[Amber] [package list]

Amber/26.0-cpeGNU-25.03-rocm (Amber-26.0-cpeGNU-25.03-rocm.eb)

Install with the EasyBuild-user module:

eb Amber-26.0-cpeGNU-25.03-rocm.eb -r

To access module help after installation and get reminded for which stacks and partitions the module is installed, use module spider Amber/26.0-cpeGNU-25.03-rocm.

EasyConfig:

# Version updated by Matteo Murdaca for LUST
#
#DOC Amber with the matching version of AmberTools, and without Python support.
easyblock = 'CMakeMake'

local_Amber_version      = '26'

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.%s' % (local_Amber_version, local_patchlevels[0], local_patchlevels[1])
versionsuffix = '-rocm'

homepage = 'https://ambermd.org/amber.html'

description = """
Amber (originally Assisted Model Building with Energy Refinement) is software
for performing molecular dynamics and structure prediction. This module provides
the pmemd MD engine (HIP/GTI build for AMD GPUs); analysis tools live in the
companion AmberTools module.
"""

toolchain = {'name': 'cpeGNU', 'version': '25.03'}
toolchainopts = {'usempi': True, 'openmp': True}

sources = [
    {'filename': 'pmemd%s.tar' % local_Amber_version},
]

patches = [
    'AmberTools26_fix_missing_MPI_LIBRARY_error.patch',
    'Amber-22_remove_undeclared_redundant_variable.patch',
    'Amber-26_remove_open-pal-link.patch',
    'Amber-26_remove_leap_requirement.patch',
    'Amber-26.0_rocm6_cuda_header.patch',
    'Amber-26.0_rocm6_cuda_header-2.patch',
    'Amber-26.0_rocm6_cuda_header-3.patch',
]

checksums = [
    'd202c57e08336e0850eeb13ec7c08eaaf747d9153100bd3459a41f1ff5a7d447',  # pmemd26.tar
    'eb72e26c860e607c1f7420e9b04ade232e0bf78d08c7da3f6d081ad58cddb01b',  # AmberTools26_fix_missing_MPI_LIBRARY_error.patch
    'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb',  # Amber-22_remove_undeclared_redundant_variable.patch
    '679eaf6350404a91e51d652aa572ea4d1cb2aa685751c55f84db59aebb93a6b2',  # Amber-26_remove_open-pal-link.patch
    '1a81b8d7419026acda7b859d4df3ea725e6d275c500b09d55ab7e8209394db3d',  # Amber-26_remove_leap_requirement.patch
    'a311d36000f4fb65e28572f4316e6578df27129abadd6f21ba9213fb1abc9463',  # Amber-26.0_rocm6_cuda_header.patch
    '4cc8679181061454d6ba4d926771866007ee70af940544e01e25d4f28abf5c3f',  # Amber-26.0_rocm6_cuda_header-2.patch
    'b7b13f9762b225cdcafe1e7025e3ecb4f0bcc78d2f46661fdb7e83f5ef45d5b4',  # Amber-26.0_rocm6_cuda_header-3.patch
]

builddependencies = [
    ('buildtools', '%(toolchain_version)s', '', True),
    ('Boost',      local_Boost_version),
]

dependencies = [
    ('cray-python',              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'),
]

local_common_opts = ' '.join([
    '-DCOMPILER=CRAY',
    '-DCMAKE_CXX_FLAGS="-O3 -ftree-vectorize -fno-math-errno -fopenmp"',
    '-DCMAKE_C_FLAGS="-O3 -ftree-vectorize -fno-math-errno -fopenmp"',
    '-DCMAKE_Fortran_FLAGS="-O3 -ftree-vectorize -fno-math-errno -fopenmp"',
    '-DBOOST_ROOT=$EBROOTBOOST',
    '-DBoost_NO_SYSTEM_PATHS=ON',
    '-DINSTALL_TESTS=ON',
    '-DPMEMD_ONLY=ON',
    '-DMPI=ON',
    '-DOPENMP=ON',
    '-DUSE_FFT=ON',
    '-DBUILD_PYTHON=OFF',
    '-DCHECK_UPDATES=OFF',
    '-DAPPLY_UPDATES=OFF',
    '-DDOWNLOAD_MINICONDA=OFF',
    '-DDISABLE_WARNINGS=ON',
    '-DCMAKE_BUILD_TYPE=Release',
    '-DCMAKE_CXX_STANDARD="17"',
    '-DHIP=ON',
    '-DGPU_TARGETS="gfx90a"',
    '-DAMDGPU_TARGETS="gfx90a"',
    '-DCMAKE_HIP_ARCHITECTURES="gfx90a"',
    '-DHIP_WARP64=ON',
    '-DCUDA_NVCC_FLAGS="--offload-arch=gfx90a -std=c++17 -I$CRAY_MPICH_DIR/include -D__HIP_PLATFORM_HCC__ -I$ROCM_PATH/include/cuda_wrappers -DcudaStream_t=hipStream_t -DcudaStreamCreate=hipStreamCreate -DcudaStreamDestroy=hipStreamDestroy -DcudaStreamSynchronize=hipStreamSynchronize"',
    '-DHIPCUDA_EMULATE_VERSION=11.5',
    '-DGTI=ON',
    '-DVKFFT=ON',
    '-DHIP_RDC=ON',
    '-DHIP_TOOLKIT_ROOT_DIR=$ROCM_PATH',
    '-DFORCE_EXTERNAL_LIBS="netcdf;blas;lapack"',
    '-DTRUST_SYSTEM_LIBS=ON',
    '-DBLAS_LIBRARIES=$CRAY_LIBSCI_PREFIX_DIR/lib/libsci_gnu_mp.so',
    '-DLAPACK_LIBRARIES=$CRAY_LIBSCI_PREFIX_DIR/lib/libsci_gnu_mp.so',
    '-DNetCDF_INCLUDES=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/include',
    '-DNetCDF_INCLUDES_F90=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/include',
    '-DNetCDF_LIBRARIES_F90=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/lib/libnetcdff.so',
    '-DNetCDF_LIBRARIES_F77=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/lib/libnetcdff.so',
    '-DNetCDF_LIBRARIES_C=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/lib/libnetcdf.so',
    '-DPnetCDF_LIBRARY=$CRAY_PARALLEL_NETCDF_PREFIX/lib/libpnetcdf.so',
    '-DPnetCDF_INCLUDE_DIR=$CRAY_PARALLEL_NETCDF_PREFIX/include',
    '-DARPACK_LIBRARY=$EBROOTARPACKMINNG/lib/libarpack.so',
    '-DMVAPICH2GDR_GPU_DIRECT_COMM=ON',
])

configopts = ' '.join([
    local_common_opts,
])

sanity_check_paths = {
    'files': ['bin/pmemd.hip'],
    'dirs': ['bin'],
}

modextravars = {
    'PMEMDHOME':  '%(installdir)s',
}

moduleclass = 'chem'

[Amber] [package list]