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/4.8.5   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/4.8.5")

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/4.8.5   2) StdEnv


[username@login1 ~]$ ml help gcc

    --------------------- Module Specific Help for "gcc/4.8.5" ---------------------
    Lua Help for Triton system gcc module



[username@login1 ~]$ ml whatis gcc
    gcc/4.8.5           : GNU compiler suite
    gcc/4.8.5           : Version: 4.8.5
    gcc/4.8.5           : Category: compiler suite
    gcc/4.8.5           : Description: C, C++ and Fortran compilers


[username@login1 ~]$ ml av

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

--------------------------- /share/mfiles/Core ----------------------------
   R/3.6.1                              (E)      anaconda3/2019.07 (E,D)
   Single-Cell-Analysis/Cellranger-atac (E)      cp2k-gpu/7.0
   Single-Cell-Analysis/Cellranger-dna  (E)      cp2k/7.0
   Single-Cell-Analysis/Cellranger      (E,D)    cuda/10.1
   StdEnv                               (L)      java/8.0
   anaconda2/2019.07                    (E)      lammps/2019.08
   anaconda3/ccs-bio                    (E)

------------------------- /share/mfiles/Compilers -------------------------
   at/12.0    gcc/4.8.5 (L)   xl/16.1.1.4 (E)

..


[username@login1 ~]$ ml show gcc
    ----------------------------------------------------------------------------
       /share/mfiles/Compilers/gcc/4.8.5.lua:
    ----------------------------------------------------------------------------
    help([[Lua Help for Triton system gcc module
    ]])
    whatis("GNU compiler suite")
    whatis("Version: 4.8.5")
    whatis("Category: compiler suite")
    whatis("Description: C, C++ and Fortran compilers")
    setenv("CC","gcc")
    setenv("CXX","g++")
    setenv("FC","gfortran")
    prepend_path("LD_LIBRARY_PATH","/usr/lib")
    prepend_path("MANPATH","/usr/man")
    prepend_path("PATH","/usr/bin")
    prepend_path("MODULEPATH","/share/mfiles/Compiler/gcc/4.8.5")
    family("compiler")

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

    Currently Loaded Modules:
      1) gcc/4.8.5   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/4.8.5   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 system gcc 4.8.5

     sets OMPI_CC, OMPI_FC, and OMPI_CXX to GNU / 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/4.8.5   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 hdf5 netcdfc netcdff cdo nco
[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

     ...

..