c1b for a full test report.

boegel

lgtm

boegel · 2025-08-18T10:53:04Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3555.doduo.os - Linux RHEL 9.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.9.18
See https://gist.github.com/boegel/9417d9fbd41a9c072344b06a08f84e4b for a full test report.

boegel · 2025-08-18T10:55:18Z

Going in, thanks @pavelToman!

adding easyconfigs: AmberTools-24.10-foss-2024a.eb and patches: Amber…

eb7472e

…Tools-24_skip-tests.patch, AmberTools-24_fix_test_missing_dirs.patch

pavelToman added the update label Aug 12, 2025

pavelToman mentioned this pull request Aug 12, 2025

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

Closed

Thyre added the 2024a issues & PRs related to 2024a common toolchains label Aug 12, 2025

boegel approved these changes Aug 18, 2025

View reviewed changes

boegel added this to the next release (5.1.2) milestone Aug 18, 2025

boegel merged commit 8a1175f into easybuilders:develop Aug 18, 2025
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{chem}[foss/2024a] AmberTools v24.10#23652

{chem}[foss/2024a] AmberTools v24.10#23652
boegel merged 1 commit intoeasybuilders:developfrom
pavelToman:20250812153607_new_pr_AmberTools2410

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Updated software AmberTools-24.10-foss-2024a.eb

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pavelToman commented Aug 12, 2025 •

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Updated software `AmberTools-24.10-foss-2024a.eb`