{chem}[foss/2026.1] AmberTools v26.1 by pavelToman · Pull Request #26555 · easybuilders/easybuild-easyconfigs

pavelToman · 2026-07-28T10:19:53Z

(created using eb --new-pr)

…ore-15.2.0.eb and patches: AmberTools-26_ignore-portability-test-differences.patch, AmberTools-26_fix-cpptraj-gzip-test.patch, AmberTools-26_fix-pytraj-install-PYTHONPATH.patch, AmberTools-26_do-not-clean-QUICK-compiler-flags.patch, AmberTools-26_skip-nonportable-tests.patch, AmberTools-26_limit-pymemembed-test-threads.patch, AmberTools-26_recythonize-pytraj.patch

github-actions · 2026-07-28T10:20:40Z

Updated software `AmberTools-26.1-foss-2026.1.eb`

Diff against AmberTools-24.10-foss-2024a.eb

easybuild/easyconfigs/a/AmberTools/AmberTools-24.10-foss-2024a.eb

diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-24.10-foss-2024a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-26.1-foss-2026.1.eb
index c8883d2bad..d3a89431eb 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-24.10-foss-2024a.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-26.1-foss-2026.1.eb
@@ -1,9 +1,9 @@
 easyblock = 'EB_Amber'
 
 name = 'AmberTools'
-local_ambertools_ver = 24
+local_ambertools_ver = 26
 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
-patchlevels = (10, 0)  # (AmberTools, Amber)
+patchlevels = (1, 0)  # (AmberTools, Amber)
 version = '%s.%s' % (local_ambertools_ver, patchlevels[0])
 
 homepage = 'https://ambermd.org/'
@@ -11,8 +11,17 @@ 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': '2024a'}
-toolchainopts = {'usempi': True}
+toolchain = {'name': 'foss', 'version': '2026.1'}
+# AmberTools regression references are sensitive to compiler-generated
+# floating-point differences, so disable CPU-specific tuning and auto-vectorization and use strict FP
+# semantics for reproducible results across supported architectures
+toolchainopts = {
+    'pic': True,
+    'usempi': True,
+    'strict': True,
+    'vectorize': False,
+    'optarch': False,
+}
 
 # download requires registration
 local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium'
@@ -30,11 +39,19 @@ patches = [
     'AmberTools-21_fix_potential_use_before_init.patch',
     'AmberTools-21_fix_rism_argument_mismatch.patch',
     'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch',
-    'AmberTools-24_fix_test_missing_dirs.patch',
-    'AmberTools-24_skip-tests.patch',
+    'AmberTools-25_fix_test_missing_dirs.patch',
+    'AmberTools-25_fix-boost.patch',
+    'AmberTools-25_fix-sander-numpy.patch',
+    'AmberTools-26_recythonize-pytraj.patch',
+    'AmberTools-26_skip-nonportable-tests.patch',
+    'AmberTools-26_do-not-clean-QUICK-compiler-flags.patch',
+    'AmberTools-26_fix-pytraj-install-PYTHONPATH.patch',
+    'AmberTools-26_fix-cpptraj-gzip-test.patch',
+    'AmberTools-26_ignore-portability-test-differences.patch',
+    'AmberTools-26_limit-pymemembed-test-threads.patch',
 ]
 checksums = [
-    {'AmberTools24.tar.bz2': '52fb4fb3370a89b7ce738a2dc3e513c2fc1943fde4b4381846d9e75cc48d840f'},
+    {'AmberTools26.tar.bz2': '5d46eef3c2bb7d5bf9e8c0c38add34406ea67e3f0e4097ac9d11d8a544538c9c'},
     {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'},
     {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch':
      '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'},
@@ -49,48 +66,108 @@ checksums = [
      '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1'},
     {'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch':
      '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f'},
-    {'AmberTools-24_fix_test_missing_dirs.patch': '1c4c44cb012b625933781e9811f1657d5ddfd14cfbf4894bb1f767995eadc3b6'},
-    {'AmberTools-24_skip-tests.patch': '290bfd539991a1f7ddb60ff8e50e56bbc99b881047727653f82b9d6377f4baa2'},
+    {'AmberTools-25_fix_test_missing_dirs.patch': '1c4c44cb012b625933781e9811f1657d5ddfd14cfbf4894bb1f767995eadc3b6'},
+    {'AmberTools-25_fix-boost.patch': 'f4ccf7dedb5aa5b289ad5f69f3c1dc808c3fcc226d7118eaba40b108688e37cc'},
+    {'AmberTools-25_fix-sander-numpy.patch': '82b875153927b8a0977022d608bbf51513ea936384f3059ecd41a37dfb004d5e'},
+    {'AmberTools-26_recythonize-pytraj.patch': '45cc8acbe61a2cc06d759972174ebca046bb174f422e76eb05a93788af41e8a2'},
+    {'AmberTools-26_skip-nonportable-tests.patch': '4d8d78d715ad89c5fc5c92300b1d5399720cf1093d4c481ed2e086645127af83'},
+    {'AmberTools-26_do-not-clean-QUICK-compiler-flags.patch':
+     '42ff0f9ab60e87cdffaddc89038a12ee8e568eb8a0e33ca043c009e5f9bb3588'},
+    {'AmberTools-26_fix-pytraj-install-PYTHONPATH.patch':
+     'f1f1d1682a97505c2ed8560d9f868d67bb44b420135d98832c63142e13ce12df'},
+    {'AmberTools-26_fix-cpptraj-gzip-test.patch': 'd80bff19ad32d7a1c9011299751c33285afc704632e0915f84d7fc86887bfa3d'},
+    {'AmberTools-26_ignore-portability-test-differences.patch':
+     '09dcb3c4b0c2219b7c1038272718cb2c07e832670b8dec2ead6eca15d33a7fa0'},
+    {'AmberTools-26_limit-pymemembed-test-threads.patch':
+     '4a89a7c6d7a36278650282f8e5d7aa6974cf9790b2b944cdfe065fcbfc68bf9c'},
 ]
 
 builddependencies = [
-    ('CMake', '3.29.3'),
-    ('pkgconf', '2.2.0'),
+    ('CMake', '3.31.11'),
+    ('pkgconf', '2.5.1'),
     ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
     ('make', '4.4.1'),
-    ('Cython', '3.0.10'),
+    ('Cython', '3.2.4'),
 ]
-
 dependencies = [
-    ('zlib', '1.3.1'),
+    ('zlib', '2.3.2'),
     ('bzip2', '1.0.8'),
-    ('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'),
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
+    ('SciPy-bundle', '2026.05'),
+    ('Perl', '5.42.0'),
+    ('Perl-bundle-CPAN', '%(perlver)s'),
+    ('Boost', '1.90.0'),
+    ('matplotlib', '3.10.9'),
+    ('netCDF', '4.10.0'),
+    ('netCDF-Fortran', '4.6.3'),
+    ('PnetCDF', '1.14.1'),
     ('Tkinter', '%(pyver)s'),
-    ('X11', '20240607'),
-    ('mpi4py', '4.0.1'),
+    ('X11', '20260518'),
+    ('mpi4py', '4.1.2'),
     ('FFTW', '3.3.10'),
-    ('netcdf4-python', '1.7.1.post2'),
-    ('PyYAML', '6.0.2'),
-    ('RDKit', '2025.03.3'),
-    ('PLUMED', '2.9.3'),
+    ('netcdf4-python', '1.7.4'),
+    ('PyYAML', '6.0.3'),
+    ('RDKit', '2026.03.4'),
+    ('PLUMED', '2.10.0'),
+    ('Biopython', '1.87'),
+    ('scikit-learn', '1.8.0'),
+    ('pydantic', '2.13.4'),
+    ('numba', '0.65.1'),
+    ('gemmi', '0.7.5'),
+    ('freesasa', '2.2.1'),
+    ('sympy', '1.14.0'),
+    ('networkx', '3.6.1'),
+    ('NLopt', '2.10.1'),
+    ('arpack-ng', '3.9.1'),
 ]
 
-_fe_toolkit_pkgs = ['edgembar', 'ndfes']
+# Avoid requiring the separate Boost.System library in the AmberTools and QUICK CMake configurations
+preconfigopts = "sed -i 's/Boost COMPONENTS thread system/Boost COMPONENTS thread/' "
+preconfigopts += "../cmake/3rdPartyTools.cmake "
+preconfigopts += "../AmberTools/src/quick/cmake/3rdPartyTools.cmake && "
+
+# Replace Amber's hard-coded -O3 with -O2 to match EasyBuild and improve numerical reproducibility
+preconfigopts += "sed -i 's/-O3/-O2/g' "
+preconfigopts += "../cmake/CompilerFlags.cmake && "
+
+# Remove the obsolete NumPy <2 upper bound from the FE-toolkit packages
+_fe_toolkit_path = "%(builddir)s/%(name)s/src/fe-toolkit/"
+_setup_path = "/src/python/setup.py"
+_fe_toolkit_pkgs = ['edgembar', 'fetkutils', 'ndfes']
+prebuildopts = """sed -i "/'numpy<2',/d" """
+for _pkg in _fe_toolkit_pkgs:
+    prebuildopts += f"{_fe_toolkit_path}{_pkg}{_setup_path} "
+prebuildopts += '&& '
+
+# Fix py3.14 compatibility -  ValueError: argument groups cannot be nested
+prebuildopts += (
+    'sed -i '
+    r"'s/group.add_argument_group(/parser.add_argument_group(/g' "
+    '../AmberTools/src/mmpbsa_py/MMPBSA_mods/commandlineparser.py && '
+)
 
 sanity_check_commands = [
-    f"python -c 'import {', '.join(_fe_toolkit_pkgs)}'",
-    "pip check",
-    "python -c 'import parmed'",
+    "sander --version",
+    "sander.MPI --version",
+    "cpptraj -h >/dev/null",
+    "tleap -h >/dev/null",
+    "antechamber -h >/dev/null",
+    "MMPBSA.py -h >/dev/null",
+    "packmol-memgen -h >/dev/null",
+    "parmed -h >/dev/null",
+    "pdb4amber -h >/dev/null",
+    "command -v quick >/dev/null",
+    "command -v quick.MPI >/dev/null",
+    "python -s -c 'import parmed'",
+    "python -s -c 'import pdb4amber'",
+    "python -s -c 'import pymsmt'",
+    "python -s -c 'import pytraj'",
+    "python -s -c 'import sander'",
+    "python -s -c 'import edgembar'",
+    "python -s -c 'import fetkutils'",
+    "python -s -c 'import ndfes'",
 ]
 
 runtest = True

Diff against AmberTools-25.2-foss-2025a.eb

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

diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2025a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-26.1-foss-2026.1.eb
index 9e8a8ba102..d3a89431eb 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-25.2-foss-2025a.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-26.1-foss-2026.1.eb
@@ -1,9 +1,9 @@
 easyblock = 'EB_Amber'
 
 name = 'AmberTools'
-local_ambertools_ver = 25
+local_ambertools_ver = 26
 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
-patchlevels = (2, 0)  # (AmberTools, Amber)
+patchlevels = (1, 0)  # (AmberTools, Amber)
 version = '%s.%s' % (local_ambertools_ver, patchlevels[0])
 
 homepage = 'https://ambermd.org/'
@@ -11,8 +11,17 @@ 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': '2025a'}
-toolchainopts = {'usempi': True}
+toolchain = {'name': 'foss', 'version': '2026.1'}
+# AmberTools regression references are sensitive to compiler-generated
+# floating-point differences, so disable CPU-specific tuning and auto-vectorization and use strict FP
+# semantics for reproducible results across supported architectures
+toolchainopts = {
+    'pic': True,
+    'usempi': True,
+    'strict': True,
+    'vectorize': False,
+    'optarch': False,
+}
 
 # download requires registration
 local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium'
@@ -31,13 +40,18 @@ patches = [
     'AmberTools-21_fix_rism_argument_mismatch.patch',
     'AmberTools-21_fix_xray_fftpack_arg_mismatch.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',
+    'AmberTools-26_recythonize-pytraj.patch',
+    'AmberTools-26_skip-nonportable-tests.patch',
+    'AmberTools-26_do-not-clean-QUICK-compiler-flags.patch',
+    'AmberTools-26_fix-pytraj-install-PYTHONPATH.patch',
+    'AmberTools-26_fix-cpptraj-gzip-test.patch',
+    'AmberTools-26_ignore-portability-test-differences.patch',
+    'AmberTools-26_limit-pymemembed-test-threads.patch',
 ]
 checksums = [
-    {'AmberTools25.tar.bz2': 'ac009b2adeb25ccd2191db28905b867df49240e038dc590f423edf0d84f8a13b'},
+    {'AmberTools26.tar.bz2': '5d46eef3c2bb7d5bf9e8c0c38add34406ea67e3f0e4097ac9d11d8a544538c9c'},
     {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'},
     {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch':
      '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'},
@@ -53,60 +67,107 @@ checksums = [
     {'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'},
+    {'AmberTools-26_recythonize-pytraj.patch': '45cc8acbe61a2cc06d759972174ebca046bb174f422e76eb05a93788af41e8a2'},
+    {'AmberTools-26_skip-nonportable-tests.patch': '4d8d78d715ad89c5fc5c92300b1d5399720cf1093d4c481ed2e086645127af83'},
+    {'AmberTools-26_do-not-clean-QUICK-compiler-flags.patch':
+     '42ff0f9ab60e87cdffaddc89038a12ee8e568eb8a0e33ca043c009e5f9bb3588'},
+    {'AmberTools-26_fix-pytraj-install-PYTHONPATH.patch':
+     'f1f1d1682a97505c2ed8560d9f868d67bb44b420135d98832c63142e13ce12df'},
+    {'AmberTools-26_fix-cpptraj-gzip-test.patch': 'd80bff19ad32d7a1c9011299751c33285afc704632e0915f84d7fc86887bfa3d'},
+    {'AmberTools-26_ignore-portability-test-differences.patch':
+     '09dcb3c4b0c2219b7c1038272718cb2c07e832670b8dec2ead6eca15d33a7fa0'},
+    {'AmberTools-26_limit-pymemembed-test-threads.patch':
+     '4a89a7c6d7a36278650282f8e5d7aa6974cf9790b2b944cdfe065fcbfc68bf9c'},
 ]
 
 builddependencies = [
-    ('CMake', '3.31.3'),
-    ('pkgconf', '2.3.0'),
+    ('CMake', '3.31.11'),
+    ('pkgconf', '2.5.1'),
     ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
     ('make', '4.4.1'),
-    ('Cython', '3.1.1'),
+    ('Cython', '3.2.4'),
 ]
-
 dependencies = [
-    ('zlib', '1.3.1'),
+    ('zlib', '2.3.2'),
     ('bzip2', '1.0.8'),
-    ('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'),
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
+    ('SciPy-bundle', '2026.05'),
+    ('Perl', '5.42.0'),
+    ('Perl-bundle-CPAN', '%(perlver)s'),
+    ('Boost', '1.90.0'),
+    ('matplotlib', '3.10.9'),
+    ('netCDF', '4.10.0'),
+    ('netCDF-Fortran', '4.6.3'),
+    ('PnetCDF', '1.14.1'),
     ('Tkinter', '%(pyver)s'),
-    ('X11', '20250521'),
-    ('mpi4py', '4.1.0'),
+    ('X11', '20260518'),
+    ('mpi4py', '4.1.2'),
     ('FFTW', '3.3.10'),
-    ('netcdf4-python', '1.7.2'),
-    ('PyYAML', '6.0.2'),
-    ('RDKit', '2025.03.4'),
-    ('PLUMED', '2.9.4'),
+    ('netcdf4-python', '1.7.4'),
+    ('PyYAML', '6.0.3'),
+    ('RDKit', '2026.03.4'),
+    ('PLUMED', '2.10.0'),
+    ('Biopython', '1.87'),
+    ('scikit-learn', '1.8.0'),
+    ('pydantic', '2.13.4'),
+    ('numba', '0.65.1'),
+    ('gemmi', '0.7.5'),
+    ('freesasa', '2.2.1'),
+    ('sympy', '1.14.0'),
+    ('networkx', '3.6.1'),
+    ('NLopt', '2.10.1'),
+    ('arpack-ng', '3.9.1'),
 ]
 
+# Avoid requiring the separate Boost.System library in the AmberTools and QUICK CMake configurations
+preconfigopts = "sed -i 's/Boost COMPONENTS thread system/Boost COMPONENTS thread/' "
+preconfigopts += "../cmake/3rdPartyTools.cmake "
+preconfigopts += "../AmberTools/src/quick/cmake/3rdPartyTools.cmake && "
+
+# Replace Amber's hard-coded -O3 with -O2 to match EasyBuild and improve numerical reproducibility
+preconfigopts += "sed -i 's/-O3/-O2/g' "
+preconfigopts += "../cmake/CompilerFlags.cmake && "
+
+# Remove the obsolete NumPy <2 upper bound from the FE-toolkit packages
 _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" """
+prebuildopts = """sed -i "/'numpy<2',/d" """
 for _pkg in _fe_toolkit_pkgs:
     prebuildopts += f"{_fe_toolkit_path}{_pkg}{_setup_path} "
 prebuildopts += '&& '
 
+# Fix py3.14 compatibility -  ValueError: argument groups cannot be nested
+prebuildopts += (
+    'sed -i '
+    r"'s/group.add_argument_group(/parser.add_argument_group(/g' "
+    '../AmberTools/src/mmpbsa_py/MMPBSA_mods/commandlineparser.py && '
+)
+
 sanity_check_commands = [
-    f"python -c 'import {', '.join(_fe_toolkit_pkgs)}'",
-    "pip check",
-    "python -c 'import parmed'",
+    "sander --version",
+    "sander.MPI --version",
+    "cpptraj -h >/dev/null",
+    "tleap -h >/dev/null",
+    "antechamber -h >/dev/null",
+    "MMPBSA.py -h >/dev/null",
+    "packmol-memgen -h >/dev/null",
+    "parmed -h >/dev/null",
+    "pdb4amber -h >/dev/null",
+    "command -v quick >/dev/null",
+    "command -v quick.MPI >/dev/null",
+    "python -s -c 'import parmed'",
+    "python -s -c 'import pdb4amber'",
+    "python -s -c 'import pymsmt'",
+    "python -s -c 'import pytraj'",
+    "python -s -c 'import sander'",
+    "python -s -c 'import edgembar'",
+    "python -s -c 'import fetkutils'",
+    "python -s -c 'import ndfes'",
 ]
 
 runtest = True

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-26.1-foss-2026.1.eb
index a5abb13998..d3a89431eb 100644
--- a/easybuild/easyconfigs/a/AmberTools/AmberTools-23.6-foss-2023a.eb
+++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-26.1-foss-2026.1.eb
@@ -1,9 +1,9 @@
 easyblock = 'EB_Amber'
 
 name = 'AmberTools'
-local_ambertools_ver = 23
+local_ambertools_ver = 26
 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
-patchlevels = (6, 0)  # (AmberTools, Amber)
+patchlevels = (1, 0)  # (AmberTools, Amber)
 version = '%s.%s' % (local_ambertools_ver, patchlevels[0])
 
 homepage = 'https://ambermd.org/'
@@ -11,8 +11,17 @@ 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'}
-toolchainopts = {'usempi': True}
+toolchain = {'name': 'foss', 'version': '2026.1'}
+# AmberTools regression references are sensitive to compiler-generated
+# floating-point differences, so disable CPU-specific tuning and auto-vectorization and use strict FP
+# semantics for reproducible results across supported architectures
+toolchainopts = {
+    'pic': True,
+    'usempi': True,
+    'strict': True,
+    'vectorize': False,
+    'optarch': False,
+}
 
 # download requires registration
 local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium'
@@ -27,15 +36,22 @@ 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-23_fix-fgetc_arm_infiniteloop.patch',
+    'AmberTools-25_fix_test_missing_dirs.patch',
+    'AmberTools-25_fix-boost.patch',
+    'AmberTools-25_fix-sander-numpy.patch',
+    'AmberTools-26_recythonize-pytraj.patch',
+    'AmberTools-26_skip-nonportable-tests.patch',
+    'AmberTools-26_do-not-clean-QUICK-compiler-flags.patch',
+    'AmberTools-26_fix-pytraj-install-PYTHONPATH.patch',
+    'AmberTools-26_fix-cpptraj-gzip-test.patch',
+    'AmberTools-26_ignore-portability-test-differences.patch',
+    'AmberTools-26_limit-pymemembed-test-threads.patch',
 ]
 checksums = [
-    {'AmberTools23.tar.bz2': 'debb52e6ef2e1b4eaa917a8b4d4934bd2388659c660501a81ea044903bf9ee9d'},
+    {'AmberTools26.tar.bz2': '5d46eef3c2bb7d5bf9e8c0c38add34406ea67e3f0e4097ac9d11d8a544538c9c'},
     {'AmberTools-20_cmake-locate-netcdf.patch': '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0'},
     {'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch':
      '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc'},
@@ -44,44 +60,114 @@ 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-23_fix-fgetc_arm_infiniteloop.patch':
-     'dde9f8e7914c491f1e1c04171bbbbda371cb12403847fb15092d023fd28fb0f5'},
+    {'AmberTools-25_fix_test_missing_dirs.patch': '1c4c44cb012b625933781e9811f1657d5ddfd14cfbf4894bb1f767995eadc3b6'},
+    {'AmberTools-25_fix-boost.patch': 'f4ccf7dedb5aa5b289ad5f69f3c1dc808c3fcc226d7118eaba40b108688e37cc'},
+    {'AmberTools-25_fix-sander-numpy.patch': '82b875153927b8a0977022d608bbf51513ea936384f3059ecd41a37dfb004d5e'},
+    {'AmberTools-26_recythonize-pytraj.patch': '45cc8acbe61a2cc06d759972174ebca046bb174f422e76eb05a93788af41e8a2'},
+    {'AmberTools-26_skip-nonportable-tests.patch': '4d8d78d715ad89c5fc5c92300b1d5399720cf1093d4c481ed2e086645127af83'},
+    {'AmberTools-26_do-not-clean-QUICK-compiler-flags.patch':
+     '42ff0f9ab60e87cdffaddc89038a12ee8e568eb8a0e33ca043c009e5f9bb3588'},
+    {'AmberTools-26_fix-pytraj-install-PYTHONPATH.patch':
+     'f1f1d1682a97505c2ed8560d9f868d67bb44b420135d98832c63142e13ce12df'},
+    {'AmberTools-26_fix-cpptraj-gzip-test.patch': 'd80bff19ad32d7a1c9011299751c33285afc704632e0915f84d7fc86887bfa3d'},
+    {'AmberTools-26_ignore-portability-test-differences.patch':
+     '09dcb3c4b0c2219b7c1038272718cb2c07e832670b8dec2ead6eca15d33a7fa0'},
+    {'AmberTools-26_limit-pymemembed-test-threads.patch':
+     '4a89a7c6d7a36278650282f8e5d7aa6974cf9790b2b944cdfe065fcbfc68bf9c'},
 ]
 
 builddependencies = [
-    ('CMake', '3.26.3'),
-    ('pkgconf', '1.9.5'),
+    ('CMake', '3.31.11'),
+    ('pkgconf', '2.5.1'),
     ('Bison', '3.8.2'),
     ('flex', '2.6.4'),
     ('make', '4.4.1'),
+    ('Cython', '3.2.4'),
 ]
-
 dependencies = [
-    ('zlib', '1.2.13'),
+    ('zlib', '2.3.2'),
     ('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'),
-    ('libreadline', '8.2'),
-    ('matplotlib', '3.7.2'),
-    ('netCDF', '4.9.2'),
-    ('netCDF-Fortran', '4.6.1'),
-    ('PnetCDF', '1.12.3'),
+    ('Python', '3.14.2'),
+    ('Python-bundle-PyPI', '2026.04'),
+    ('SciPy-bundle', '2026.05'),
+    ('Perl', '5.42.0'),
+    ('Perl-bundle-CPAN', '%(perlver)s'),
+    ('Boost', '1.90.0'),
+    ('matplotlib', '3.10.9'),
+    ('netCDF', '4.10.0'),
+    ('netCDF-Fortran', '4.6.3'),
+    ('PnetCDF', '1.14.1'),
     ('Tkinter', '%(pyver)s'),
-    ('X11', '20230603'),
-    ('mpi4py', '3.1.4'),
+    ('X11', '20260518'),
+    ('mpi4py', '4.1.2'),
+    ('FFTW', '3.3.10'),
+    ('netcdf4-python', '1.7.4'),
+    ('PyYAML', '6.0.3'),
+    ('RDKit', '2026.03.4'),
+    ('PLUMED', '2.10.0'),
+    ('Biopython', '1.87'),
+    ('scikit-learn', '1.8.0'),
+    ('pydantic', '2.13.4'),
+    ('numba', '0.65.1'),
+    ('gemmi', '0.7.5'),
+    ('freesasa', '2.2.1'),
+    ('sympy', '1.14.0'),
+    ('networkx', '3.6.1'),
+    ('NLopt', '2.10.1'),
+    ('arpack-ng', '3.9.1'),
+]
+
+# Avoid requiring the separate Boost.System library in the AmberTools and QUICK CMake configurations
+preconfigopts = "sed -i 's/Boost COMPONENTS thread system/Boost COMPONENTS thread/' "
+preconfigopts += "../cmake/3rdPartyTools.cmake "
+preconfigopts += "../AmberTools/src/quick/cmake/3rdPartyTools.cmake && "
+
+# Replace Amber's hard-coded -O3 with -O2 to match EasyBuild and improve numerical reproducibility
+preconfigopts += "sed -i 's/-O3/-O2/g' "
+preconfigopts += "../cmake/CompilerFlags.cmake && "
+
+# Remove the obsolete NumPy <2 upper bound from the FE-toolkit packages
+_fe_toolkit_path = "%(builddir)s/%(name)s/src/fe-toolkit/"
+_setup_path = "/src/python/setup.py"
+_fe_toolkit_pkgs = ['edgembar', 'fetkutils', 'ndfes']
+prebuildopts = """sed -i "/'numpy<2',/d" """
+for _pkg in _fe_toolkit_pkgs:
+    prebuildopts += f"{_fe_toolkit_path}{_pkg}{_setup_path} "
+prebuildopts += '&& '
+
+# Fix py3.14 compatibility -  ValueError: argument groups cannot be nested
+prebuildopts += (
+    'sed -i '
+    r"'s/group.add_argument_group(/parser.add_argument_group(/g' "
+    '../AmberTools/src/mmpbsa_py/MMPBSA_mods/commandlineparser.py && '
+)
+
+sanity_check_commands = [
+    "sander --version",
+    "sander.MPI --version",
+    "cpptraj -h >/dev/null",
+    "tleap -h >/dev/null",
+    "antechamber -h >/dev/null",
+    "MMPBSA.py -h >/dev/null",
+    "packmol-memgen -h >/dev/null",
+    "parmed -h >/dev/null",
+    "pdb4amber -h >/dev/null",
+    "command -v quick >/dev/null",
+    "command -v quick.MPI >/dev/null",
+    "python -s -c 'import parmed'",
+    "python -s -c 'import pdb4amber'",
+    "python -s -c 'import pymsmt'",
+    "python -s -c 'import pytraj'",
+    "python -s -c 'import sander'",
+    "python -s -c 'import edgembar'",
+    "python -s -c 'import fetkutils'",
+    "python -s -c 'import ndfes'",
 ]
 
 runtest = True

pavelToman · 2026-07-28T10:21:34Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-07-28T10:30:08Z

@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=26555 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_26555 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 11062

Test results coming soon (I hope)...

Details

- notification for comment with ID 5102898805 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 · 2026-07-28T10:57:24Z

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 4 (total: 26 mins 48 secs) (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.8, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/1ea041f45dffc401619b9feb54c86cb1 for a full test report.

pavelToman · 2026-07-28T11:05:48Z

Test report by @boegelbot FAILED Build succeeded for 2 out of 4 (total: 26 mins 48 secs) (2 easyconfigs in total) jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.8, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25 See https://gist.github.com/boegelbot/1ea041f45dffc401619b9feb54c86cb1 for a full test report.

Missing CMake patch - fixed

pavelToman · 2026-07-28T11:05:56Z

@boegelbot please test @ jsc-zen3

boegelbot · 2026-07-28T11:10:07Z

@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=26555 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_26555 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 11063

Test results coming soon (I hope)...

Details

- notification for comment with ID 5103312637 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).

Thyre · 2026-07-28T11:14:00Z

Why should we add CMake v3.31.8 when v3.31.11 exists already?

pavelToman · 2026-07-28T12:43:24Z

There are still some problems to solve:

packmol-memgen 2026.3.25 requires pdb2pqr, which is not installed.
proprep 1.0.0 requires pdb2pqr, which is not installed.
proprep 1.0.0 has requirement biopython<1.86,>=1.83, but you have biopython 1.87.
proprep 1.0.0 has requirement numpy<2.0,>=1.26, but you have numpy 2.4.6.

pavelToman · 2026-07-28T13:29:52Z

Test report by @pavelToman
SUCCESS
Build succeeded for 2 out of 2 (total: 2 hours 4 mins 28 secs) (1 easyconfigs in total)
node4417.skiddo.os - Linux RHEL 9.6, x86_64, AMD EPYC 9755 128-Core Processor, Python 3.9.21
See https://gist.github.com/pavelToman/3677643cd776ec8bf501dc6b3b0922f6 for a full test report.

boegelbot · 2026-07-28T13:56:24Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (total: 2 hours 46 mins 0 secs) (2 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.8, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.25
See https://gist.github.com/boegelbot/79cc303b04e5064e7334456f5b7ecc22 for a full test report.

pavelToman added the update label Jul 28, 2026

github-actions Bot added the 2026.1 issues & PRs related to 2026.1 common toolchains label Jul 28, 2026

pavelToman mentioned this pull request Jul 28, 2026

PhyStack - python bundles with foss/2026.1 vscentrum/vsc-software-stack#650

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100 tasks

add cmake patch

924e126

pavelToman added the AI-assisted AI-assisted contributions label Jul 28, 2026

pavelToman added 3 commits July 28, 2026 13:22

Update AmberTools-26.1-foss-2026.1.eb - cmake version

3c1cce2

DeleteCMake-3.31.8

25b98e2

Delete easybuild/easyconfigs/c/CMake/CMake-3.31.8-GCCcore-15.2.0.eb

ca8d1ef

pavelToman changed the title ~~{chem,devel}[GCCcore/15.2.0,foss/2026.1] AmberTools v26.1, CMake v3.31.8~~ {chem}[foss/2026.1] AmberTools v26.1 Jul 28, 2026

pavelToman mentioned this pull request Jul 28, 2026

{chem}[foss/2025b] Ambertools 26 #26453

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{chem}[foss/2026.1] AmberTools v26.1 - #26555

{chem}[foss/2026.1] AmberTools v26.1#26555
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