Difference between revisions of "HPC:Main Page"
| Line 19: | Line 19: | ||
Please also refer the man pages for bsub, bjobs, bkill, bhist, bqueues and bhosts. | Please also refer the man pages for bsub, bjobs, bkill, bhist, bqueues and bhosts. | ||
* <strong>bsub <job script></strong> : submit a job description file for execution | * <strong>bsub <job script></strong> : submit a job description file for execution | ||
| − | * <strong>bsub -Is bash</strong> : request a node for interactive use | + | * <strong>bsub -Is bash</strong> : request a node for interactive use |
* <strong>bjbos <jobid></strong> : show the status of a job | * <strong>bjbos <jobid></strong> : show the status of a job | ||
* <strong>bjbos -l <jobid></strong> : show more details about the job | * <strong>bjbos -l <jobid></strong> : show more details about the job | ||
| Line 25: | Line 25: | ||
* <strong>bjobs -u <user></strong> : display jobs queued or running for a single user | * <strong>bjobs -u <user></strong> : display jobs queued or running for a single user | ||
* <strong>bjobs -u all</strong> : to see all jobs | * <strong>bjobs -u all</strong> : to see all jobs | ||
| + | |||
| + | === Default Submission Constraints === | ||
| + | Please note that all submissions, both batch and interactive sessions, on the cluster <b>have a default memory limit of 3GB</b>. To request more memory for a given request, you can use one of the other queues that allow jobs to request and use more than 3GB. For example, to run a batch job that needs 5GB of RAM | ||
| + | <pre> | ||
| + | bsub -q plus <job_script> | ||
| + | </pre> | ||
| + | Where -q tells the LSF scheduler that you wish to use the "plus" queue which allows up to 6GB of RAM usage per slot. | ||
| + | |||
| + | To request more than 6GB of RAM use the "-q max_mem64" | ||
Revision as of 22:40, 18 November 2013
High Performance Computing at PennMedicine is supported by the Enterprise Research Applications (ERA) group within Penn Medicine Academic Computing Services (PMACS). Please send requests and report problems to Jason/Rikki/Anand
Contents
Accounts
For Account requests please contact Jason Hughes/Rikki Godshall or Anand Srinivasan
Other Pages
Connecting
Currently, secure shell (SSH) is the only supported method of connecting to the cluster. The login machine name is consign.pmacs.upenn.edu You should probably add "ServerKeepAliveInterval 60" to your SSH client's configuration.
After your account is created, you can connect using your PMACS credentials.
Guidelines
Don't run compute-intensive tasks on the cluster head node (consign). Use an interactive node (bsub -Is bash) instead. Please read the man page for 'bsub' and the documentation linked below.
Common Commands (IBM Platform LSF)
Please also refer the man pages for bsub, bjobs, bkill, bhist, bqueues and bhosts.
- bsub <job script> : submit a job description file for execution
- bsub -Is bash : request a node for interactive use
- bjbos <jobid> : show the status of a job
- bjbos -l <jobid> : show more details about the job
- bkill <jobid> : cancel a job
- bjobs -u <user> : display jobs queued or running for a single user
- bjobs -u all : to see all jobs
Default Submission Constraints
Please note that all submissions, both batch and interactive sessions, on the cluster have a default memory limit of 3GB. To request more memory for a given request, you can use one of the other queues that allow jobs to request and use more than 3GB. For example, to run a batch job that needs 5GB of RAM
bsub -q plus <job_script>
Where -q tells the LSF scheduler that you wish to use the "plus" queue which allows up to 6GB of RAM usage per slot.
To request more than 6GB of RAM use the "-q max_mem64"
