Cluster Usage Notes | mtholder.github.io/home/

Various development tools and utilities (git, svn, gdb, python2.6 etc.) have been installed on " /share/apps/ ". Adding " /share/apps/bin/ " to your path should give you access to these.
The full gcc suite, except gcc java, has been built and installed under " /share/apps/opt/gcc ". If you add " /share/apps/opt/gcc/bin " to your path, then you will have the entire suite available to you on both the head node and the compute nodes.
We try to keep the core system clean of actual domain-specific programs and libraries. This means that particular programs or supporting libraries that you need for your work should be built, installed, and run from a subdirectory off your home directories.

We use the Sun Grid Engine for all job scheduling.
Every job should be annotated with the maximum amount of memory it is expected to consume using the " -l h_vmem " flag (which defaults to a value of 1G).
In most cases, you will be submitting jobs to the " general. q " queue.

A simple job submission script would look like:

#! /bin/sh
#$ -cwd
#$ -V
#$ -q "general.q"
#$ -l h_vmem=2G
~/path/to/program file.dat

A parallel job submission script:

#! /bin/sh
#$ -cwd
#$ -V
#$ -q "general.q"
#$ -l h_vmem=2G
#$ -pe mpi_general 4
/opt/openmpi/bin/mpirun -np 4 ~/path/to/program file.dat

Firewall rules on kywjibo currently only permit access from machines in Haworth or Dyche. If you are trying to access from outside these buildings, you will need to first log in to a gateway machine in either one of these buildings, and from there login to kwyjibo. This entire process can be wrapped up a simple alias:
```
alias kwyjibo='ssh -t REMOTE.GATEWAY.IP ssh 129.237.24.139'
```
Similarly, you can mount your kwyjibo home directory as a subdirectory of your home directory on your gateway machine, thus simplifying file transfers. On OS X machines, you will need to install sshfs for OS from here , after which you would:
```
$ mkdir ~/kwyjibo
$ /Applications/sshfs/bin/mount_sshfs 129.237.24.139  ~/kwyjibo
```
While on Linux/UNIX machines, assuming you have sshfs installed::
```
$ mkdir ~/kwyjibo
$ sshfs 129.237.24.139 ~/kwyjibo
```