This is the tenth and final blog post in a series of articles about using the CCEB cluster. An overview of the series is available here. This post includes all the commands and references used throughout the series.
The commands presented below are sometimes generalizations of what was presented throughout the series.
# Change the working directory cd # List folders/files in a directory ls # Report working directory pwd # Move files or directories mv # Copy files or directories cp # Summons the manual man # Create a directory mkdir # Removes a directory rmdir # Removes files or a directory rm # Clear the screen/command board in Terminal clear # Uses all files with the pattern indicated in the command applied *pattern* # Creates an empty text file touch
ssh -X pennkey@scisub
# Screen the session while on the scisub host screen # Check how many screens you have open screen -ls # Resuming a screen screen -r
# Full bsub for an interactive session bsub -Is -q cceb_interactive -m "silver01" -n 8 -R "span[hosts=1] rusage[mem=5000]" -M 10000 "bash"
# R code to detect the number of cores requested by bsub # Recall parallel::detectCores() does not report the proper number Sys.getenv('LSB_DJOB_NUMPROC')
bsub -q cceb_normal \ -J "jobname[1-n]%5" \ -m "silver02" \ -R "rusage[mem=5000]" \ -M 10000 \ -n 8 \ -o /project/taki3/amv/cluster/normal_session_examples/example_output.txt \ Rscript /project/taki3/amv/cluster/normal_session_examples/normal_example.R
# Get the normal batch job index in R Sys.getenv("LSB_JOBINDEX")
# Show queues bqueues -u alval # List execution host information bhosts # Check a queues traffic bjobs -u all | grep cceb # List all your jobs (pending and running) bjobs # List all running jobs bjobs -r # List all pening jobs bjobs -p # List all suspended jobs bjobs -s # List summary information bjobs -sum # Estimate run time bjobs -WF # Check history of current jobs running bhist # Use the job name to peek bpeek -J "jobname" # Use the job ID to peek bpeek 2147852 # Suspend or pause a job bstop # Resume a job bresume # Kill a job bkill # Check live machine usage -- must be run on execution host (i.e. after bsub) top
bqueues - Display information about queues.
bhosts - Display information about execution hosts.
bjobs - Check job status .
bhist - Check job and task status history and summary.
bpeek - Peek into job to view output.
bstop - Suspend a job.
bresume - Resume a suspended job.
bkill - Terminate a job.