{chem}[foss/2025a] AmberTools v25.2 by pavelToman · Pull Request #23420 · easybuilders/easybuild-easyconfigs

pavelToman · 2025-07-15T14:56:13Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#578
requires:

…pi-2025a.eb, netCDF-Fortran-4.6.2-gompi-2025a.eb and patches: AmberTools-25_parmed-update.patch, AmberTools-25_fix_test_missing_dirs.patch

github-actions · 2025-07-15T14:56:44Z

Updated software `AmberTools-25.2-foss-2025a.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-2025a.eb
index ca7d8074aa..9e8a8ba102 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2025a.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': '2025a'}
 toolchainopts = {'usempi': True}
 
 # download requires registration
@@ -27,14 +27,17 @@ 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',
+    'AmberTools-25_parmed-update.patch',
+    'AmberTools-25_fix-boost.patch',
+    'AmberTools-25_skip-tests.patch',
+    'AmberTools-25_fix-sander-numpy.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 +46,67 @@ 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'},
+    {'AmberTools-25_parmed-update.patch': '2216c7883be026ce48aac7589f75749f2a42ec74f6e3ceba378d762403c50924'},
+    {'AmberTools-25_fix-boost.patch': 'f4ccf7dedb5aa5b289ad5f69f3c1dc808c3fcc226d7118eaba40b108688e37cc'},
+    {'AmberTools-25_skip-tests.patch': '3de155ba9eedcbe84eb44962e9a5e66fda9d9dfff9ad50a356750baa286f8e21'},
+    {'AmberTools-25_fix-sander-numpy.patch': '82b875153927b8a0977022d608bbf51513ea936384f3059ecd41a37dfb004d5e'},
 ]
 
 builddependencies = [
-    ('CMake', '3.26.3'),
-    ('pkgconf', '1.9.5'),
+    ('CMake', '3.31.3'),
+    ('pkgconf', '2.3.0'),
     ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
     ('make', '4.4.1'),
+    ('Cython', '3.1.1'),
 ]
 
 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', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('Perl', '5.40.0'),
+    ('Perl-bundle-CPAN', '5.40.0'),
+    ('Boost', '1.88.0'),
     ('libreadline', '8.2'),
-    ('matplotlib', '3.7.2'),
-    ('netCDF', '4.9.2'),
-    ('netCDF-Fortran', '4.6.1'),
-    ('PnetCDF', '1.12.3'),
+    ('matplotlib', '3.10.3'),
+    ('netCDF', '4.9.3'),
+    ('netCDF-Fortran', '4.6.2'),
+    ('PnetCDF', '1.14.0'),
     ('Tkinter', '%(pyver)s'),
-    ('X11', '20230603'),
-    ('mpi4py', '3.1.4'),
+    ('X11', '20250521'),
+    ('mpi4py', '4.1.0'),
+    ('FFTW', '3.3.10'),
+    ('netcdf4-python', '1.7.2'),
+    ('PyYAML', '6.0.2'),
+    ('RDKit', '2025.03.4'),
+    ('PLUMED', '2.9.4'),
+]
+
+_fe_toolkit_path = "%(builddir)s/%(name)s/src/fe-toolkit/"
+_setup_path = "/src/python/setup.py"
+_fe_toolkit_pkgs = ['edgembar', 'fetkutils', 'ndfes']
+# recythonize pytraj files - python3.13 compability
+prebuildopts = "cd %(builddir)s/%(name)s/src/pytraj && find . -name '*.cpp' -delete && python setup.py --cythonize && "
+prebuildopts += "cd %(builddir)s/easybuild_obj && "
+# unpin numpy version restriction in fe-toolkit pkgs
+prebuildopts += """sed -i "/'numpy<2',/d" """
+for _pkg in _fe_toolkit_pkgs:
+    prebuildopts += f"{_fe_toolkit_path}{_pkg}{_setup_path} "
+prebuildopts += '&& '
+
+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-2025a.eb
index 5d584ac768..9e8a8ba102 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2025a.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': '2025a'}
 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 +26,87 @@ 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',
+    'AmberTools-25_parmed-update.patch',
+    'AmberTools-25_fix-boost.patch',
+    'AmberTools-25_skip-tests.patch',
+    'AmberTools-25_fix-sander-numpy.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'},
+    {'AmberTools-25_parmed-update.patch': '2216c7883be026ce48aac7589f75749f2a42ec74f6e3ceba378d762403c50924'},
+    {'AmberTools-25_fix-boost.patch': 'f4ccf7dedb5aa5b289ad5f69f3c1dc808c3fcc226d7118eaba40b108688e37cc'},
+    {'AmberTools-25_skip-tests.patch': '3de155ba9eedcbe84eb44962e9a5e66fda9d9dfff9ad50a356750baa286f8e21'},
+    {'AmberTools-25_fix-sander-numpy.patch': '82b875153927b8a0977022d608bbf51513ea936384f3059ecd41a37dfb004d5e'},
 ]
 
 builddependencies = [
-    ('Bison', '3.7.6'),
-    ('pkg-config', '0.29.2'),
-    ('CMake', '3.21.1'),
+    ('CMake', '3.31.3'),
+    ('pkgconf', '2.3.0'),
+    ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
-    ('make', '4.3'),
+    ('make', '4.4.1'),
+    ('Cython', '3.1.1'),
 ]
 
 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', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('Perl', '5.40.0'),
+    ('Perl-bundle-CPAN', '5.40.0'),
+    ('Boost', '1.88.0'),
+    ('libreadline', '8.2'),
+    ('matplotlib', '3.10.3'),
+    ('netCDF', '4.9.3'),
+    ('netCDF-Fortran', '4.6.2'),
+    ('PnetCDF', '1.14.0'),
     ('Tkinter', '%(pyver)s'),
-    ('X11', '20210802'),
+    ('X11', '20250521'),
+    ('mpi4py', '4.1.0'),
+    ('FFTW', '3.3.10'),
+    ('netcdf4-python', '1.7.2'),
+    ('PyYAML', '6.0.2'),
+    ('RDKit', '2025.03.4'),
+    ('PLUMED', '2.9.4'),
+]
+
+_fe_toolkit_path = "%(builddir)s/%(name)s/src/fe-toolkit/"
+_setup_path = "/src/python/setup.py"
+_fe_toolkit_pkgs = ['edgembar', 'fetkutils', 'ndfes']
+# recythonize pytraj files - python3.13 compability
+prebuildopts = "cd %(builddir)s/%(name)s/src/pytraj && find . -name '*.cpp' -delete && python setup.py --cythonize && "
+prebuildopts += "cd %(builddir)s/easybuild_obj && "
+# unpin numpy version restriction in fe-toolkit pkgs
+prebuildopts += """sed -i "/'numpy<2',/d" """
+for _pkg in _fe_toolkit_pkgs:
+    prebuildopts += f"{_fe_toolkit_path}{_pkg}{_setup_path} "
+prebuildopts += '&& '
+
+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-2025a.eb
index a7fbe6089c..9e8a8ba102 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2025a.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': '2025a'}
 toolchainopts = {'usempi': True}
 
 # download requires registration
@@ -26,65 +26,87 @@ 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',
+    'AmberTools-25_parmed-update.patch',
+    'AmberTools-25_fix-boost.patch',
+    'AmberTools-25_skip-tests.patch',
+    'AmberTools-25_fix-sander-numpy.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'},
+    {'AmberTools-25_parmed-update.patch': '2216c7883be026ce48aac7589f75749f2a42ec74f6e3ceba378d762403c50924'},
+    {'AmberTools-25_fix-boost.patch': 'f4ccf7dedb5aa5b289ad5f69f3c1dc808c3fcc226d7118eaba40b108688e37cc'},
+    {'AmberTools-25_skip-tests.patch': '3de155ba9eedcbe84eb44962e9a5e66fda9d9dfff9ad50a356750baa286f8e21'},
+    {'AmberTools-25_fix-sander-numpy.patch': '82b875153927b8a0977022d608bbf51513ea936384f3059ecd41a37dfb004d5e'},
 ]
 
 builddependencies = [
-    ('CMake', '3.21.1'),
-    ('pkg-config', '0.29.2'),
-    ('Bison', '3.7.6'),
+    ('CMake', '3.31.3'),
+    ('pkgconf', '2.3.0'),
+    ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
-    ('make', '4.3'),
+    ('make', '4.4.1'),
+    ('Cython', '3.1.1'),
 ]
 
 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', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('Perl', '5.40.0'),
+    ('Perl-bundle-CPAN', '5.40.0'),
+    ('Boost', '1.88.0'),
+    ('libreadline', '8.2'),
+    ('matplotlib', '3.10.3'),
+    ('netCDF', '4.9.3'),
+    ('netCDF-Fortran', '4.6.2'),
+    ('PnetCDF', '1.14.0'),
     ('Tkinter', '%(pyver)s'),
-    ('X11', '20210802'),
+    ('X11', '20250521'),
+    ('mpi4py', '4.1.0'),
+    ('FFTW', '3.3.10'),
+    ('netcdf4-python', '1.7.2'),
+    ('PyYAML', '6.0.2'),
+    ('RDKit', '2025.03.4'),
+    ('PLUMED', '2.9.4'),
+]
+
+_fe_toolkit_path = "%(builddir)s/%(name)s/src/fe-toolkit/"
+_setup_path = "/src/python/setup.py"
+_fe_toolkit_pkgs = ['edgembar', 'fetkutils', 'ndfes']
+# recythonize pytraj files - python3.13 compability
+prebuildopts = "cd %(builddir)s/%(name)s/src/pytraj && find . -name '*.cpp' -delete && python setup.py --cythonize && "
+prebuildopts += "cd %(builddir)s/easybuild_obj && "
+# unpin numpy version restriction in fe-toolkit pkgs
+prebuildopts += """sed -i "/'numpy<2',/d" """
+for _pkg in _fe_toolkit_pkgs:
+    prebuildopts += f"{_fe_toolkit_path}{_pkg}{_setup_path} "
+prebuildopts += '&& '
+
+sanity_check_commands = [
+    f"python -c 'import {', '.join(_fe_toolkit_pkgs)}'",
+    "pip check",
+    "python -c 'import parmed'",
 ]
 
 runtest = True

Updated software `PLUMED-2.9.4-foss-2025a.eb`

Diff against PLUMED-2.9.3-foss-2024a.eb

easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.3-foss-2024a.eb

diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.3-foss-2024a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.4-foss-2025a.eb
index 0e44fc2634..0d61800b40 100644
--- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.3-foss-2024a.eb
+++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.4-foss-2025a.eb
@@ -1,7 +1,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'PLUMED'
-version = '2.9.3'
+version = '2.9.4'
 
 homepage = 'https://www.plumed.org'
 description = """PLUMED is an open source library for free energy calculations in molecular systems which
@@ -11,24 +11,24 @@ description = """PLUMED is an open source library for free energy calculations i
  The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
 """
 
-toolchain = {'name': 'foss', 'version': '2024a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'usempi': 'True'}
 
-source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
-sources = [SOURCE_TGZ]
-checksums = ['2ba5095bc7c7cfde1ca95780c1240d852b7dc1b00c9de5b31e607120449ff827']
+source_urls = ['https://github.com/plumed/plumed2/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['3068ab5e28cbae38b582d128fecac14c820762244d8eb87ad6030f04f96ecd78']
 
 builddependencies = [
-    ('xxd', '9.1.1275'),
+    ('xxd', '9.1.1457'),
+    ('Cython', '3.1.1'),
 ]
 
 dependencies = [
     ('zlib', '1.3.1'),
     ('GSL', '2.8'),
-    ('Python', '3.12.3'),
-    ('SciPy-bundle', '2024.05'),
-    ('Cython', '3.0.10'),  # Cython is not included in Python-bundle-PyPI > 2023
-    ('Boost', '1.85.0'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('Boost', '1.88.0'),
 ]
 
 preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '

Diff against PLUMED-2.9.2-foss-2023b.eb

easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.2-foss-2023b.eb

diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.2-foss-2023b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.4-foss-2025a.eb
index 3ed5ad9b82..0d61800b40 100644
--- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.2-foss-2023b.eb
+++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.4-foss-2025a.eb
@@ -1,7 +1,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'PLUMED'
-version = '2.9.2'
+version = '2.9.4'
 
 homepage = 'https://www.plumed.org'
 description = """PLUMED is an open source library for free energy calculations in molecular systems which
@@ -11,23 +11,24 @@ description = """PLUMED is an open source library for free energy calculations i
  The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
 """
 
-toolchain = {'name': 'foss', 'version': '2023b'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'usempi': 'True'}
 
-source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
-sources = [SOURCE_TGZ]
-checksums = ['6fc23fe31074ad6b7a0eb9e2441fce5b3d92514d0d87206594c59c75e4c83d6e']
+source_urls = ['https://github.com/plumed/plumed2/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['3068ab5e28cbae38b582d128fecac14c820762244d8eb87ad6030f04f96ecd78']
 
 builddependencies = [
-    ('xxd', '9.1.0307'),
+    ('xxd', '9.1.1457'),
+    ('Cython', '3.1.1'),
 ]
 
 dependencies = [
-    ('zlib', '1.2.13'),
-    ('GSL', '2.7'),
-    ('Python', '3.11.5'),
-    ('SciPy-bundle', '2023.11'),
-    ('Boost', '1.83.0'),
+    ('zlib', '1.3.1'),
+    ('GSL', '2.8'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('Boost', '1.88.0'),
 ]
 
 preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '

Diff against PLUMED-2.9.0-foss-2023a.eb

easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2023a.eb

diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2023a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.4-foss-2025a.eb
index b08db49309..0d61800b40 100644
--- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2023a.eb
+++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.4-foss-2025a.eb
@@ -1,7 +1,7 @@
 easyblock = 'ConfigureMake'
 
 name = 'PLUMED'
-version = '2.9.0'
+version = '2.9.4'
 
 homepage = 'https://www.plumed.org'
 description = """PLUMED is an open source library for free energy calculations in molecular systems which
@@ -11,23 +11,24 @@ description = """PLUMED is an open source library for free energy calculations i
  The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
 """
 
-toolchain = {'name': 'foss', 'version': '2023a'}
+toolchain = {'name': 'foss', 'version': '2025a'}
 toolchainopts = {'usempi': 'True'}
 
-source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
-sources = [SOURCE_TGZ]
-checksums = ['534db9ccb9446844f3e99ecdff091ad79c014ce9c4afe212c1536e19f85ab0d1']
+source_urls = ['https://github.com/plumed/plumed2/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['3068ab5e28cbae38b582d128fecac14c820762244d8eb87ad6030f04f96ecd78']
 
 builddependencies = [
-    ('xxd', '9.0.2112'),
+    ('xxd', '9.1.1457'),
+    ('Cython', '3.1.1'),
 ]
 
 dependencies = [
-    ('zlib', '1.2.13'),
-    ('GSL', '2.7'),
-    ('Python', '3.11.3'),
-    ('SciPy-bundle', '2023.07'),
-    ('Boost', '1.82.0'),
+    ('zlib', '1.3.1'),
+    ('GSL', '2.8'),
+    ('Python', '3.13.1'),
+    ('SciPy-bundle', '2025.06'),
+    ('Boost', '1.88.0'),
 ]
 
 preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '

pavelToman · 2025-07-15T15:00:45Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-07-15T15:40:12Z

@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=23420 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23420 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7250

Test results coming soon (I hope)...

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it is of no use to you (unless you think I have a bug, which I don't).

pavelToman · 2025-07-15T16:00:20Z

Test report by @pavelToman
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node4205.shinx.os - Linux RHEL 9.4, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/468a8aeaa37a3b72dad8cfd8cd978042 for a full test report.

pavelToman · 2025-07-15T16:13:53Z

Test report by @pavelToman
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node4005.donphan.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 570.133.20, Python 3.9.18
See https://gist.github.com/pavelToman/3310561288eaec8a48bd76c34359961a for a full test report.

boegelbot · 2025-07-15T16:54:22Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/03b8addab925972d02faeafd0737e6a0 for a full test report.

pavelToman · 2025-07-17T10:23:26Z

there is a problem with python packages the AmberTools installs internally. The EB_Amber easyblock does not check python stuff by pip check.
After the check -> some of the py stuff is not compatible with numpy 2.x

EDIT: added patch to fix numpy 2 compability + update parmed patch

…mpi-2025a.eb

…asyconfigs into 20250715165609_new_pr_AmberTools251

pavelToman · 2025-07-21T15:11:49Z

@boegelbot please test @ jsc-zen3

boegelbot · 2025-07-21T15:20:09Z

@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=23420 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_23420 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7299

Test results coming soon (I hope)...

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pavelToman · 2025-07-21T16:06:21Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4244.shinx.os - Linux RHEL 9.4, x86_64, AMD EPYC 9654 96-Core Processor, Python 3.9.18
See https://gist.github.com/pavelToman/4a83a8d868b2ce84a9d600bee927579e for a full test report.

boegelbot · 2025-07-21T16:10:47Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.21
See https://gist.github.com/boegelbot/f4074564861b64805d01ca9d96410045 for a full test report.

verdurin · 2025-07-25T14:35:27Z

@pavelToman looking at RDKit. Wonder if you could help with updating Amber itself? Or do you only need AmberTools`?

pavelToman · 2025-07-28T07:39:06Z

@pavelToman looking at RDKit. Wonder if you could help with updating Amber itself? Or do you only need AmberTools`?

I need only AmberTools for Open Force Field Toolkit: #23439
For now I either fight with new jax-0.6.2, but maybe I will have some time this week to look into Amber

…asyconfigs into 20250715165609_new_pr_AmberTools251

easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2025a.eb

laraPPr · 2025-07-30T12:50:16Z

Test report by @laraPPr
FAILED
Build succeeded for 2 out of 3 (1 easyconfigs in total)
node3536.doduo.os - Linux RHEL 9.4 (Plow), x86_64, AMD EPYC 7552 48-Core Processor, Python 3.9.18
See https://gist.github.com/laraPPr/7bda3b0691303622a4214ea6f9d4616b for a full test report.

pavelToman · 2025-08-04T15:50:28Z

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

boegelbot · 2025-08-04T16:00:13Z

@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=23420 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_23420 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7485

Test results coming soon (I hope)...

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boegelbot · 2025-08-04T17:30:05Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3868
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
jsczen3c2.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/d77a894a8d94ad582fcd04d776e2dc4a for a full test report.

pavelToman · 2025-08-06T08:32:53Z

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

boegelbot · 2025-08-06T08:40:09Z

@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=23420 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_23420 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7499

Test results coming soon (I hope)...

Details

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boegelbot · 2025-08-06T10:17:54Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3868
FAILED
Build succeeded for 1 out of 2 (2 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/44dba2ad8d872c1d99d6a2643911c0cf for a full test report.

easybuild/easyconfigs/a/AmberTools/AmberTools-25_skip-2048-wat-tests.patch

pavelToman · 2025-08-12T08:26:43Z

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

boegelbot · 2025-08-12T08:30:09Z

@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=23420 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_23420 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 7547

Test results coming soon (I hope)...

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boegelbot · 2025-08-12T10:35:30Z

Test report by @boegelbot
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3868
SUCCESS
Build succeeded for 2 out of 2 (2 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/a16bb0a61a295b76c480d36321e0c75b for a full test report.

pavelToman · 2025-08-12T11:18:22Z

Test report by @pavelToman
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node4001.donphan.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 570.133.20, Python 3.9.18
See https://gist.github.com/pavelToman/2e5b1583d24eec7d04249cc0760a2a7a for a full test report.

pavelToman · 2025-08-12T13:39:59Z

@laraPPr could you test it again on doduo? Should work now

boegel · 2025-08-13T07:21:03Z

@pavelToman Test report from doduo is coming up...

boegel · 2025-08-13T07:31:57Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3868
FAILED
Build succeeded for 0 out of 2 (2 easyconfigs in total)
node3534.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/379f837b72a45521318c607b043070f9 for a full test report.

edit: ignore this failure, I was also rebuilding FFTW.MPI to test easybuilders/easybuild-easyblocks#3884...

boegel · 2025-08-13T10:37:32Z

Test report by @boegel
Using easyblocks from PR(s) easybuilders/easybuild-easyblocks#3868
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3534.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/99f7a1d00a4c27cb5c95648b92e48ba3 for a full test report.

boegel

lgtm

requested changes made

boegel · 2025-08-18T08:43:22Z

Going in, thanks @pavelToman!

adding easyconfigs: AmberTools-25.1-foss-2025a.eb, PnetCDF-1.14.0-gom…

6c24d29

…pi-2025a.eb, netCDF-Fortran-4.6.2-gompi-2025a.eb and patches: AmberTools-25_parmed-update.patch, AmberTools-25_fix_test_missing_dirs.patch

pavelToman added the update label Jul 15, 2025

pavelToman mentioned this pull request Jul 15, 2025

updated of Python packages on top of Python 3.13 for courses (Py4Sci) vscentrum/vsc-software-stack#578

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25 tasks

pavelToman marked this pull request as draft July 17, 2025 10:22

pavelToman added 2 commits July 18, 2025 10:37

Delete easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.2-go…

d8c5fc5

…mpi-2025a.eb

Delete easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.14.0-gompi-2025a.eb

8dbb83f

pavelToman changed the title ~~{data}[gompi/2025a] AmberTools v25.1, PnetCDF v1.14.0, netCDF-Fortran v4.6.2~~ {chem}[foss/2025a] AmberTools v25.1 Jul 18, 2025

branfosj and others added 3 commits July 18, 2025 12:57

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

5f3f199

…asyconfigs into 20250715165609_new_pr_AmberTools251

update to v25.2 + Boost.patch + update parmed.patch

e055b34

add updated parmed.patch

9697d0f

pavelToman marked this pull request as ready for review July 21, 2025 15:11

pavelToman mentioned this pull request Jul 21, 2025

{bio,chem,numlib}[foss/2025a] OpenForceField-Toolkit v0.16.9, Pint v0.24.4, nglview v3.1.4 #23439

Merged

pavelToman changed the title ~~{chem}[foss/2025a] AmberTools v25.1~~ {chem}[foss/2025a] AmberTools v25.2 Jul 21, 2025

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

db1155b

…asyconfigs into 20250715165609_new_pr_AmberTools251

laraPPr previously requested changes Jul 29, 2025

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Update AmberTools-25.2-foss-2025a.eb

087bdae

boegel added this to the 5.x milestone Jul 31, 2025

fix tests + add plumed

35f4818

pavelToman mentioned this pull request Aug 4, 2025

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

Merged

Update PLUMED-2.9.4-foss-2025a.eb

345be39

Thyre added the 2025a issues & PRs related to 2025a common toolchains label Aug 6, 2025

pavelToman mentioned this pull request Aug 6, 2025

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

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boegel reviewed Aug 6, 2025

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easybuild/easyconfigs/a/AmberTools/AmberTools-25_skip-2048-wat-tests.patch Outdated Show resolved Hide resolved

maxim-masterov mentioned this pull request Aug 7, 2025

{chem}[GCC/14.2.0] Libint v2.11.1 w/ lmax 6 cp2k, libvori v220621, libxsmm v1.17 #23593

Merged

add patches to fix tests + numpy v2 in sander

c5fa793

boegel modified the milestones: 5.x, next release (5.1.2) Aug 13, 2025

boegel approved these changes Aug 18, 2025

View reviewed changes

boegel merged commit b723634 into easybuilders:develop Aug 18, 2025
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sheepforce mentioned this pull request Sep 19, 2025

ambertools: broken on current master Nix-QChem/NixOS-QChem#736

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Updated software AmberTools-25.2-foss-2025a.eb

Updated software PLUMED-2.9.4-foss-2025a.eb

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Updated software `AmberTools-25.2-foss-2025a.eb`

Updated software `PLUMED-2.9.4-foss-2025a.eb`

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