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: [] ]