HPC Test Cluster

  • You can login on the submit host hpcs03.op.umcutrecht.nl. This host is available from outside. If you access the cluster from outside, use hpcs01/02 as a stepping stone.

  • Please try to compile, install and run your software and let us know what doesn't work.

  • You can not submit jobs yet. (Actually you can, but please don't; I'm going to break this, repeatedly, over the next few days). For now, feel free to do a (small) test run on the submit host.

  • The "modules" system works, and already provides some packages. Suggestions for more packages/versions welcome.

  • Use the "module" command to list and use packages like R, Python and Java:

[mmarinus@hpcs03 ~]$ R --version
-bash: R: command not found
[mmarinus@hpcs03 ~]$ module avail

--------------------------------- /hpc/local/CentOS7/modulefiles/Lang ----------------------------------
   Java/1.8.0_60    R/3.2.2    python/2.7.10 (D)    python/3.4.3

------------------------------- /hpc/local/CentOS7/modulefiles/dev_tools -------------------------------

   (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".

[mmarinus@hpcs03 ~]$ module load R
[mmarinus@hpcs03 ~]$ R --version
WARNING: ignoring environment value of R_HOME
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see

  • Every now and then I notice some strange delays. This could be related to the fact that your homedirectory is served from a machine in the "old" cluster. Let me know if you also notice this.

-- Martin Marinus - 2015-10-08


This topic: HPC > WebHome > TestCluster
Topic revision: r2 - 2015-10-09 - MartinMarinus
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