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lsf.txt
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lsf.txt
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# LSF
* Load Sharing Facility
* http:https://www.ebi.ac.uk/systems-srv/public-wiki/index.php/EBI_Good_Computing_Guide
* python inferface: https://pypi.python.org/pypi/bsub/0.3.3
# lsmake
* run make targets in parallel
* default: run on local host with 1 cpu
lsmake [makeoptions] [target] //
-j n // use n cpus
-c m // run m jobs per cpu
-R resources
-m hostname
-V // verbose, print hosts
-y // print summary at the end
# bsub
-R "rusage[mem=100]" -M 100 // request 100 MB
-R 'select[panfs_nobackup_research]' // select filesystem
-R "select[model=XeonE52670]" // cpu model
-n ncpu // minimum number of CPUs
-o file // append stdout to file
file%J // substitute %J by job id
-e file // append stderr to file
-oo, -ee // overwrite instead of append
-cwd dir // change to dir before executing command, logs in dir
-XF // X11 forwarding
-J job_name
# queues
-q research-rh6 // research queue (default)
-q production-rh6 // production jobs run with higher priority
-q dungeon // long runnning (>7 days) jobs
## Interactive job
bsub -Is bash // interactive tmux
bsub -Is tmux // interactive tmux
bsub -Ip ipython console // interactive console
bsub -Ip -XF ipython console // interactive job with X11 forwarding
# bjobs
bjobs -l ID // detailed information
bjobs -a // show all (including finished jobs)
# bkill
bkill 0 // kill all jobs
bkill -h /groupname 0 // kill all jobs of group
# Groups
bgadd -L 2 /groupname // group with 2 slots (max 2 jobs)
bgmod -L 10 /groupname // change slots
bjgroup -s /groupname // get info
bsub -g /groupname -o …. -e …. // submit using group
bkill -g /groupname 0 // kill jobs of group
# General infos
lsid // show current cluster
lsload -E // show current load
lshosts // show spec of nodes
bqueues // show all queues
# EBI file exchange
http:https://www.ebi.ac.uk/systems-srv/mp/file-exchange/
* 500 MB single files
* 2.5 GB total
* Alternative: EBI Google Drive
# EBI backups
* cd ~/.snapshot // invisible by ls -a