{chem}[foss/2025a] AmberTools v25.2

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

@@ -0,0 +1,114 @@
+easyblock = 'EB_Amber'
+
+name = 'AmberTools'
+local_ambertools_ver = 25
+# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php
+patchlevels = (2, 0)  # (AmberTools, Amber)
+version = '%s.%s' % (local_ambertools_ver, patchlevels[0])
+
+homepage = 'https://ambermd.org/'
+description = """AmberTools consists of several independently developed packages that work well by themselves,
+ 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}
+
+# 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 = [{
+    'download_filename': local_download_credentials,
+    'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver,
+}]
+patches = [
+    'AmberTools-20_cmake-locate-netcdf.patch',
+    'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
+    'AmberTools-20_fix_xblas_missing_make_dependency.patch',
+    'AmberTools-21_CMake-FlexiBLAS.patch',
+    'AmberTools-21_fix_incorrect_dvout_call.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-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 = [
+    {'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', '3.31.3'),
+    ('pkgconf', '2.3.0'),
+    ('Bison', '3.8.2'),
+    ('flex', '2.6.4'),
+    ('make', '4.4.1'),
+    ('Cython', '3.1.1'),
+]
+
+dependencies = [
+    ('zlib', '1.3.1'),
+    ('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'),
+    ('Tkinter', '%(pyver)s'),
+    ('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
+
+moduleclass = 'chem'

easybuild/easyconfigs/a/AmberTools/AmberTools-25_fix-boost.patch

@@ -0,0 +1,13 @@
+New Boost (here v1.88) needs newer cxx standard to work
+From: https://aur.archlinux.org/cgit/aur.git/tree/0001-Use-cxx14-for-Boost.patch?h=ambertools
+Added by: Pavel Tomanek (Inuits)
+--- a/AmberTools/src/moft/CMakeLists.txt	2025-02-12 17:09:45.031074795 +0100
++++ b/AmberTools/src/moft/CMakeLists.txt	2025-02-12 17:08:16.999758347 +0100
+@@ -4,6 +4,7 @@
+
+ target_include_directories(metatwist PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+ target_compile_options(metatwist PRIVATE ${OPT_CXXFLAGS})
++target_compile_features(metatwist PRIVATE cxx_std_14)
+ target_link_libraries(metatwist fftw boost_program_options boost_iostreams boost_regex boost_system boost_timer boost_chrono boost_filesystem boost_graph)
+
+ install(TARGETS metatwist DESTINATION ${BINDIR})

easybuild/easyconfigs/a/AmberTools/AmberTools-25_fix-sander-numpy.patch

@@ -0,0 +1,21 @@
+Fix numpy syntax to be compatible with v2
+--- AmberTools/src/pysander/sander/__init__.py.orig	2025-08-08 11:21:39.084040000 +0200
++++ AmberTools/src/pysander/sander/__init__.py	2025-08-08 11:22:44.758277000 +0200
+@@ -83,7 +83,7 @@
+     # numpy arrays to solve this quickly, but in cases where the coordinates
+     # are given as a list (or tuple) of Vec3's (or tuples), this requires
+     # separate handling
+-    positions = _np.array(positions, copy=False, subok=True)
++    positions = _np.asarray(positions)
+     positions = positions.flatten()
+     natom = _pys.natom()
+     if len(positions) != natom * 3:
+@@ -260,7 +260,7 @@
+                 box = rst.box
+
+         # Convert from numpy arrays to regular arrays
+-        coordinates = _np.array(coordinates, copy=False, subok=True)
++        coordinates = _np.asarray(coordinates)
+         coordinates = coordinates.flatten().tolist()
+         if box is None or box is False:
+             box = _np.zeros(6)

easybuild/easyconfigs/a/AmberTools/AmberTools-25_fix_test_missing_dirs.patch

@@ -0,0 +1,17 @@
+Make sure test_amber_clean.sh dosen't try to cd into a possibly missing directory.
+--- test/test_amber_clean.sh.orig	2025-07-14 13:34:48.866262000 +0200
++++ test/test_amber_clean.sh	2025-07-14 13:35:44.941307000 +0200
+@@ -1273,7 +1273,11 @@
+ echo $delete_list | xargs /bin/rm -f
+
+ # Remove cuda remd test output
+-cd cuda/remd && make clean && cd ../..
++if [ -d "cuda/remd" ]; then
++    cd cuda/remd && make clean && cd ../..
++fi
+
+ # Remove hip remd test output
+-cd hip/remd && make clean && cd ../..
++if [ -d "hip/remd" ]; then
++    cd hip/remd && make clean && cd ../..
++fi