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Modules

Environment modules#

Software is provided on Sherlock under the form of loadable environment modules.

Software is only accessible via modules

The use of a module system means that most software is not accessible by default and has to be loaded using the module command. This mechanism allows us to provide multiple versions of the same software concurrently, and gives users the possibility to easily switch between software versions.

Sherlock uses Lmod to manage software installations. The modules system helps setting up the user's shell environment to give access to applications, and make running and compiling software easier. It also allows us to provide multiple versions of the same software, that would otherwise conflict with each other, and abstract things from the OS sometimes rigid versions and dependencies.

When you first log into Sherlock, you'll be presented with a default, bare bone environment with minimal software available. The module system is used to manage the user environment and to activate software packages on demand. In order to use software installed on Sherlock, you must first load the corresponding software module.

When you load a module, the system will set or modify your user environment variables to enable access to the software package provided by that module. For instance, the $PATH environment variable might be updated so that appropriate executables for that package can be used.

Module categories#

Modules on Sherlock are organized by scientific field, in distinct categories. This is to limit the information overload that can result when displaying the full list of available modules. Given the large diversity of the Sherlock user population, all users are not be interested in the same kind of software, and high-energy physicists may not want to see their screens cluttered with the latest bioinformatics packages.

Module categories

You will first have to load a category module before getting access to individual modules. The math and devel categories are loaded by default, and modules in those categories can be loaded directly

For instance, to be able to load the gromacs module, you'll first need to load the chemistry module. This can be done in a single command, by specifying first the category, then the actual application module name:

$ module load chemistry gromacs

The math and devel categories, which are loaded by default, provide direct access to compilers, languages, and MPI and numerical libraries.

For a complete list of software odule categories, please refer to the list of available software

Searching for a module

To know how to access a module, you can use the module spider <module_name> command. It will search through all the installed modules, even if they're masked, and display instructions to load them. See the Examples section for details.

Module usage#

The most common module commands are outlined in the following table. module commands may be shortened with the ml alias, with slightly different semantics.

Module names auto-completion

The module command supports auto-completion, so you can just start typing the name of a module, and press Tab to let the shell automatically complete the module name and/or version.

Module command Short version Description
module avail ml av List available software1
module spider gromacs ml spider gromacs Search for particular software
module keyword blas ml key blas Search for blas in module names and descriptions
module whatis gcc ml whatis gcc Display information about the gcc module
module help gcc ml help gcc Display module specific help
module load gcc ml gcc Load a module to use the associated software
module load gsl/2.3 ml gsl/2.3 Load specific version of a module
module unload gcc ml -gcc Unload a module
module swap gcc icc ml -gcc icc Swap a module (unload gcc and replace it with icc)
module purge ml purge Remove all modules2
module save foo ml save foo Save the state of all loaded modules in a collection named foo
module restore foo ml restore foo Restore the state of saved modules from the foo collection

Additional module sub-commands are documented in the module help command. For complete reference, please refer to the official Lmod documentation.

Module properties#

Multiple versions

When multiple versions of the same module exist, module will load the one marked as Default (D). For the sake of reproducibility, we recommend always specifying the module version you want to load, as defaults may evolve over time.

To quickly see some of the modules characteristics, module avail will display colored property attributes next to the module names. The main module properties are:

  • S: Module is sticky, requires --force to unload or purge
  • L: Indicate currently loaded module
  • D: Default module that will be loaded when multiple versions are available
  • r: Restricted access, typically software under license. Contact us for details
  • g: GPU-accelerated software, will only run on GPU nodes
  • m: Software supports parallel execution using MPI

Searching for modules#

You can search through all the available modules for either:

  • a module name (if you already know it), using module spider
  • any string within modules names and descriptions, using module keyword

For instance, if you want to know how to load the gromacs module, you can do:

$ module spider gromacs

If you don't know the module name, or want to list all the modules that contain a specific string of characters in their name or description, you can use module keyword. For instance, the following command will list all the modules providing a BLAS library:

$ module keyword blas

Examples#

Listing#

To list all the modules that can be loaded, you can do:

$ ml av

-- math -- numerical libraries, statistics, deep-learning, computer science ---
   R/3.4.0             gsl/1.16             openblas/0.2.19
   cudnn/5.1  (g)      gsl/2.3       (D)    py-scipystack/1.0_py27 (D)
   cudnn/6.0  (g,D)    imkl/2017.u2         py-scipystack/1.0_py36
   fftw/3.3.6          matlab/R2017a (r)

------------------ devel -- compilers, MPI, languages, libs -------------------
   boost/1.64.0          icc/2017.u2           python/2.7.13    (D)
   cmake/3.8.1           ifort/2017.u2         python/3.6.1
   cuda/8.0.61    (g)    impi/2017.u2   (m)    scons/2.5.1_py27 (D)
   eigen/3.3.3           java/1.8.0_131        scons/2.5.1_py36
   gcc/6.3.0      (D)    julia/0.5.1           sqlite/3.18.0
   gcc/7.1.0             llvm/4.0.0            tbb/2017.u2
   h5utils/1.12.1        nccl/1.3.4     (g)    tcltk/8.6.6
   hdf5/1.10.0p1         openmpi/2.0.2  (m)

-------------- categories -- load to make more modules available --------------
   biology      devel (S,L)    physics    system
   chemistry    math  (S,L)    staging    viz

  Where:
   S:  Module is Sticky, requires --force to unload or purge
   r:  Restricted access
   g:  GPU support
   L:  Module is loaded
   m:  MPI support
   D:  Default Module

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

Searching#

To search for a specific string in modules names and descriptions, you can run:

$ module keyword numpy
---------------------------------------------------------------------------

The following modules match your search criteria: "numpy"
---------------------------------------------------------------------------

  py-scipystack: py-scipystack/1.0_py27, py-scipystack/1.0_py36
    The SciPy Stack is a collection of open source software for scientific
    computing in Python. It provides the following packages: numpy, scipy,
    matplotlib, ipython, jupyter, pandas, sympy and nose.

---------------------------------------------------------------------------
[...]
$ ml key compiler
---------------------------------------------------------------------------

The following modules match your search criteria: "compiler"
---------------------------------------------------------------------------

  cmake: cmake/3.8.1
    CMake is an extensible, open-source system that manages the build
    process in an operating system and in a compiler-independent manner.

  gcc: gcc/6.3.0, gcc/7.1.0
    The GNU Compiler Collection includes front ends for C, C++, Fortran,
    Java, and Go, as well as libraries for these languages (libstdc++,
    libgcj,...).

  icc: icc/2017.u2
    Intel C++ Compiler, also known as icc or icl, is a group of C and C++
    compilers from Intel

  ifort: ifort/2017.u2
    Intel Fortran Compiler, also known as ifort, is a group of Fortran
    compilers from Intel

  llvm: llvm/4.0.0
    The LLVM Project is a collection of modular and reusable compiler and
    toolchain technologies. Clang is an LLVM native C/C++/Objective-C
    compiler,

---------------------------------------------------------------------------
To get information about a specific module, especially how to load it, the following command can be used:
$ module spider gromacs

-------------------------------------------------------------------------------
  gromacs: gromacs/2016.3
-------------------------------------------------------------------------------
    Description:
      GROMACS is a versatile package to perform molecular dynamics, i.e.
      simulate the Newtonian equations of motion for systems with hundreds to
      millions of particles.

    Properties:
      GPU support      MPI support

    You will need to load all module(s) on any one of the lines below before
    the "gromacs/2016.3" module is available to load.

      chemistry

Loading#

Loading a category module allows to get access to field-specific software:

$ ml chemistry
$ ml av

------------- chemistry -- quantum chemistry, molecular dynamics --------------
   gromacs/2016.3 (g,m)    vasp/5.4.1 (g,r,m)

-- math -- numerical libraries, statistics, deep-learning, computer science ---
   R/3.4.0             gsl/1.16             openblas/0.2.19
   cudnn/5.1  (g)      gsl/2.3       (D)    py-scipystack/1.0_py27 (D)
   cudnn/6.0  (g,D)    imkl/2017.u2         py-scipystack/1.0_py36
   fftw/3.3.6          matlab/R2017a (r)

------------------ devel -- compilers, MPI, languages, libs -------------------
   boost/1.64.0          icc/2017.u2           python/2.7.13    (D)
   cmake/3.8.1           ifort/2017.u2         python/3.6.1
   cuda/8.0.61    (g)    impi/2017.u2   (m)    scons/2.5.1_py27 (D)
   eigen/3.3.3           java/1.8.0_131        scons/2.5.1_py36
   gcc/6.3.0      (D)    julia/0.5.1           sqlite/3.18.0
   gcc/7.1.0             llvm/4.0.0            tbb/2017.u2
   h5utils/1.12.1        nccl/1.3.4     (g)    tcltk/8.6.6
   hdf5/1.10.0p1         openmpi/2.0.2  (m)

-------------- categories -- load to make more modules available --------------
   biology          devel (S,L)    physics    system
   chemistry (L)    math  (S,L)    staging    viz

[...]

Reseting the modules environment#

If you want to reset your modules environment as it was when you initially connected to Sherlock, you can use the ml reset command: it will remove all the modules you have loaded, and restore the original state where only the math and devel categories are accessible.

If you want to remove all modules from your environment, including the default math and devel modules, you can use ml --force purge.

Loading modules in jobs#

In order for an application running in a Slurm job to have access to any necessary module-provided software packages, we recommend loading those modules in the job script directly. Since Slurm propagates all user environment variables by default, this is not strictly necessary, as jobs will inherit the modules loaded at submission time. But to make sure things are reproducible and avoid issues, it is preferable to explicitly load the modules in the batch scripts.

module load commands should be placed right after #SBATCH directives and before the actual executable calls. For instance:

#!/bin/bash
#SBATCH ...
#SBATCH ...
#SBATCH ...

ml reset
ml load gromacs/2016.3

srun gmx_mpi ...

Custom modules#

Users are welcome and encouraged to build and install their own software on Sherlock. To that end, and to facilitate usage or sharing of their custom software installations, they can create their own module repositories.

See the Software Installation page for more details.

Lab-provided software#

PI groups and Labs can share their software installations and modules with the whole Sherlock community of users, and let everyone benefit from their tuning efforts and software developments.

Those modules are available in the specific labs category, and organized by lab name.

For instance, listing the available lab modules can be done with:

$ ml labs
$ ml av
-------------------- labs -- lab-contributed software ----------------------
   poldrack

To get information about a specific lab module:

$ ml show poldrack
----------------------------------------------------------------------------
   /share/software/modules/labs/poldrack.lua:
----------------------------------------------------------------------------
prepend_path("MODULEPATH","/home/groups/russpold/modules")
whatis("Name:        poldrack")
whatis("Version:     1.0")
whatis("Category:    labs")
whatis("URL:         https://github.com/poldracklab/lmod_modules")
whatis("Description: Software modules contributed by the Poldrack Lab.")

And to list the available software modules contributed by the lab:

$ ml poldrack
$ ml av

------------------------ /home/groups/russpold/modules -------------------------
   afni/17.3.03           freesurfer/6.0.1            gsl/2.3      (D)
   anaconda/5.0.0-py36    fsl/5.0.9                   pigz/2.4
   ants/2.1.0.post710     fsl/5.0.11           (D)    remora/1.8.2
   c3d/1.1.0              git-annex/6.20171109        xft/2.3.2
[...]

  1. If a module is not listed here, it might be unavailable in the loaded modules categories, and require loading another category module. Search for not-listed software using the module spider command. 

  2. The math and devel category modules will not be unloaded with module purge as they are "sticky". If a user wants to unload a sticky module, they must specify the --force option.