[Amber] [package list]

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

Install with the EasyBuild-user module:

eb AmberTools-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/AmberTools-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_AmberTools_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 = 'AmberTools'
version = '%s.%s.%s' % (local_AmberTools_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 the analysis tools; the pmemd MD engine (HIP/GTI build for AMD GPUs) lives in the
companion AmberTools module.
"""

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

sources = [
    {'filename': 'ambertools%s.tar.bz2' % local_AmberTools_version, 'alt_location': 'AmberTools'},
]

patches = [
    'AmberTools26_cpptraj_cmake.patch',
    'AmberTools26_cpptraj.patch',
    'AmberTools26_HIP.patch',
    'AmberTools26_HIP_2.patch',
    'AmberTools26_HIP_3.patch',
    'AmberTools26_HIP_4.patch',
    'AmberTools26_HIP_5.patch',
    'AmberTools26_HIP_6.patch',
    'AmberTools26_HIP_7_cudaMemset.patch',
    'AmberTools26_nth_cpptraj.patch',
    'AmberTools26_fix_missing_MPI_LIBRARY_error.patch',
]


checksums = [
    '5d46eef3c2bb7d5bf9e8c0c38add34406ea67e3f0e4097ac9d11d8a544538c9c',  # ambertools26.tar.bz2
    'b596fa67f85b0314f064d3119533a63135b32d999e81737c3fa61d1fc4ec8467',  # AmberTools26_cpptraj_cmake.patch
    '685cb2809b986a083ecc22726c1c17b3d0a7b53b4373f432725a0b77f8383302',  # AmberTools26_cpptraj.patch
    'aa7a7cdf3038f869b8fddd65ba1998a0bbb4d437e8e7de025a746581b732c2e1',  # AmberTools26_HIP.patch
    '69a7829cd63a38449c7c48eb046a05f27dc98731b5c07c4aba25844ac509877c',  # AmberTools26_HIP_2.patch
    '7656ea4ea1e72b843ff95e1e37c4f5eec793d76366ed22591809dabea8540e69',  # AmberTools26_HIP_3.patch
    '81a61d5a53f8bddd28f4d4dc6b41a56e523273421d889c579212c6aca9337413',  # AmberTools26_HIP_4.patch
    'ac04bb27e125e8efa1fd30ac379ca461639c3c97c8b3df5d9d7a3aac08021c2e',  # AmberTools26_HIP_5.patch
    'd5973040d8178d722629762d49656d47a537216605986b6b7f7e6d52e7cd5b3e',  # AmberTools26_HIP_6.patch
    '7d1b667853b366db0a8858b198a619777193625274c5625db80f992c93959a9d',  # AmberTools26_HIP_7_cudaMemset.patch
    '18f848df67f46926b84159ed6f8b218c178ff4391c3d1b8a0d9fe342ec8aff9b',  # AmberTools26_nth_cpptraj.patch
    'eb72e26c860e607c1f7420e9b04ade232e0bf78d08c7da3f6d081ad58cddb01b',  # AmberTools26_fix_missing_MPI_LIBRARY_error.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'),
]

configopts = ' '.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=$EBROOTBOOST',
    '-DBoost_NO_SYSTEM_PATHS=ON',
    '-DINSTALL_TESTS=ON',
    '-DMPI=ON',
    '-DOPENMP=ON',
    '-DUSE_FFT=ON',
    '-DBUILD_PYTHON=OFF',
    '-DCHECK_UPDATES=OFF',
    '-DAPPLY_UPDATES=OFF',
    '-DDOWNLOAD_MINICONDA=OFF',
    '-DCMAKE_BUILD_TYPE=Release',
    '-DCMAKE_CXX_STANDARD="17"',
    '-DHIP=ON',
    '-DGPU_TARGETS="gfx90a"',
    '-DAMDGPU_TARGETS="gfx90a"',
    '-DCMAKE_HIP_ARCHITECTURES="gfx90a"',
    '-DHIP_WARP64=ON',
    '-DCUDA_NVCC_FLAGS="--offload-arch=gfx90a -std=c++17 -I$CRAY_MPICH_DIR/include -D__HIP_PLATFORM_HCC__"',
    '-DHIPCUDA_EMULATE_VERSION=11.5',
    '-DGTI=ON',
    '-DVKFFT=ON',
    '-DHIP_RDC=ON',
    '-DHIP_TOOLKIT_ROOT_DIR=$ROCM_PATH',
    '-DFORCE_EXTERNAL_LIBS="netcdf;fftw;blas;lapack;pnetcdf;arpack"',
    '-DTRUST_SYSTEM_LIBS=ON',
    '-DBLAS_LIBRARIES=$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',
])

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

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

moduleclass = 'chem'

[Amber] [package list]