Proper usage of /tmp

  • Please include as a last line on your scripts something like “rm -rf
    $TMPDIR” in order to make sure that there’s no data left on the node
    after your job terminated. See link below for further info: How to submit a job
  • If your jobs fail, you can use the script ‘’ on the
    submit host to clean out any remaining data on the nodes. Please use it,
    but only when you have a lot of jobs that failed.
  • Please don’t write gigabytes of data. There’s 130GB free space on the
    c2-x, if you managed to fill this up you did something wrong.
  • Please be considerate. If you fuck up the cluster, you block all
    other users and, in terms of near deadlines like now, tempers rise

Read More

GCC 4.4 and ARGoS on the IRIDIA cluster

EDIT: With the new installation of the cluster, gcc44 is the default compiler, so you don’t need this anymore. Actually it might be possible that leaving these settings will prevent you from compiling. Remove them in case you have cmake problems (such as: CMake Error: Error required internal CMake variable not set, cmake may be not be built correctly. Missing variable is: CMAKE_C_COMPILER)

On the IRIDIA cluster, GCC 4.4 is available under the commands gcc44/g++44.

In order to use this with CMake and ARGoS2, you can either set the appropriate environment variables or simply add a

set(CMAKE_C_COMPILER "gcc44")

before the version check in the main CMakeList of *each* of your packages.

On a side note, I fixed the missing packages for ARGoS 1, so that old experiments can again be compiled.

Read More

SSH host key changed

As the operating system was replaced completely, the SSH host key of majorana changed as well.

If you get an error message from your ssh client upon trying to connect to majorana, follow the instructions to delete the cached key (usually in ~/.ssh/known_hosts).

Read More

How do I get mails about my jobs status?

From the manual:

The qsub -m command requests email to be sent to the user who submitted a job or to the email addresses specified by the -M flag if certain events occur. See the qsub(1) man page for a description of the flags. An argument to the -m option specifies the events. The following arguments are available:

  • b – Send email at the beginning of the job.
  • e – Send email at the end of the job.
  • a – Send email when the job is rescheduled or aborted (for example, by using the qdel command).
  • s – Send email when the job is suspended.
  • n – Do not send email. n is the default.

Use a string made up of one or more of the letter arguments to specify several of these options with a single -m option. For example, -m be sends email at the beginning and at the end of a job.

Thus, you can simply change your submit script like this:

#$ -m a,s
#$ -M,
#$ -cwd

This sends a mail to the two specified email addresses if the job is rescheduled or aborted. If you omit -M, the mail is send to the user who submitted the job.

Read More