= Program:module = '''module''' is a utility used to manage multiple compilers on a single system, as well as set environment variables for other programs and utilities. === Available Modules === The following command will list all available modules. {{{ [tulaneID@cypress1 ~]$ module avail -------------------------------------------------------- /cm/local/modulefiles -------------------------------------------------------- cluster-tools/7.0 ipmitool/1.8.13 openldap cmd module-git openmpi/gcc/64/1.8.2-mlnx-ofed2 dot module-info shared freeipmi/1.3.4 mvapich2/gcc/64/2.0rc1-mlnx-ofed2 use.own intel/mic/sdk/3.3 null version ------------------------------------------------------- /cm/shared/modulefiles -------------------------------------------------------- acml/gcc/64/5.3.1 cuda60/profiler/6.0.37 lapack/gcc/64/3.5.0 acml/gcc/fma4/5.3.1 cuda60/toolkit/6.0.37 lapack/open64/64/3.5.0 acml/gcc/mp/64/5.3.1 default-environment mpich/ge/gcc/64/3.1 acml/gcc/mp/fma4/5.3.1 fftw2/openmpi/gcc/64/double/2.1.5 mpich/ge/open64/64/3.1 acml/gcc-int64/64/5.3.1 fftw2/openmpi/gcc/64/float/2.1.5 mpiexec/0.84_432 acml/gcc-int64/fma4/5.3.1 fftw2/openmpi/open64/64/double/2.1.5 mvapich/gcc/64/1.2rc1 acml/gcc-int64/mp/64/5.3.1 fftw2/openmpi/open64/64/float/2.1.5 mvapich/open64/64/1.2rc1 acml/gcc-int64/mp/fma4/5.3.1 fftw3/openmpi/gcc/64/3.3.3 mvapich2/gcc/64/2.0b acml/open64/64/5.3.1 fftw3/openmpi/open64/64/3.3.3 mvapich2/open64/64/2.0b acml/open64/fma4/5.3.1 gcc/4.8.2 netcdf/gcc/64/4.3.1.1 acml/open64/mp/64/5.3.1 globalarrays/openmpi/gcc/64/5.3 netcdf/open64/64/4.3.1.1 acml/open64/mp/fma4/5.3.1 globalarrays/openmpi/open64/64/5.3 netperf/2.6.0 acml/open64-int64/64/5.3.1 hadoop/HAL/Cloudera/2.3.0-cdh5.1.2 open64/4.5.2.1 acml/open64-int64/fma4/5.3.1 hdf5/1.6.10 openblas/dynamic/0.2.8 acml/open64-int64/mp/64/5.3.1 hdf5_18/1.8.12 openmpi/gcc/64/1.8.1 acml/open64-int64/mp/fma4/5.3.1 hive/HAL/Cloudera/1.2.0-bin openmpi/open64/64/1.8.1 blacs/mpichge/gcc/64/1.1patch03 hpl/2.1 pbspro/12.2.1.140292 blacs/openmpi/gcc/64/1.1patch03 hwloc/1.8.1 pig/HAL/Cloudera/0.12.0-cdh5.1.2 blacs/openmpi/open64/64/1.1patch03 intel/compiler/64/14.0/2013_sp1.3.174 scalapack/gcc/64/1.8.0 blas/gcc/64/1 intel-cluster-checker/2.1.2 scalapack/open64/64/1.8.0 blas/open64/64/1 intel-cluster-runtime/ia32/3.6 sge/2011.11p1 bonnie++/1.97.1 intel-cluster-runtime/intel64/3.6 slurm/14.03.0 cmgui/7.0 intel-cluster-runtime/mic/3.6 spark/HAL/Cloudera/1.4.0-bin-hadoop2.3 cuda60/blas/6.0.37 intel-tbb-oss/ia32/42_20140601oss torque/4.2.6.1 cuda60/fft/6.0.37 intel-tbb-oss/intel64/42_20140601oss tulane/intel-psxe/2015 cuda60/nsight/6.0.37 iozone/3_420 ------------------------------------------------------- /share/apps/modulefiles ------------------------------------------------------- anaconda/2.1.0 fftw/2.1.5/single metis/5.1.0 plink/1.07 bbcp/amd64_rhel60 fftw/3.3.4 mosaik/2.2.3 python/2.7.10 berkeleygw/1.1-beta2 gcc/4.7.4 mpich/3.1.4 R/3.1.2 boost/1.57.0 git/2.4.1 ncbi-blast/2.2.30+ rsem/1.2.19 bowtie/1.1.1 gnuplot/5.0.1 netcdf/4.3.2 samtools/0.1.19 bowtie2/2.2.4 hdf5/1.8.14 netcdf-cxx4/4.2.1 samtools/1.1 cmake/3.0.2 hdf5-parallel/1.8.14 netcdf-fortran/4.4.1 star/2.4.0i diamond/0.6.12 ibamr/0.1-rc1 openmpi/1.8.4 sundials/2.5.0 eigen/3.2.4 idev parmetis/4.0.3 tinker/7.1.2 emacs/24.4 intel-psxe/2015-update1 petsc/3.4.5 tophat/2.0.13 espresso/5.1.2 matlab/r2013b petsc/3.5.2 visit/2.9.2 fftw/2.1.5/double(default) matlab/r2015a petsc/3.5.3 vtk/6.1.0 }}} === Loading & Unloading Modules === This will load the Intel Parallel Studio XE which contains the Intel compiler suite: {{{ [tulaneID@cypress1 ~]$ module load intel-psxe }}} To unload the same package: {{{ [tulaneID@cypress1 ~]$ module unload intel-psxe }}} === Listing Loaded Modules === {{{ [tulaneID@cypress1 ~]$ module load intel-psxe [tulaneID@cypress1 ~]$ module list Currently Loaded Modulefiles: 1) slurm/14.03.0 2) idev 3) intel-psxe/2015-update1 }}} [http://modules.sourceforge.net/ Details] === Using $HOME/.modulerc === This file can be used to load or to define your own environment during each login. An example looks like this: {{{ #%Module module load intel-psxe/2016 }}} A .modulerc begins with the magic cookie, '#%Module'. ==== Define your own module ==== Compiling software in a user directory then defining personal environment modules is useful when software one needs are not installed on Cypress, or the installed ones are not of the desired version. For example, [http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ SuperLU] is not available on the main module. Download the source codes, and compile and install it, for example, on '''/lustre/project/dpg/local/SuperLU_5.2.1''' Create a [http://modules.sourceforge.net/man/modulefile.html module-definition] file, for example, as '''/lustre/project/dpg/local/modulefiles/SuperLU/5.2.1''' where the directory name '''SuperLU''' is the software name without version number, and the file name, '''5.2.1''' is the version number. The file looks like this: {{{ #%Module1.0 -*- tcl -*- ## ## modulefile ## module-whatis "a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations." set curMod [module-info name] if { [ module-info mode load ] } { system "/bin/logger -p local0.info 'module_load: $curMod.'" } conflict SuperLU/4.3 module load intel-psxe/2016 set INSTALL_ROOT /lustre/project/dpg/local/SuperLU_5.2.1 prepend-path PATH $INSTALL_ROOT/bin prepend-path LD_LIBRARY_PATH $INSTALL_ROOT/lib prepend-path LIBRARY_PATH $INSTALL_ROOT/lib setenv SLU_DIR $INSTALL_ROOT }}} Edit your '''.modulerc''' that looks like this: {{{ #%Module module use /lustre/project/dpg/local/modulefiles }}} Now your new module will be listed and you can load it with the usual commands. {{{ [tulaneID@cypress1 ~]$ module avail ------------------------------------------------ /lustre/project/dpg/local/modulefiles ------------------------------------------------ SuperLU/5.2.1 -------------------------------------------------------- /cm/local/modulefiles -------------------------------------------------------- cluster-tools/7.0 ipmitool/1.8.13 openldap : : }}} === Next Section === [[cypress/using|Job Submissions]]