.. _options: *********************************** Installing ChemShell: Setup Options *********************************** Help for the ChemShell setup options can be generated with the command ``setup --help``. The output of this command is provided below: :: usage: setup [-h] [-v] [--debug] [-fc] [-cc] [-cpc] [-fflags [...]] [-cflags [...]] [-ldflags [...]] [--ld_path [...]] [--math_header_macros] [-j] [-O] [-i8] [-f128] [--cmake] [--arch] [--python_root_dir] [--prepend-pythonpath] [-mkl] [--mkl_flags] [--mkl_compile_flags] [--blas] [--lapack] [--fftw] [--fftw_link_flags] [--fftw_include_dir] [--scalapack ] [--scalapack_flags] [-mpi [MPI]] [--mpi_include_path] [--mpi_lib_path] [--mpi_libraries] [-mpiexec] [--tcl_include_path] [--no-pip] [-clean [...]] [-rb [REBUILD ...]] [--rebuild-without-download] [--castep] [--cp2k ] [--cp2k-reinstall] [--fhiaims] [--gamess-uk] [--lsdalton ] [--nwchem ] [--dl_poly ] [--gulp] [--namd] [--dl_field] [--dl_monte ] [--dl_monte_htk] [--ga] [--ga-no-configure] [--ga-armci-network] [--aten] [--charmm-ff-version] [--charmm-ff] [--bse] [--pdb2pqr] [--propka] [--platform] [--force-serial [FORCE_SERIAL]] [--load-modules [...]] [--unload-modules [...]] Py-ChemShell Installer For a guide to the setup options please see the INSTALL file or consult the installation section in the ChemShell manual. ---------------------------------------------------------------------- Basic options: -h, --help Show this help message and exit -v, --version Show program's version number and exit --debug Compile in a debug mode by using debug flags and print verbose screen output ---------------------------------------------------------------------- Compile/Link options: Use these options to choose compilers and their compile/link flags and specify paths to libraries -fc , --fc , --fortran-compiler Specify Fortran compiler [ default: ifort ] -cc , --cc , --c-compiler Specify C compiler [ default: icx ] -cpc , --cpc , --cpp-compiler Specify C++ compiler [ default: ] -fflags [ ...], --fflags [ ...] Fortran compiler flags [ default: [] ] -cflags [ ...], --cflags [ ...] C compiler flags [ default: [] ] -ldflags [ ...], --ldflags [ ...] Extra link flags to add [ default: [] ] --ld_path [ ...] Specify ld library path [ default: [] ] --math_header_macros Resolve the incompatibility between Intel math.h and the system math.h [ default: -U__linux__ -U__USE_MISC -U__NetBSD__ -D__FreeBSD__ -U__PURE_INTEL_C99_HEADERS__ ] -j , --jobs Specify the number of make jobs to run simultaneously for building external programs (`make -j` command, no argument for no limit) [ default: 4 ] -O , -opt , --opt Specify compiler optimisation level [ default: 2 ] -i8, --i8 Build 64-bit binary [ default: False ] -f128, --f128 Impose -D_Float128=__float128 to fix the conflict between Intel 17 and gcc 7 [ default: False ] --cmake Specify the CMake command [ default: cmake ] --arch Override the ChemShell build architecture that is otherwise automatically detected according to the compilers [ default: ] --python_root_dir Specify path to the root directory of a Python 3 installation. [ default: ] --prepend-pythonpath Path(s) to additional Python packages to prepend to sys.path (NB: not the environment variable PYTHONPATH); seperate with : when there are more than one; package paths prepended will override the default system ones if there are duplicates [ default: ] -mkl , --mkl Enable Intel MKL and specify MKL library path [ default: ] --mkl_flags Intel MKL arguments for linking [ default: ] --mkl_compile_flags Intel MKL arguments for compiling [ default: ] --blas Specify BLAS path [ default: default ]. If "default", find_package will be used; otherwise provide a path directly to the object (i.e. usually libblas.so/libblas.a)or a complete set of compilation flags. --lapack Specify LAPACK path [ default: default ] If "default", find_package will be used; otherwise provide a path directly to the object (i.e. usually liblapack.so/libblapack.a)or a complete set of compilation flags. --fftw Specify the path to FFTW library directory [ default: ] --fftw_link_flags Specify the FFTW linker flags[ default: ] --fftw_include_dir Specify the full path of directory containing FFTW header files [ default: ] --scalapack [] Path to ScaLAPACK library directory: ScaLAPACK switched on using default settings if no argument provided [ default: ] --scalapack_flags ScaLAPACK arguments for linking [ default: ] -mpi [MPI], --mpi [MPI] [Specify MPI implementation] to enable MPI parallel build, for example: --mpi or --mpi=openmpi or --mpi=intel [default: False] --mpi_include_path Include path(s) for MPI header, for example: --mpi_include_path=/usr/lib/x86_64-linux- gnu/openmpi/include [ default: ] --mpi_lib_path Specify MPI lib path (use semicolon ";" if there are more than one), for example: --mpi_lib_path=/usr/lib/x86_64-linux-gnu/openmpi/lib; this will override the MPI option chosen by Fortran compiler [ default: ] --mpi_libraries MPI shared libraries separated by semicolon (;) [ default: ] -mpiexec , --mpiexec Executable program of MPI: could be mpirun.openmpi or mpiexec.openmpi for OpenMPI if the latter coexists with Intel MPI in your system [ default: ] --tcl_include_path Include path(s) for Tcl header files [ default: ] --no-pip [Not to upgrade pip version nor install Python dependencies using pip [default: False] -clean [ ...], --clean [ ...] Clear the existing compilation -rb [REBUILD ...], --rebuild [REBUILD ...], --recompile [REBUILD ...] Specify module(s) of the external codes/drivers/addons to recompile [ default: [] ] --rebuild-without-download, --recompile-without-download Do not redownload source code before rebuilding the external code [ default: False ] ---------------------------------------------------------------------- QM codes: Compile/Install optional support for external QM codes --castep Enable direct linking to a pre-compiled CASTEP library and specify location of CASTEP library [ default: ] --cp2k [] Enable CP2K build: download CP2K from the GitHub repository if no parameter is given; otherwise specify CP2k location--the directory where dft, diesel, etc are contained [ default: False ] --cp2k-reinstall Force to reinstall CP2K libraries [ default: False ] --fhiaims Enable direct linking to a pre-compiled FHI-aims library and specify location of FHI-aims library [ default: ] --gamess-uk Enable GAMESS-UK and specify GAMESS-UK location--the directory where dft, diesel, etc are contained [ default: ] --lsdalton [] Enable LSDALTON and optionally specify LSDALTON location--either the directory where source is contained or a tarball; if no parameter given the official GitLab repository is used [ default: False ] --nwchem [] Enable direct linking to pre-compiled NWChem libraries by specifying NWChem root location; if no location is specified NWChem will be downloaded from the official repository [ default: False ] ---------------------------------------------------------------------- MM codes: Compile/Install optional support for external MM codes --dl_poly [] Enable DL_POLY 5 and optionally specify DL_POLY 5 location--either the directory where source is contained or a tarball; if no parameter given the official GitLab repository is used [ default: False ] --gulp Enable GULP and specify GULP location--either the directory where Src is contained or a tarball [ default: ] --namd Enable NAMD and specify NAMD location: either the directory where Src is contained or a tarball [ default: None ] ---------------------------------------------------------------------- Drivers: Compile/Install optional drivers --dl_field Specify the DL_FIELD location [ default: ] --dl_monte [] Enable DL_MONTE build: download DL_MONTE from the GitLab repository if no parameter is given; otherwise specify DL_MONTE location--the directory where dft, diesel, etc are contained [ default: False ] --dl_monte_htk DL_MONTE HTK GitLab repository; or the directory where subdirectories "doc", "examples", and "htk" are contained [ default: https://gitlab.com/dl_monte/dlmontepython.git ] --ga Enable Global Arrays (GA) and specify a GA location [ default: GA in the NWChem distribution ] --ga-no-configure Skip GA configure [ default: False ] --ga-armci-network Specify NWChem ARMCI_NETWORK flag (see https://nwchemgit.github.io/ARMCI.html for options) [ default: MPI-PR ] ---------------------------------------------------------------------- Add-ons: Compile/Install additional add-ons --aten Download and compile the Aten GUI (see: www.projectaten.com) [ default: False ] --charmm-ff-version Version of CHARMM forcefield files to install, see --charmm-ff [ default: c36_jul21 ] --charmm-ff Download CHARMM forcefield files from http://mackerell.umaryland.edu/charmm_ff.shtml and install to chemsh/data/charmm. See INSTALL if your machine cannot access the internet [ default: False ] --bse, --molssi-bse Download and install BSE (Basis Set Exchange). See INSTALL if your machine cannot access the internet [ default: False ] --pdb2pqr Download and install PDB2PQR. See INSTALL if your machine cannot access the internet [ default: False ] --propka Download and install PROPKA (You do not have to use this argument if you use --pdb2pqr already because PDB2PQR contains PROPKA) [ default: False ] ---------------------------------------------------------------------- Platform options: Use presets for supported HPC platforms --platform Choose the platform type [ default: ] --force-serial [FORCE_SERIAL] Enforce a serial build without MPI (only valid for HPC platforms defaulted to --mpi) [default: False] --load-modules [ ...] Modules to load using the Environment Modules system [ default: [] ] --unload-modules [ ...] Modules to unload using the Environment Modules system [ default: [] ]