Tag Archives: farnam

Farnam partition

The absolute path is "/ysm-gpfs/pi/gerstein/". Please put most of your data here.

After creating the folder (don’t forget to set up chmod the way you like), then you can create a soft link your folder back to your home folder for quick access.

ln -s [your folder under pi] [the soft link under your home folder (aka ~/xx )]

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Instructions on setting up ssh desktop clients for Farnam

1) It is possible to set up ssh such that you only have to authenticate once; subsequent ssh’s reuse that connection. Please see our detailed instructions here:

http://research.computing.yale.edu/support/hpc/user-guide/ssh-sample-configuration

2) We have detailed instructions on how to use Cyberduck and Winscp to connect using duo on our website. Please see:
http://research.computing.yale.edu/support/hpc/user-guide/transfer-files-or-cluster

I believe it is also possible to use filezilla after doing a similar configuration to avoid the creation of new connections, but don’t see the need, given that cyberduck and winscp are both usable.

Farnam dedicated queue

There is a hard limit on the number of cores available per user at Farnam general queue (QOSMaxCpuPerUserLimit). As an alternative, the gerstein group has a large dedicated partition (pi_gerstein) which has no per user limit.

Use the parameter –partition pi_gerstein or -p pi_gerstein when submiting jobs to Farnam’s slurm.