Amber/24.0-cpeGNU-25.03-AmberTools-24.0-rocm-cray-python-3.11.7 (Amber-24.0-cpeGNU-25.03-AmberTools-24.0-rocm-cray-python-3.11.7.eb)
Install with the EasyBuild-user module:
To access module help after installation and get reminded for which stacks and partitions the module is installed, usemodule spider Amber/24.0-cpeGNU-25.03-AmberTools-24.0-rocm-cray-python-3.11.7.
EasyConfig:
# Version updated by Emanuele Vitali for LUST
#
#DOC Amber with the matching version of AmberTools, and support for Cray Python.
easyblock = 'CMakeMake'
local_craypython_version = '3.11.7'
local_Amber_version = '24'
local_AmberTools_version = '24'
local_arpack_ng_version = '3.9.1' # https://github.com/opencollab/arpack-ng/tags
local_Boost_version = '1.88.0' # https://www.boost.org/
local_Perl_version = '5.40.0' # https://www.perl.org/get.html
local_zlib_version = '1.3.1' # https://zlib.net/
local_bzip2_version = '1.0.8' # http://www.bzip.org/downloads.html
# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php
local_patchlevels = (0, 0) # (AmberTools, Amber)
name = 'Amber'
version = '%s.%s' % (local_Amber_version, local_patchlevels[1])
versionsuffix = '-AmberTools-%s.%s-rocm-cray-python-%s' % (local_AmberTools_version, local_patchlevels[0], local_craypython_version)
homepage = 'https://ambermd.org/amber.html'
description = """
Amber (originally Assisted Model Building with Energy Refinement) is software
for performing molecular dynamics and structure prediction.
"""
toolchain = {'name': 'cpeGNU', 'version': '25.03'}
toolchainopts = {'usempi': True, 'openmp': True}
sources = [
{'filename': '%%(name)s%s.tar.bz2' % local_Amber_version},
{'filename': 'AmberTools%s.tar.bz2' % local_AmberTools_version, 'alt_location': 'AmberTools'},
]
patches = [
'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
'Amber-22_remove_undeclared_redundant_variable.patch',
'Amber-24_remove_open-pal-link.patch',
'Amber-24_cusparse_LinearSolvers_ugly_fix.patch',
'AmberTools-24_pythonbuild_dirty_hack.patch',
'Amber-24-patch_wrappers_c.patch',
'Amber-24-patch_peptide_c.patch',
'Amber-24-cmakelists_protobuf_ugly.patch',
'Amber-24-cpptraj_configure_ugly.patch',
'Amber-24-protobuf_configure.patch',
'Amber-24-configure2_cpp11to14.patch',
'Amber-24-nlopc_cmake11to14.patch',
'Amber-24-cpptraj_cmake.patch',
'Amber-24-compilationOptionsc++bump.patch',
]
checksums = [
'74a7dbc4530f6302ae1efe723ba54d0fcdb03bce2b7231663ce5afc2c5660076', # Amber24.tar.bz2
'52fb4fb3370a89b7ce738a2dc3e513c2fc1943fde4b4381846d9e75cc48d840f', # AmberTools24.tar.bz2
'210b0fb2a33e9cf00e8deb991420a027095d569ef752b1b9442915ec9f378be3', # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch
'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb', # Amber-22_remove_undeclared_redundant_variable.patch
'5878b2cb0525a4501b2679dd17fe3321ddc5a9d389f0d73d51c8ae3f6e705a5e', # Amber-24_remove_open-pal-link.patch
'576fb8416b8a0427702d85dc785047d7c70234c780a74a1ae06cb298bc3d72fa', # Amber-24_cusparse_LinearSolvers_ugly_fix.patch
'cb466158590cb635c656ec76f64c0e2f3b98eee7971f6a68e6d061ed523cfed7', # AmberTools-24_pythonbuild_dirty_hack.patch
'a2bf7e1259e97806944828a4c974735b289c79a27d909a41625470d38b154e00', # Amber-24-patch_wrappers_c.patch
'3bb4b562864eaf4fb6b7d80fee79c15068e7697bbee0458355350881aa9ab01a', # Amber-24-patch_peptide_c.patch
'43692bb2294fa589a74055e99cde317c02113697ad1b760c3810e6d4b4c45ae1', # Amber-24-cmakelists_protobuf_ugly.patch
'afc5c8a9402f3506210ad2df4fe5cdd0ae38f325a2946b7d653ab4d6aadbd1ab', # Amber-24-cpptraj_configure_ugly.patch
'f9eab7a9486f8bfda8bf1cc92e71f627df8ce3f7fc808c5d448b7730d4a8708c', # Amber-24-protobuf_configure.patch
'56e4fc44fd63a43fc2db75d2299d674edc16c437fe6ac9b8cb957d1dc22aa3d4', # Amber-24-configure2_cpp11to14.patch
'34bb57390e8884c0ec96c0fbe628582be358d5045218e35bc784854c4586f284', # Amber-24-nlopc_cmake11to14.patch
'bf9c3364cc2453894bf0baf2982ba9e3aacbaf132fbd7b447176c75c432598ce', # Amber-24-cpptraj_cmake.patch
'c01c4def814ee49267fe3638e76e9f1974e2d2e4d895752e5b8266b5ed7f451b', # Amber-24-compilationOptionsc++bump.patch
]
builddependencies = [
('buildtools', '%(toolchain_version)s', '', True),
('Boost', local_Boost_version),
]
dependencies = [
(f'cray-python/{local_craypython_version}', EXTERNAL_MODULE),
('cray-fftw', EXTERNAL_MODULE),
('cray-hdf5-parallel', EXTERNAL_MODULE),
('cray-parallel-netcdf', EXTERNAL_MODULE),
('cray-netcdf-hdf5parallel', EXTERNAL_MODULE),
('rocm', EXTERNAL_MODULE),
('zlib', local_zlib_version),
('bzip2', local_bzip2_version),
('Perl', local_Perl_version),
('arpack-ng', local_arpack_ng_version, '-OpenMP'),
]
configopts = ' '.join([
'-D COMPILER=CRAY',
'-D CMAKE_CXX_STANDARD="14"',
'-D CMAKE_CXX_FLAGS="-O3 -ftree-vectorize -fno-math-errno -fopenmp"',
'-D CMAKE_C_FLAGS="-O3 -ftree-vectorize -fno-math-errno -fopenmp"',
'-D CMAKE_Fortran_FLAGS="-O3 -ftree-vectorize -fno-math-errno -fopenmp" ',
'-D BOOST_ROOT=$EBROOTBOOST',
'-D Boost_NO_SYSTEM_PATHS=ON '
'-D MPI=ON',
'-D OPENMP=ON',
'-D USE_FFT=ON',
'-D BUILD_PYTHON=ON',
'-D SKIP_PYTHON_PACKAGE_CHECKS=ON',
'-D CHECK_UPDATES=OFF',
'-D APPLY_UPDATES=FALSE',
'-D DOWNLOAD_MINICONDA=OFF',
'-D HIP=ON',
'-D GPU_TARGETS="gfx90a"',
'-D AMDGPU_TARGETS="gfx90a"',
'-D HIP_WARP64=ON',
'-D CUDA_NVCC_FLAGS="--offload-arch=gfx90a -std=c++14 -I$CRAY_MPICH_DIR/include"',
'-D CMAKE_HIP_ARCHITECTURES="gfx90a"',
'-D GTI=TRUE',
'-D VKFFT=ON',
'-D HIP_RDC=ON',
'-D HIP_TOOLKIT_ROOT_DIR=$ROCM_PATH',
'-D HIPCUDA_EMULATE_VERSION="10.1"',
'-D FORCE_EXTERNAL_LIBS="netcdf;fftw;blas;lapack;pnetcdf;arpack"',
'-D TRUST_SYSTEM_LIBS=TRUE',
'-D BLAS_LIBRARIES=$CRAY_LIBSCI_PREFIX_DIR/lib/libsci_gnu_mp.so',
'-D LAPACK_LIBRARIES=$CRAY_LIBSCI_PREFIX_DIR/lib/libsci_gnu_mp.so',
'-D NetCDF_INCLUDES=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/include',
'-D NetCDF_INCLUDES_F90=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/include',
'-D NetCDF_LIBRARIES_F90=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/lib/libnetcdff.so',
'-D NetCDF_LIBRARIES_F77=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/lib/libnetcdff.so '
'-D NetCDF_LIBRARIES_C=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/lib/libnetcdf.so',
'-D PnetCDF_LIBRARY=$CRAY_PARALLEL_NETCDF_PREFIX/lib/libpnetcdf.so',
'-D PnetCDF_INCLUDE_DIR=$CRAY_PARALLEL_NETCDF_PREFIX/include',
'-D ARPACK_LIBRARY=$EBROOTARPACKMINNG/lib/libarpack.so',
'-D MVAPICH2GDR_GPU_DIRECT_COMM=ON',
])
sanity_check_paths = {
'files': ['bin/pmemd.hip'],
'dirs': [''],
}
modextravars = {
'AMBERHOME' : '%(installdir)s',
}
moduleclass = 'chem'