CBIR operates a scientific computational resource to help CBIR users to preprocess and
analyze neuroimaging data. Due to high load on this resource, we recommend that users
postpone their jobs until evening and weekend house. Please see Sung Yu or Peter Kochunov
if additional computation capacity is needed, it maybe available through collaborative
agreement with the
institute for genomic science
or off-campus vendors.
Frequently Asked Questions
- New user orientation
- Sung Yu does weekly classes for new users. Please schedule the time at syu at mprc.umaryland.edu.
- How do I log in?
- You will receive a welcome email from Sung Yu that will include temporary account password and your assigned login node.
- CBIR implements a two-step authentication process. Please download
Google Authenticator app. It can be installed on your smart phone or tablet or used within browser environment.
- Your welcoming email will include a Q-Code that ties your smart phone with the CBIR account. The Google Authenticator will provide you with a six digit numeric code to be entered as a part of your login process. Please note that the Q-Code in the welcome email will expire in 24 hours.
- You'll need to install a SSH client if you don't already have one. Then SSH to the ip address provided in your welcome email.
- How do I change my password?
- You can use the command '
yppasswd' to change your password on either of the login nodes.
- How can I stay informed about system changes?
- Sung Yu maintains a mailing list that includes all MPRC accounts.
- If you use off-site account, please ask Sung to include it on the list.
- Can I run jobs on the login nodes?
- Login nodes are a shared resource. They also serve as cluster masters. Please do not run any jobs on the login nodes.
- Why isn't my job running?
- The PBS cluster jobs can be debugged by running command '
checkjob -v JOBID'. It should provide information regarding the source of the failure.
- It's taking forever to transfer my files. How can I transfer them faster?
- Please note that for security reasons, data transfer bandwidth from CBIR is capped.
- Please see Sung Yu if you have a large dataset to transfer outside of the CBIR/UMB network.
- 'Disk quota exceeded'
- Hard quota of 500GB is maintained for home directory. Please see Sung Yu if you need large temporal space for data analyses. Investigators are expected to maintain their own analysis data space. Please see Sung Yu for more details.
- Why are my #PBS options being ignored?
- Make sure that your #PBS options come before any commands in your shell script. Once the queuing system encounters a command, it quits looking for #PBS options, so these options will be ignored.
- Scientific Software
- CBIR maintains a large library of scientific software on /data/brutus_data0/freeware.
- It includes multiple versions of matlab, FSL, SOLAREclipse, AFNI, Free Surfer, SPM and many others.
- You are welcome to install software in your home directory. However, if that software to be used by more than one user, please ask Sung to install in the public space.
- Data Back Up
- Please note that regular backup of user home space is user's responsibility.
- CBIR only does monthly backups of the home directory.
- Back up of project scratch space is responsibility of individual users. Please see Sung Yu on the available options.