Dear Users,

We frequently see jobs dying because of faulty scripts. This is part of a development cycle. After all: Who is perfect?

There are other ways than trying to correct the script post mortem - and saving time. One is to just check the syntax without executing a script:

$ bash -n scriptname

Another, very powerful tool is this on-line shell checker tool.

Your HPC-Team


Customizing bqueues

Many of you have noticed the increasing number of queues. This can be confusing when you just want to check the current status of the queues you're allowed to use. But there is an easy way to change this. You can tell bqueues to show just "your" queues by calling it using

bqueues -u $USER

If you want bqueues to always show your queues only, you can just add an alias to your .bashrc (found in your home-directory). Here, is a simple command to add it to your .bashrc-file:

echo '# Customizing bqueues to show only your queues'  >> ~/.bashrc
echo 'alias bqueues="\bqueues -u $USER"' >> ~/.bashrc

Now, either you call

source ~/.bashrc

Or you wait until your next login to Mogon and the changes will be active.

If you want to see all queues again, you have to call unalias bqueues . Then bqueues is back to "normal" for the current shell.

Your HPC Team

New Policy: Limited number of files in home directories

Dear Users,


As consequence of the recently increased quota in mogon home directories some users have been saving an excess amount of files in their home directory (fs1).

Due to performance reasons we therefore have to limit the number of files allowed in home directories to 1 million. Policies are linked in our wiki, this one can be found here.

Thank you for your consideration.

Posted on | Posted in Ticker

Python 3.5 with numpy linked against MKL

Dear Users,


We now provide a new version of Python -- 3.5-- as usual along with a great number of scientific Python modules. In particular, numpy, the basic array library, is compiled against Intel's MKL resulting in a tremendous speed-up when dealing with numerical computations, e.g. matrix multiplication.


See our wiki entry for more details.

Profiling on Mogon

We strive to offer Profiling tools for high performance computing. If you develop software, please check out our documentation on Intel's Vtune software, also Allinea, both are parallel profiling tools. (Documentation for Allinea on Mogon is forthcoming.)

If interested drop us a mail at hpc@uni-mainz.de to arrange a slot during the Thursdays Workshop.

New Module: R Version 3.2.2

We are pleased to announce the installation of the statistical software R, version 3.2.2, in a new module. This module includes many packages, including Bioconductor package. Parallelisation support is included. Check out the local R documentation.