How to Discover Available Software¶

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Command	Description
`module spider <software>`	Query if `<software>` is available
`module load <software>`	Load `<software` into environment
`module list`	List loaded software packages
`module rm <software>`	Remove previously loaded `<software>` from environment
`module unload <software>`	Same as `module rm <software>`
`module purge`	Remove all previously loaded `<software>` from environment

CRC uses the Lmod Environment Modules tool to manage and provision software applications. The command module spider <software> (1) shows if a package is available. For example, (2)

Throughout the examples, we use the conventional syntax <variable> to represent a placeholder for an expected value that the user will provide.

module spider <software>

commandoutput

module spider python

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  python:
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
    Description:
      Anaconda is the leading open data science platform powered by Python.

     Versions:
        python/anaconda2.7-4.2.0_westpa
        python/anaconda2.7-4.2.0
        python/anaconda2.7-4.4.0_genomics
        python/anaconda2.7-5.2.0_westpa
        python/anaconda2.7-5.2.0
        python/anaconda2.7-2018.12_westpa
        python/anaconda3.5-4.2.0-dev
        python/anaconda3.5-4.2.0
        python/anaconda3.6-5.2.0_deeplabcut
        python/anaconda3.6-5.2.0_leap
        python/anaconda3.6-5.2.0
        python/anaconda3.7-5.3.1_genomics
        python/anaconda3.7-2018.12_westpa
        python/anaconda3.7-2019.03_astro_bagpipes-0.8.2
        python/anaconda3.7-2019.03_astro_bagpipes-0.8.8-alt
        python/anaconda3.7-2019.03_astro_bagpipes-0.8.8
        python/anaconda3.7-2019.03_astro
        python/anaconda3.7-2019.03_deformetrica
        python/anaconda3.7-2019.03
        python/anaconda3.8-2020.11
        python/anaconda3.9-2021.11
        python/anaconda3.10-2022.10
        python/bioconda-2.7-5.2.0
        python/bioconda-3.6-5.2.0
        python/bioconda-3.7-2019.03
        python/intel-3.5
        python/intel-3.6_2018.3.039
        python/intel-3.6_2019.2.066
        python/intel-3.6
        python/ondemand-jupyter-python3.8
        python/ondemand-jupyter-python3.9
        python/ondemand-jupyter-python3.10
        python/ondemand-jupyter-python3.11
        python/3.7.0-dev
        python/3.7.0-fastx
        python/3.7.0

     Other possible modules matches:
        biopython  openslide-python

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  To find other possible module matches do:
      module -r spider '.*python.*'

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  For detailed information about a specific "python" module (including how to load the modules) use the module's full name.
  For example:

     $ module spider python/ondemand-jupyter-python3.9
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

will show all the available Python versions. Repeating this command with a version-specific Python will display how to load the package and if there are any dependencies:

module spider <specific software>

commandoutput

module spider python/anaconda3.10-2022.10

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  python: python/anaconda3.10-2022.10
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
    Description:
      Anaconda is the leading open data science platform powered by Python. Compatible with gcc/8.2.0

     Other possible modules matches:
        biopython, openslide-python

    You will need to load all module(s) on any one of the lines below before the "python/anaconda3.10-2022.10" module is available to load.

      gcc/8.2.0

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  To find other possible module matches do:
      module -r spider '.*python/anaconda3.10-2022.10.*'

As instructed by the output of the python/anaconda3.10-2022.10 module, you will need to load the gcc/8.2.0 package before loading the version-specific Python. The command to load a software package is module load <software>. You can load the packages one at a time or all on the same commandline, making sure that the depedencies are loaded first:

module load <software>

commandalternative command

module load gcc/8.2.0
module load python/anaconda3.10-2022.10

module load gcc/8.2.0 python/anaconda3.10-2022.10

To show all the software that had been loaded into your environment, use the command module list:

module list

commandoutput

module list

Currently Loaded Modules:
  1) gcc/8.2.0   2) python/anaconda3.10-2022.10

To remove a software package from your environment, use the command module rm <software>:

module rm <software>

commandoutput

module list
module rm python/anaconda3.10-2022.10
module list

{kimwong@login1.crc.pitt.edu ~}$module list

Currently Loaded Modules:
  1) gcc/8.2.0   2) python/anaconda3.10-2022.10

[kimwong@login1.crc.pitt.edu ~]$module rm python/anaconda3.10-2022.10
[kimwong@login1.crc.pitt.edu ~]$module list
No modules loaded
[kimwong@login1.crc.pitt.edu ~]$

You should have noticed in the output that removal of the python/anaconda3.10-2022.10 module also removes gcc/8.2.0. This is because the latter was a dependency for the Python module. What happens if you were to remove the dependency first? Let's load the modules again and try it out:

module rm <software>

commandoutput

module load gcc/8.2.0 python/anaconda3.10-2022.10
module list
module rm gcc/8.2.0
module list

[kimwong@login1.crc.pitt.edu ~]$module load gcc/8.2.0 python/anaconda3.10-2022.10
[kimwong@login1.crc.pitt.edu ~]$module list

Currently Loaded Modules:
  1) gcc/8.2.0   2) python/anaconda3.10-2022.10

[kimwong@login1.crc.pitt.edu ~]$module rm gcc/8.2.0

Inactive Modules:
  1) python/anaconda3.10-2022.10

[kimwong@login1.crc.pitt.edu ~]$module list

Currently Loaded Modules:
  None found.

Inactive Modules:
  1) python/anaconda3.10-2022.10

[kimwong@login1.crc.pitt.edu ~]$

The removal of the dependent software makes the main software module inactive, which has the same effect as a module rm <software>. Now, suppose you have a few software packages loaded. Do you need to remove each package individually or is there a single global remove command? The command is module purge:

module purge

commandoutput

module load gcc/8.2.0 python/anaconda3.10-2022.10 r/3.6.0
module list
module purge
module list

[kimwong@login1.crc.pitt.edu ~]$module load gcc/8.2.0 python/anaconda3.10-2022.10 r/3.6.0
[kimwong@login1.crc.pitt.edu ~]$module list

Currently Loaded Modules:
  1) gcc/8.2.0                     3) java/1.8.0_181-oracle   5) bzip2/1.0.6   7) pcre/8.40     9) gsl/2.5     11) hdf5/1.10.4   13) gdal/2.4.2     15) r/3.6.0
  2) python/anaconda3.10-2022.10   4) zlib/1.2.9              6) xz/5.2.3      8) curl/7.52.1  10) jags/4.3.0  12) netcdf/4.6.3  14) openmpi/1.8.8

[kimwong@login1.crc.pitt.edu ~]$module purge
[kimwong@login1.crc.pitt.edu ~]$module list
No modules loaded
[kimwong@login1.crc.pitt.edu ~]$