[Amber] [package list]

Amber/22.0-cpeGNU-22.08-AmberTools-22.3 (Amber-22.0-cpeGNU-22.08-AmberTools-22.3.eb)

Install with the EasyBuild-user module:

eb Amber-22.0-cpeGNU-22.08-AmberTools-22.3.eb -r

To access module help after installation and get reminded for which stacks and partitions the module is installed, use module spider Amber/22.0-cpeGNU-22.08-AmberTools-22.3.

EasyConfig:

easyblock = 'CMakeMake'

name = 'Amber'

local_amber_ver = 22
local_ambertools_ver = 22
# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php
patchlevels = (3, 0)  # (AmberTools, Amber)
version = '%s.%s' % (local_amber_ver, patchlevels[1])
versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0])

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': '22.08'}
toolchainopts = {'usempi': True, 'openmp': True}

sources = [
    '%%(name)s%s.tar.bz2' % local_amber_ver,
    {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'},
]

patches = [
     'AmberTools-20_cmake-locate-netcdf.patch',
     'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch',
     'Amber-22_remove_undeclared_redundant_variable.patch',
]

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

dependencies = [
    ('cray-python', EXTERNAL_MODULE),
    ('cray-fftw', EXTERNAL_MODULE),
    ('cray-hdf5-parallel/1.12.1.5', EXTERNAL_MODULE),
    ('cray-parallel-netcdf', EXTERNAL_MODULE),
    ('cray-netcdf-hdf5parallel', EXTERNAL_MODULE),
    ('Boost', '1.79.0', ''),
    ('arpack-ng', '3.9.0', '-OpenMP'),
]

preconfigopts = 'cd ../amber22_src && ./update_amber --update && cd build && '

configopts  = '-D COMPILER=CRAY '
configopts += '-D MPI=ON '
configopts += '-D OPENMP=ON '
configopts += '-D STATIC=ON ' 
configopts += '-D CHECK_UPDATES=FALSE '
configopts += '-D APPLY_UPDATES=FALSE '
configopts += '-D DOWNLOAD_MINICONDA=FALSE '
configopts += '-D BUILD_PYTHON=OFF '
configopts += '-D FORCE_EXTERNAL_LIBS="netcdf;fftw;blas;lapack;pnetcdf;arpack" '
configopts += '-D TRUST_SYSTEM_LIBS=TRUE '
configopts += '-D BLAS_LIBRARIES=$CRAY_LIBSCI_PREFIX_DIR/lib/libsci_gnu_mp.so '
configopts += '-D LAPACK_LIBRARIES=$CRAY_LIBSCI_PREFIX_DIR/lib/libsci_gnu_mp.so '
configopts += '-D NetCDF_INCLUDES=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/include '
configopts += '-D NetCDF_INCLUDES_F90=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/include '
configopts += '-D NetCDF_LIBRARIES_F90=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/lib/libnetcdff.so '
configopts += '-D NetCDF_LIBRARIES_F77=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/lib/libnetcdff.so ' 
configopts += '-D NetCDF_LIBRARIES_C=$CRAY_NETCDF_HDF5PARALLEL_PREFIX/lib/libnetcdf.so '
configopts += '-D PnetCDF_LIBRARY=$CRAY_PARALLEL_NETCDF_PREFIX/lib/libpnetcdf.so '
configopts += '-D PnetCDF_INCLUDE_DIR=$CRAY_PARALLEL_NETCDF_PREFIX/include '
configopts += '-D ARPACK_LIBRARY=$EBROOTARPACKMINNG/lib/libarpack.so '

prebuildopts = 'cd ../amber22_src/build && '

preinstallopts = 'cd ../amber22_src/build && '

moduleclass = 'chem'

[Amber] [package list]