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Accesing Galaxy

Accesing Galaxy. You have to SSH in to galaxy using ssh2 protocol, for Windows use PUTTY with ssh2 enabled for Unix/Linux please do bash-2.05$ssh -2 galaxy.ams.sunysb.edu bash-2.05$ssh2 galaxy.ams.sunysb.edu. The PATH environment variable. Please make sure that

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Accesing Galaxy

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  1. Accesing Galaxy You have to SSH in to galaxy using ssh2 protocol, for Windows use PUTTY with ssh2 enabled for Unix/Linux please do bash-2.05$ssh -2 galaxy.ams.sunysb.edu bash-2.05$ssh2 galaxy.ams.sunysb.edu

  2. The PATH environment variable Please make sure that "/usr/local/mpi/bin/" is in your path under bash-2.05$env | grep PATH you should get something like blah blah blah PATH=/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin PATH part is important, change it using declare -x PATH="/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/usr/local/mpi/bin" this way you have access to /usr/local/mpi/bin where all mpi executables reside.

  3. Compiling Jobs with mpi** You can compile the programs with mpicc, mpif77, mpiCC or mpif90. Do mpicc -o mpitest mpitest.c -lm or First mpicc -c mpitest.c Then mpicc -o mpitest mpitest.o Assuming your path is correct.

  4. Submitting Jobs To GalaxyPart 1 To run the mpi program please do execute "nodes" to make sure you have what to run on. bash-2.05$nodes avail alloc resv down nodes: 4 20 0 3 star: 0 0 0 0 nova: 0 0 0 0 vega: 0 0 0 0 orion: 0 0 0 0 aries: 0 0 0 0 p1000: 0 16 0 1 a1200: 4 4 0 2 This mans that all nodes are allocated.

  5. Submitting Jobs To GalaxyPart 2 however if you had something like: avail alloc resv down nodes: 6 18 0 3 star: 0 0 0 0 nova: 0 0 0 0 vega: 0 0 0 0 orion: 0 0 0 0 aries: 0 0 0 0 p1000: 4 12 0 1 a1200: 2 6 0 2 You can run a job on two nodes, you have 3 available p1000 to run the jobs on since one of them is down.

  6. Submitting Jobs To GalaxyPart 3 Thus do mpirun -pbs -p4ssport 12345 -np 3 mpitest

  7. OpenPbs Part 1 To check if your job is running please do "qstat" (hare you are interfacing with OpenPbs - the portable batch system which is an advanced parallel job scheduler and management tool you can do "man pbs" to find out more about it) Job id Name User Time Use S Queue ---------------- ---------------- ---------------- -------- - ----- 481.starzero ibkim895 ibkim 11:27:38 R starzero 482.starzero ibkim337 ibkim 11:37:52 etc.. What you see here are user jobs catalloged with Job id’s and User names, also the time that the jobs were executing on Galaxy.

  8. OpenPbs Part 2 the state of your job is S where - the job state: E - Job is exiting after having run. H - Job is held. Q - job is queued, eligable to run or routed. R - job is running. T - job is being moved to new location. W - job is waiting for its execution time (-a option) to be reached. S - (Unicos only) job is suspend. Taken from "man qstat"

  9. Galaxy Web Page Please check the galaxy web page for more information, http://galaxy.ams.sunysb.edu Please click on Portable Batch System (PBS) link to get to Job submission "how-to" and User Info You will find all this information usefull. This is the basic information you need to run jobs on Galaxy.

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