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Brain is a small computing cluster running Rocks 7. The cluster currently consists of 16 compute nodes, and 1 head node with a total capacity of 464 cores, and approximately 6.2TB of RAM. Cluster nodes are interconnected via 2x 10Gb Ethernet.
This Wiki will serve as the primary source for cluster documentation. It will be divided into two major topic groups, cluster administration, and end-user tasks. In cases where a topic must reference potentially sensitive information, that information should be stored on the DEOHS Portal, and a reference link provided.
Brain doesn't have access to the department's main network storage. You will need to transfer any data or code you are working on to Brain. Once you are no longer working a particular dataset on Brain, you should remove the dataset from your Brain account.
R Studio Desktop is installed on Brain. You'll need to connect to the cluster using X2Go. Once connected request an interactive computing session, and activate the R and R Studio environments.
Alternatively, you can use R Studio Server via your browser. For details, see https://github.com/deohs/ehbrain/wiki/RStudio-Server
The problem is most likely, one of the following:
- You need to specify the full hostname of the database server you wish to reach.
- The database server firewall isn't configured to allow access from Brain.
- Your database user account isn't authorized to access the database from Brain.
If the problem isn't the hostname, you'll need to contact EHIT for assistance.
Software (including R packages) should be compiled and installed via the head node.
Most likely you have forgot to change your Unix primary group, to the group your queue requires. Make sure, you run "newgrp WORKGROUP", before you run qlogin or qsub.
Each group that sponsors brain, has a group folder located in /share/groups. Within each group folder, we automatically create an "apps" directory, for your storing software you install, along with a modulefiles sub-directory for Environment Modules.
No. Brain's storage system isn't backed up. Each user or group is responsible for backing up the files they wish to protect.
Most likely you are trying to build R packages on one of the compute nodes, rather than the frontend. All software compilation should be done on the front end, as the compute nodes lack compilers and development libraries.
Brain users can contact EHIT for assistance in getting connected, installing software, etc. The primary means of contact is via email to ehit[at]uw.edu (replace the [at] with @). Additional contact methods can be found on Portal.