Summary and Version Information
|Description||Numerical computation library for python, esp for machine learning|
|Categories||Computerscience, Numerical Analysis, Research|
|0.9.0||theano/0.9.0/python/2/nocuda|| Deepthought2 HPCC
|N||No GPU support|
|1.0.1||theano/1.0.1/nocuda|| Deepthought2 HPCC
|N||No GPU support|
*: Packages labelled as "available" on an HPC cluster means that it can be used on the compute nodes of that cluster. Even software not listed as available on an HPC cluster is generally available on the login nodes of the cluster (assuming it is available for the appropriate OS version; e.g. RedHat Linux 6 for the two Deepthought clusters). This is due to the fact that the compute nodes do not use AFS and so have copies of the AFS software tree, and so we only install packages as requested. Contact us if you need a version listed as not available on one of the clusters.
In general, you need to prepare your Unix environment to be able to use this software. To do this, either:
module load MODFOO
where TAPFOO and MODFOO are one of the tags in the tap
and module columns above, respectively. The
tap command will
print a short usage text (use
-q to supress this, this is needed
in startup dot files); you can get a similar text with
module help MODFOO. For more information on
the tap and module commands.
For packages which are libraries which other codes get built against, see the section on compiling codes for more help.
Tap/module commands listed with a version of current will set up for what we considered the most current stable and tested version of the package installed on the system. The exact version is subject to change with little if any notice, and might be platform dependent. Versions labelled new would represent a newer version of the package which is still being tested by users; if stability is not a primary concern you are encouraged to use it. Those with versions listed as old set up for an older version of the package; you should only use this if the newer versions are causing issues. Old versions may be dropped after a while. Again, the exact versions are subject to change with little if any notice.
In general, you can abbreviate the module tags. If no version is given, the default current version is used. For packages with compiler/MPI/etc dependencies, if a compiler module or MPI library was previously loaded, it will try to load the correct build of the package for those packages. If you specify the compiler/MPI dependency, it will attempt to load the compiler/MPI library for you if needed.
The keras, tensorflow, and theano packages are not natively installed on the Deepthought2 cluster for various technical reasons. What is provided instead are Singularity containers which have versions of both python2 and python3 installed with these packages.
To use these python packages, you must load the appropriate environmental
module load theano) and then launch the python
interpretter inside the Singularity container. To help with this,
the following helper/wrapper scripts have been provided:
theano-python2will invoke a Theano-enabled python2 interpretter within the container. Any arguments given will be passed to the python command, so you can do something like
theano-python3will behave as above, but invoke a Theano-enabled python3 interpretter within the container.
theano-cache-python2will run the
theano-cachecommand (using python2) inside the container. Any arguments given will be passed to the theano-cache command.
theano-nose-python2will run the
theano-nosecommand (using python2) inside the container. Any arguments given will be passed to the theano-nose command.
theano-nose, respectively, but invoke python3 variants of the named script.
In all cases, any arguments given to the wrapper scripts are passed directly to the python interpretter running within the container. E.g., you can provide the name of a python script, and that script will run in the python interpretter running inside your container. Your home and lustre directories are accessible from within the container, so you can read and write to files in those directories as usual.
Note that if you load the keras environmental module and then issue the
python command, you will start up a natively installed python
interpretter which does NOT have the theano, etc. python modules
installed. You need to start one of the python interpretters inside the
container to get these modules --- you can either do that using the correct
singularity command, or use the friendlier wrapper scripts
It is hoped that for most users, the "containerization" of these packages should not cause any real issues, and hopefully not even really be noticed. However, there are some limitations to the use of containers:
- In general, you will not have access to natively installed software, just
the software included in the container. So even if some package
foois installed natively on Deepthought2, it is likely not accessible from within the container (unless it was also installed inside that container).
- You will not likely be able to use python
virtualenvscripts to install new python modules for use within the container, as that will be installing packages natively, which would not then be available inside the container.
However, you are permitted to create your own Singularity containers and use them on the Deepthought2 cluster. You will need to have root access on some system (e.g. a workstation or desktop) to create your own Singularity containers (we cannot provide you root access on the Deepthought2 login or compute nodes), but if you have such you can build your own containers. You can also copy the system provided containers and edit them. More details can be found under the software page for Singularity.