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Available Software

At this time the cluster has Anaconda and Cuda installed for work on systems like Tensorflow and Pytorch. The preferred method of installing software is to work off of Anaconda environments. If you need additional software installed please email rc@zi.columbia.edu to request it.

Environment Modules

Axon uses a system of environmental modules, specifically using a piece of software called lmod, which allows people to specify the version of the program they want to run. This enables the cluster to seamlessly have multiple versions of a single program. Below is an example of how environment modules work:

Python before and after loading a module
[aa3301@axon ~]$ python --version
Python 2.7.5
[aa3301@axon ~]$ which python
/usr/bin/python
[aa3301@axon ~]$ ml anaconda3-2019.03
[aa3301@axon ~]$ python --version
Python 3.7.3
[aa3301@axon ~]$ which python
/share/apps/anaconda3-2019.03/bin/python

In the example above when we log in and run Python we get the default system python, but if we run ml (which can also be run as module load) and load anaconda we get a much newer version with a bunch of modules already installed.

Running the ml (or module list) will show you the currently loaded modules, and ml av (or module avail) will show you the available modules to load:

More module commands
[aa3301@axon ~]$ ml

Currently Loaded Modules:
  1) anaconda3-2019.03



[aa3301@axon ~]$ ml av

--------------------------------------------------------------------------- /share/modulefiles ----------------------------------------------------------------------------
   anaconda3-2019.03 (L)    cuda/9.2.88      cuda/10.1.168 (D)    cudnn/7.5.1-10.0       cudnn/7.6.1.34-10.1 (D)    kilosort2       matlab/2017b    matlab/2018b (D)
   cuda/9.0.176             cuda/10.0.130    cudnn/7.3.0          cudnn/7.6.1.34-10.0    gcc/4.9.1                  matlab/2017a    matlab/2018a

  Where:
   L:  Module is loaded
   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".

The ml alias is convenient shortcut to most commands. If you type ml and press tab it will show you all the possible completion the same is true of the module load command:

Use tab completion to navigate the modules
[aa3301@axon ~]$ ml
add                  cuda/10.1.168        cudnn/7.5.1-10.0     gcc/4.9.1            load                 matlab/2018b         show                 unuse
anaconda3-2019.03    cuda/9.0.176         cudnn/7.6.1.34-10.0  help                 matlab               purge                sl                   update
avail                cuda/9.2.88          cudnn/7.6.1.34-10.1  keyword              matlab/2017a         restore              spider               use
cuda                 cudnn                delete               kilosort2            matlab/2017b         rm                   swap                 whatis
cuda/10.0.130        cudnn/7.3.0          gcc                  list                 matlab/2018a         save                 unload
[aa3301@axon ~]$ ml load cud
cuda                 cuda/10.1.168        cuda/9.2.88          cudnn/7.3.0          cudnn/7.6.1.34-10.0
cuda/10.0.130        cuda/9.0.176         cudnn                cudnn/7.5.1-10.0     cudnn/7.6.1.34-10.1
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