Triton Software Modules¶

Triton software versions (and dependencies) are deployed through Lmod, an upgraded Environment Modules suite.

https://lmod.readthedocs.io/en/latest/010_user.html

Module Commands¶

Shortcut commands are also available :

Command	Shortcut	Description
module list	ml	list currently loaded modules
module avail	ml av	list available modules, based on currently loaded hierarchies (compilers, libraries, etc.)
module avail pkgName1	ml av pkgName1	search available modules, based on currently loaded hierarchies
module is-avail pkgName1	ml is-avail pkgName1	check if module(s) can be loaded, based on currently loaded hierarchies
module spider	ml spider	list all modules
module spider pkgName1	ml spider pkgName1	search all modules
module keyword word1	ml keyword word1	search module help and whatis for word(s)
module spider pkgName1/Version	ml spider pkgName1/Version	show how to load a specific module
module load pkgName1	ml pkgName1	load module(s) by name (default version)
module load pkgName1/Version	ml pkgName1/Version	load module(s) by name and version
module unload pkgName1	ml -pkgName1	unload module(s) by name
module reset	ml reset	reset to system defaults
module restore	ml restore	reset to user defaults, if they exist
module help pkgName1	ml help pkgName1	show module help info
module whatis pkgName1	ml whatis pkgName1	show module version info
module show pkgName1	ml show pkgName1	show module environment changes

Triton Standard Environment¶

The StdEnv on Triton contains the default configurations for the cluster.

show loaded modules with module list or ml
show StdEnv settings with module show StdEnv or ml show StdEnv

[username@login1 ~]$ ml

    Currently Loaded Modules:
      1) gcc/8.3.1   2) StdEnv

[username@login1 ~]$ ml show StdEnv
    ----------------------------------------------------------------------------
       /share/mfiles/Core/StdEnv.lua:
    ----------------------------------------------------------------------------
    help([[  Lua Help for the Standard Environment module configurations on Triton
    ]])
    whatis("Description: loads standard environment modules")
    load("gcc/8.3.1")

Triton available modules¶

Available modules at login include the compilers under “Compilers”, compiler-independent modules under “Core”, and modules dependent on the currently loaded compiler.

*Note :* some modulefiles are marked (E) for Experimental. As with all software, please report any issues to hpc@ccs.miami.edu.

show loaded modules with module list or ml
show module help info with module help NAME or ml help NAME
show module whatis info with module whatis NAME or ml whatis NAME
show available modules with module avail or ml av
show module settings with module show NAME or ml show NAME
load a module with module load NAME or ml NAME

[username@login1 ~]$ ml

    Currently Loaded Modules:
      1) gcc/8.3.1   2) StdEnv


[username@login1 ~]$ ml help gcc

    --------------------- Module Specific Help for "gcc/8.3.1" ---------------------
    The GNU Compiler Collection includes front ends for C, C++, Objective-C,
    Fortran, Ada, and Go, as well as libraries for these languages.



[username@login1 ~]$ ml whatis gcc
    gcc/8.3.1           : Name : gcc
    gcc/8.3.1           : Version : 8.3.1
    gcc/8.3.1           : Target : power9le


[username@login1 ~]$ ml av
    ----------------------- /share/mfiles/Compiler/gcc/8.3.1 -----------------------
       R/3.6.3                libxsmm/1.16.1         (E)
       R/4.0.3                ncview/2.1.8           (D)
       R/4.0.5         (D)    netcdf-c/4.8.0
       R/4.1.0                netcdf-fortran/4.5.3
       cmake/3.19.2           openbabel/3.0.0
       cmake/3.20.2    (D)    openblas/0.3.13
       ffmpeg/4.3.2           openblas/0.3.14        (D)
       fftw/3.3.9      (D)    openfoam/2012          (D)
       gdal/2.4.4             openmpi/4.0.5
       gdal/3.3.0      (D)    openssl/1.1.1k
       gromacs/2021.1         pandoc/2.7.3
       gsl/2.6                parallel-netcdf/1.12.2
       hdf5/1.10.7            perl/5.32.1
       jags/4.3.0             plumed/2.8.0
       lammps/20200721        python/3.8.10
       lammps/20210310 (D)    smpi/10.02
       libgit2/1.1.0          wrf/4.2
       libicov/1.16

    ------------------------ /usr/share/Modules/modulefiles ------------------------
       dot    module-info    modules    null    use.own

    ------------------------------ /share/mfiles/Core ------------------------------
       StdEnv                (L)      lammps/2019.08
       anaconda2/2019.07     (E)      libiconv/1.16
       anaconda3/biohpc      (E)      libpciaccess/0.13.5
       anaconda3/2019.07     (E)      libxml2/2.9.9
       anaconda3/2019.10     (E,D)    ncl/6.3.0
       anaconda3/2020.11     (E)      ncview/2.1.2
       cellranger-atac/3.0.2 (E)      netlib-scalapack/2.0.2
       cellranger-dna/3.0.2  (E)      numactl/2.0.12
       cellranger/3.0.2      (E)      openblas/0.3.7
       cmake/3.20.2                   openfoam/2006
       cp2k/6.1                       vmd/1.9.4              (E)
       cuda/10.1                      wml/1.6.1              (E)
       cuda/10.2             (D)      wml/1.6.2              (E)
       fftw/3.3.8                     wml/1.7.0              (E,D)
       gaussian/16                    wml_anaconda3/2019.10  (E)
       java/8.0              (D)      xz/5.2.4
       java/8.0-6.5                   zlib/1.2.11

    --------------------------- /share/mfiles/Compilers ----------------------------
       at/12.0          gcc/7.4.0        gcc/8.4.0
       gcc/4.8.5 (D)    gcc/8.3.1 (L)    xl/16.1.1.4 (E)

      Where:
       D:  Default Module
       E:  Experimental
       L:  Module is loaded

    Use "module spider" to find all possible modules.
    Use "module keyword key1 key2 ..." to search for all possible modules matching
    any of the "keys".

..


[username@login1 ~]$ ml show gcc
    ----------------------------------------------------------------------------
       /share/mfiles/Compilers/gcc/8.3.1.lua:
    ----------------------------------------------------------------------------
    whatis("Name : gcc")
    whatis("Version : 8.3.1")
    whatis("Target : power9le")
    help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
    Fortran, Ada, and Go, as well as libraries for these languages.]])
    prepend_path("MODULEPATH","/share/mfiles/Compiler/gcc/8.3.1")
    family("compiler")
    prepend_path("INFOPATH","/opt/rh/devtoolset-8/root/usr/share/info")
    prepend_path("LD_LIBRARY_PATH","/opt/rh/devtoolset-8/root/usr/lib64:/opt/rh/devtoolset-8/root/usr/lib:/opt/rh/devtoolset-                       8/root/usr/lib64/dyninst:/opt/rh/devtoolset-8/root/usr/lib/dyninst:/opt/rh/devtoolset-8/root/usr/lib64:/opt/rh/devtoolset-8/root/usr/lib")
    prepend_path("MANPATH","/opt/rh/devtoolset-8/root/usr/share/man")
    prepend_path("PATH","/opt/rh/devtoolset-8/root/usr/bin")
    prepend_path("PKG_CONFIG_PATH","/opt/rh/devtoolset-8/root/usr/lib64/pkgconfig")
    prepend_path("PYTHONPATH","/opt/rh/devtoolset-8/root/usr/lib64/python2.7/site-packages:/opt/rh/devtoolset-8/root/usr/lib/python2.7/site-packages")
    setenv("PCP_DIR","/opt/rh/devtoolset-8/root")
    setenv("PERL5LIB","/opt/rh/devtoolset-8/root//usr/lib64/perl5/vendor_perl:/opt/rh/devtoolset-8/root/usr/lib/perl5:/opt/rh/devtoolset-8/root//usr/share/perl5/vendor_perl")

[username@login1 ~]$ ml smpi
[username@login1 ~]$ ml

    Currently Loaded Modules:
      1) gcc/8.3.1   2) StdEnv   3) smpi/10.02

Triton module hierarchies¶

Switch to a different compiler with the module swap command. Any dependent modules should also swap, if both versions exist. The SMPI module has both a gcc version, and an at/12.0 version.

show currently loaded modules with ml
show smpi module help with ml help smpi
switch from gcc to at with ml swap gcc at or ml -gcc at
- note the Lmod “reload” message for the smpi module
- (confirm smpi is loaded with ml)
show smpi module help with ml help smpi (a different smpi module)
reset to Triton defaults with ml reset

[username@login1 ~]$ ml

Currently Loaded Modules:
  1) StdEnv   2) gcc/8.3.1   3) smpi/10.02

    [username@login1 ~]$ ml help smpi

    -------------------- Module Specific Help for "smpi/10.02" ---------------------
      Lua Help file for IBM smpi 10.02 with devtoolset-8 GCC suite

      gcc version 8.3.1

      sets OMPI_CC, OMPI_FC, and OMPI_CXX to AT gcc suite

[username@login1 ~]$ ml -gcc at

Due to MODULEPATH changes, the following have been reloaded:
  1) smpi/10.02

[username@login1 ~]$ ml

Currently Loaded Modules:
  1) at/12.0   2) StdEnv   3) smpi/10.02

[username@login1 ~]$ ml help smpi

    -------------------- Module Specific Help for "smpi/10.02" ---------------------
      Lua Help file for IBM smpi 10.02 with Triton IBM AT 12.0 gcc suite

      gcc version 8.3.1

      sets OMPI_CC, OMPI_FC, and OMPI_CXX to AT gcc suite

[username@login1 ~]$ ml reset
Resetting modules to system default. Reseting $MODULEPATH back to system default. All extra directories will be removed from $MODULEPATH.
[username@login1 ~]$ ml

    Currently Loaded Modules:
      1) gcc/8.3.1   2) StdEnv

More hierarchies and dependencies¶

Dependency modules can be loaded in the same command, without waiting for them to appear in the output for module list (ml av).

Example : cdo, nco, and netcdff depend on “netcdfc”. Netcdfc depends on “hdf5”. They can be loaded in sequence, starting with the first dependency, “hdf5”.

[username@login1 ~]$ ml gcc/4.8.5 hdf5 netcdfc netcdff cdo nco
    The following have been reloaded with a version change:
    1) gcc/8.3.1 => gcc/4.8.5

[username@login1 ~]$ ml

    Currently Loaded Modules:
      1) gcc/4.8.5         4) netcdfc/4.7.4 (E)   7) cdo/1.9.8 (E)
      2) StdEnv            5) netcdff/4.5.3 (E)
      3) hdf5/1.8.16 (E)   6) nco/4.9.3     (E)

To view dependent modules in ml av, first load their prerequisites.

“Behind the scenes”

After an hdf5 module is loaded, any available netcdfc modules will show in ml av output :

load the default hdf5 module with ml hdf5
show loaded modules with ml
show available modules with ml av : netcdfc module now available to load
load the default netcdfc module with ml netcdfc
show newly available modules with ml av : netcdff, nco, and cdo now available to load

[username@login1 ~]$ ml hdf5
[username@login1 ~]$ ml

    Currently Loaded Modules:
      1) gcc/4.8.5   2) StdEnv   3) hdf5/1.8.16 (E)


[username@login1 ~]$ ml av

    ------------------- /share/mfiles/Library/gcc485/hdf5/1.8.16 -------------------
       netcdfc/4.7.4 (E)

    ----------------------- /share/mfiles/Compiler/gcc/4.8.5 -----------------------
       hdf5/1.8.16   (E,L)    myGCCdependentProgram/1.0 (S)    openmpi/3.1.4
       hwloc/1.11.11          openBLAS/0.3.7                   smpi/10.02

     ...

..

Once both hdf5 and netcdfc are loaded, ml av shows the next set of dependent modules :

[username@login1 ~]$ ml netcdfc
[username@login1 ~]$ ml

    Currently Loaded Modules:
      1) gcc/4.8.5   2) StdEnv   3) hdf5/1.8.16 (E)   4) netcdfc/4.7.4 (E)

[username@login1 ~]$ ml av

    ------------ /share/mfiles/Library/gcc485/netcdfc/4.7.4/hdf5/1.8.16 ------------
       cdo/1.9.8 (E)    nco/4.9.3 (E)    netcdff/4.5.3 (E)

    ------------------- /share/mfiles/Library/gcc485/hdf5/1.8.16 -------------------
       netcdfc/4.7.4 (E,L)

    ----------------------- /share/mfiles/Compiler/gcc/4.8.5 -----------------------
       hdf5/1.8.16   (E,L)    myGCCdependentProgram/1.0 (S)    openmpi/3.1.4
       hwloc/1.11.11          openBLAS/0.3.7                   smpi/10.02

     ...

..