Genetic code

January 8th, 2008

The standard code, definining which amino acid to build from which combination of nucleic acids can be read from the image below.

Standard Codon Set
DNA triplet codes (Codonsonne/Codesonne)

Job Scheduling systems on HPCs

January 4th, 2008

LSF

The Load Sharing Facility system from IBM Platform can be used to run high performance compute ressources (HPC). It allows the scheduling of computational tasks (jobs) and load balancing of the machines that are part of the compute farm or cluster.

Basic tasks:

  • send jobs to farm:
    bsub -o output.txt script_name.pl -p parameter_1
  • specify ressource requirments:
    bsub -R 'model=IBMBC2800' job
    bsub 'select[mem>1000] rusage[mem=1000] job'

    limit access to database:
    select[ecs4<100] rusage[ecs4my3353=10:duration=10:decay=1]
  • kill jobs:
    bkill 0
    bkill jobid
  • example to kill specific jobs:
    bjobs | grep long | awk '{ print $1 }' | xargs bkill
    force-kill: bkill -r <ID>
  • Check jobs:
    bpeek jobid
  • Check farm machines:
    bhosts -w | more

Grid Engine

The Oracle Grid engine is a similar system based on an open-source software project supported by Sun.

Basic Usage:

  • Submit jobs
    qsub job,
    e.g. for shell scripts:
    qsub -cwd -e run.err -o run.out run_me.sh
    and for binaries:
    qsub -cwd -e run.err -o run.out -b y program.exe
    use -cwd to run job from current dir and write job results here use -V to pass in all environmental variables
  • kill jobs
    qdel jobid
    qdel -u user
  • Show host/job/queue status
    qhost
    qstat
    qstat -j jobid
    qstat -q

    or just: qstat | grep <username>
    more details:
    qstat -j jobid -explain E
  • queue details/available nodes:qstat -g c

Job status codes:

    qw - Queued and waiting
    w  - Job waiting
    s  - Job suspended
    t  - Job transferring and about to start
    r  - Job running
    h  - Job hold
    R  - Job restarted
    d  - Job has been marked for deletion
    Eqw - An error occurred with the job

More details: HowTo and Installation & User manual,notes.