Getting access to BioHPC Linux nodes

You may be asked to compute on BioHPC's ECCO Linux nodes (f.i., for very long-running jobs, or for very large memory).

Request an account

Go to the BioHPC account request page, requesting specifically joining the ECCO group and lv39 (Lars') "lab"

Reserve a node

• Go to BioHPC Reservations page, choose "Restricted", and reserve a node:
  • cbsuecco02: up to 7 days
  • all others: up to 3 days
  • in both cases, renewable

Access a node

See Getting Started Guide, but SSH is the best path (if you don't need graphical applications).

Notes

Shared directory

Your default home directory (/home/NETID) is not shared among group users (same as on CISER). Use /home/ecco_lv39 instead.

Using Docker

The BioHPC docker command is docker1. All files that are shared via the -v option must reside on /workdir/NETID and cannot be shared across nodes. To get the files to /workdir/NETID, the following commands can be used, assuming that your files are in /home/ecco_lv39/Workspace/aearep-$AEAREP:

• Sync to workdir:

AEAREP=12345
[[ -d /workdir/$(id -nu) ]] || mkdir /workdir/$(id -nu)
rsync -auv /home/ecco_lv39/Workspace/aearep-$AEAREP/ /workdir/$(id -nu)/aearep-$AEAREP/

• Sync back to shared drive (once computations are done, or at any time

AEAREP=12345
rsync -auv /workdir/$(id -nu)/aearep-$AEAREP/ /home/ecco_lv39/Workspace/aearep-$AEAREP/