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=== Access ===

==== Login to the headnode ====

You can submit jobs to the cluster from the head node: snapx.Stanford.EDU (sorry about the name, the head node will be renamed to ilh soon). First SSH to the headnode:

ssh your_cs_id@snapx.Stanford.EDU

Use your CSID username and password to login to the headnode.

==== Preparing your job ====

Preparing your job for the scheduler is as simple as adding a few comments to a script that runs your program. Here is an example:

#PBS -N my_job_name
#PBS -l nodes=1:ppn=1
#PBS -l walltime=01:10:00

echo "I am running on:"
sleep 20

The comment lines that start with the PBS keyword let you select different PBS options:

 * #PBS -N: lets you specify a friendly job name
 * #PBS -l nodes=1:ppn=1: specifies that I would like my job to run on a single node (nodes) and on a single core (ppn)
 * #PBS -l walltime=01:10:00: specifies the amount of real time I anticipate that my script will need to finish. Please note that the scheduler will terminate my script if it does not finish in time.

For a more comprehensive list of resources that you can slecify with #PBS -l see here: http://www.clusterresources.com/torquedocs/2.1jobsubmission.shtml. Note however, that there is currently only one queue without very many parameters set.

Make sure that your job uses data from:

 * Your CS home directory (whatever is under /afs/cs.stanford.edu/u/your_csid on hulk, rocky and snapx, please note that user home directories are not yet available under /u/your_csid on snapx)
 * Network mounted directories from rocky and hulk:
  * /dfs/hulk/0
  * /dfs/rocky/0

Here is an example of a bit more complex script to run an MPI job (copied from http://csc.cnsi.ucsb.edu/docs/running-jobs-torque):

#PBS -l nodes=2:ppn=4

# Make sure that we are in the same subdirectory as where the qsub command
# is issued.

# make a list of allocated nodes(cores)
cat $PBS_NODEFILE > nodes

# How many cores total do we have?
NO_OF_CORES=`cat $PBS_NODEFILE | egrep -v '^#'\|'^$' | wc -l | awk '{print $1}'`

# Just for kicks, see which nodes we got.

# Run the executable. *DO NOT PUT* a '&' at the end!!
mpirun -np $NO_OF_CORES -machinefile nodes ./pi3 >& log

==== Submitting your job ====

Now that your job is prepared you have to submit it to the resource manager. Use qsub to submit your jobs:

qsub myjob.sh

Make sure you run qsub from your CS home directory or from a network mounted filesystem (see above). Once the job is finished output data will wait for you in the same directory and there will be two additional files that end in e<job#> and o<job#>. These two are stderr and stdout, respectively.

==== Check the status of your job ====

You can check what is happening with your job with the qstat command:

qstat jobid

jobid is the number that the resource manager assigned to your job (the first number qsub will output after you successfully submit a job).

==== Other useful commands ====

 * qdel job_id: deletes your job
 * qstat -q: lists all queues
 * qstat -a: lists all jobs
 * qstat -au userid: lists all jobs submitted by userid
 * pbsnodes: list status of all the compute nodes

More coming soon...

Infolab cluster

Beta warning

If Google can keep things in Beta, why can't we? So.. beware... Things might break. Please join the mailing list and report any glitches that you come across.


  • 2 head nodes
  • 2 development nodes
  • 36 compute nodes:
    • 1152 cores
    • 2.25 TB RAM
  • Each node:
    • 2x AMD Opteron 6276 (Interlagos) @2.3GHz - 3.2GHz, 16 cores/CPU, AMD64, VT
    • 64 GB RAM
    • 2 TB local HDD

Mailing list

There is a mailing list for all those interested in what is currently happening with the cluster and the configuration of the cluster:


We decided that it is not good to have a split personality that is why we now have a set of nodes dedicated to the compute cluster and another set of nodes dedicated to a hadoop cluster.

  • Compute cluster:

    • TORQUE resource manager, MAUI job scheduler
    • Nodes: iln01-iln28
    • Submission node: ilhead1
  • Hadoop cluster
    • Apache Hadoop
    • Nodes: iln29-iln36
    • Submission node: iln29