ModulesOnLochness
From NJIT-ARCS HPC Wiki
Lmod
Lmod is used to to manage modules on Lochness and Stheno. The software stack on Lochness and Stheno is new. Submit scripts will need to be adjusted to account for the new lmod system.
For more information on Lmod check the user manual.
module available
Lmod presents a hierarchal view of the available modules. This means that the view of available modules changes depending on the module loaded by the user.
$ module available ----------------------------------------------------- /opt/site/modulefiles ------------------------------------------------------ cuda/10.0.130 julia/1.0.4 matlab/2019a polyflow/20.1.0 (D) python/3.8 (D) cuda/10.1.243 matlab/2018a matlab/2020a (D) python/3.6 raspa2/2.0 cuda/10.2.89 (D) matlab/2018b polyflow/19.4.0 python/3.7 vim/8.2 -------------------------------------------------- /opt/ohpc/pub/modulefiles ---------------------------------------------------- EasyBuild/3.9.2 cmake/3.15.4 gnu8/8.3.0 papi/5.7.0 singularity/3.4.1 autotools gnu/5.4.0 intel/19.0.4.243 pmix/2.2.2 valgrind/3.15.0 charliecloud/0.9.7 gnu7/7.3.0 intel/19.1.0.166 (D) prun/1.3
There are 3 versions of gnu compilers and 2 versions of intel compilers. Load the 'gnu8' compiler
$ module load gnu8 $ module available ------------------------------------------------- /opt/ohpc/pub/moduledeps/gnu8 -------------------------------------------------- R/3.5.3 impi/2019.4.243 metis/5.1.0 ocr/1.0.1 pdtoolkit/3.25 scotch/6.0.6 gsl/2.5 impi/2019.6.166 (D) mpich/3.3.1 openblas/0.3.5 plasma/2.8.0 superlu/5.2.1 hdf5/1.10.5 likwid/4.3.4 mvapich2/2.3.1 openmpi3/3.1.4 py2-numpy/1.15.3 ----------------------------------------------------- /opt/site/modulefiles ------------------------------------------------------ cuda/10.0.130 julia/1.0.4 matlab/2019a polyflow/20.1.0 (D) python/3.8 (D) cuda/10.1.243 matlab/2018a matlab/2020a (D) python/3.6 raspa2/2.0 cuda/10.2.89 (D) matlab/2018b polyflow/19.4.0 python/3.7 vim/8.2 --------------------------------------------------- /opt/ohpc/pub/modulefiles ---------------------------------------------------- EasyBuild/3.9.2 cmake/3.15.4 gnu8/8.3.0 (L) papi/5.7.0 singularity/3.4.1 autotools gnu/5.4.0 intel/19.0.4.243 pmix/2.2.2 valgrind/3.15.0 charliecloud/0.9.7 gnu7/7.3.0 intel/19.1.0.166 (D) prun/1.3
Notice that various new modules are now available including various MPI distributions.
module spider
module spider provides information on the software installed and how to load the modules necessary to run the software. For example to find netcdf:
$ module spider netcdf
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netcdf:
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Description:
C Libraries for the Unidata network Common Data Form
Versions:
netcdf/4.5.0
netcdf/4.6.1
netcdf/4.6.3
Other possible modules matches:
netcdf-cxx netcdf-fortran pnetcdf
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To find other possible module matches execute:
$ module -r spider '.*netcdf.*'
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For detailed information about a specific "netcdf" module (including how to load the modules) use the module's full name.
For example:
$ module spider netcdf/4.6.3
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Use the full version to get more information.
$ module spider netcdf/4.6.3
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netcdf: netcdf/4.6.3
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Description:
C Libraries for the Unidata network Common Data Form
You will need to load all module(s) on any one of the lines below before the "netcdf/4.6.3" module is available to load.
gnu8/8.3.0 impi/2019.4.243
gnu8/8.3.0 impi/2019.6.166
gnu8/8.3.0 mpich/3.3.1
gnu8/8.3.0 mvapich2/2.3.1
gnu8/8.3.0 openmpi3/3.1.4
intel/19.0.4.243 impi/2019.4.243
intel/19.0.4.243 impi/2019.6.166
intel/19.0.4.243 mpich/3.3.1
intel/19.0.4.243 mvapich2/2.3.1
intel/19.1.0.166 impi/2019.4.243
intel/19.1.0.166 impi/2019.6.166
intel/19.1.0.166 mpich/3.3.1
intel/19.1.0.166 mvapich2/2.3.1
Help:
This module loads the NetCDF C API built with the gnu8 compiler
toolchain and the mpich MPI stack.
Note that this build of NetCDF leverages the HDF I/O library and requires linkage
against hdf5. Consequently, the phdf5 package is loaded automatically with this module.
A typical compilation step for C applications requiring NetCDF is as follows:
$CC -I$NETCDF_INC app.c -L$NETCDF_LIB -lnetcdf -L$HDF5_LIB -lhdf5
Version 4.6.3
Following the instructions above , to load netcdf/4.6.3 compiled with openmpi3 based on the gnu8 compilers, the command would be:
$ module load gnu8/8.3.0 openmpi3/3.1.4 netcdf/4.6.3 $ module list Currently Loaded Modules: 1) gnu8/8.3.0 2) openmpi3/3.1.4 3) phdf5/1.10.5 4) netcdf/4.6.3
Note the phd5/1.10.5 is automatically loaded as a dependency.
It is useful to use regular expressions to search through the hierarchy to find software packages. For example:
$ module -r spider '.*netcdf.*'
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netcdf:
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Description:
C Libraries for the Unidata network Common Data Form
Versions:
netcdf/4.5.0
netcdf/4.6.1
netcdf/4.6.3
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For detailed information about a specific "netcdf" module (including how to load the modules) use the module's full name.
For example:
$ module spider netcdf/4.6.3
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netcdf-cxx:
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Description:
C++ Libraries for the Unidata network Common Data Form
Versions:
netcdf-cxx/4.3.0
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For detailed information about a specific "netcdf-cxx" module (including how to load the modules) use the module's full name.
For example:
$ module spider netcdf-cxx/4.3.0
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netcdf-fortran:
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Description:
Fortran Libraries for the Unidata network Common Data Form
Versions:
netcdf-fortran/4.4.4
netcdf-fortran/4.4.5
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For detailed information about a specific "netcdf-fortran" module (including how to load the modules) use the module's full name.
For example:
$ module spider netcdf-fortran/4.4.5
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pnetcdf:
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Description:
A Parallel NetCDF library (PnetCDF)
Versions:
pnetcdf/1.8.1
pnetcdf/1.9.0
pnetcdf/1.12.0
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For detailed information about a specific "pnetcdf" module (including how to load the modules) use the module's full name.
For example:
$ module spider pnetcdf/1.12.0
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