Equipment¶
Scanner¶
The BSIC houses a Siemens 3-Tesla MAGNETOM Cima.X scanner featuring Gemini Gradients (whole-body performance of 200 mT/m at 200 T/m/s) with 64-channel head coils and 8- and 16-channel body coils.
Computational Cluster¶
BSIC operates a scientific computational resource to help BSIC 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 William Burroughs 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¶
How do I log in?
You will receive a welcome email from William Burroughs that will include temporary account password and your assigned login node. BSIC 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 BSIC 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 passwd to change your password on either of the login nodes.
How can I stay informed about system changes?
William Burroughs maintains a mailing list for all accounts created on the cluster.
Can I run jobs on the login nodes?
Please do not run any jobs on the login node. Running computationally intensive jobs on the login node can cause problems for other users. Processes causing problems on the login node may be terminated without notice.
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 BSIC is capped. Please see William Burroughs if you have a large dataset to transfer outside of the BSIC/UMB network.
Disk quota exceeded
Hard quota of 500GB is maintained for home directory. Please see William Burroughs if you need large temporal space for data analyses. Investigators are expected to maintain their own analysis data space. Please see William Burroughs 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.
Where can I find x program?
BSIC maintains a large library of scientific software in $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 William Burroughs to install in the public space.
Is there a backup of my data?
Please note that regular backup of user home space is user's responsibility. BSIC only does monthly backups of the home directory. Back up of project scratch space is responsibility of individual users. Please see William Burroughs on the available options.