EBI Cluster Guide

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Cluster Specifications

Compute Nodes

  • 24 Nodes
  • Dell Poweredge 1950 Servers
  • 8 cores 2.8 GHz Intel CPUs per Node
  • 16 Gigabytes of RAM per Node
  • 200GB of Temp space on /state/partition1
  • 1TB of temp space on /state/partition2

Storage

NO DATA is backed up on this system

  • 40TB Raid array
    • Shared using NFS
    • Located at /home/scratch
  • 7TB Raid array
    • Shared with NFS
    • Located at /home/
    • Contains user home directories


How To Get Cluster Access

EBI Affiliated

  • If you are a member of EBI or an EBI affiliate you may send an email to help@igb.illinois.edu requesting access to the cluster. We will forward your email to get you access.
  • You must also request your professor or theme leader to e-mail us at help@igb.uiuc.edu approving your access, unless you are a fellow.

Cluster Rules

  • Running jobs on the head node are strictly prohibited. Running jobs on the head node could cause the entire cluster to crash and affect everyone's jobs on the cluster. Any program found to be running on the headnode will be stopped immediately and your account could be locked. You can start an interactive session to login to a node to manual run programs.
  • Installing Software Please email help@igb.illinois.edu for any software requests. Compiled software will be installed in /home/apps. If its a standard RedHat package (rpm), it will be installed in their default locations on the nodes.
  • Creating or Moving over Programs: Programs you create or move to the cluster should be first tested by you outside the cluster for stability. Once your program is stable, then it can be moved over to the cluster for use. Unstable programs that cause problems with the cluster can result in your account being locked.  Programs should only be added by CNRG personnel and not compiled in your home directory.
  • Reserving Memory: TORQUE allows the user to specify the amount of memory they want their program to use.. If your job tries to use more memory than you have reserved, the job will automatically get shutdown. Make sure to specify the correct amount of memory.
  • Reserving Nodes and Processors: For each job, you must reserve the correct number of nodes and processors. By default you are reserved 1 processor on 1 node. If you are running a multiple processor job or a MPI job you need to reserve the appropriate amount. If you do not reserve the correct amount, the cluster will shutdown your job. Failure to comply with this policy will result in your account being locked.

How To Log Into The Cluster

  • You will need to use an SSH client to connect.

On Windows

PuTTYbiocluster.PNG

  • Hit Open and login using your IGB account credentials.

On Mac OS X

  • Simply open the terminal under Go >> Utilities >> Terminal
  • Type in ssh username@ebi-cluster.igb.illinois.edu where username is your NetID.
  • Hit the Enter key and type in your IGB password.

How To Submit A Cluster Job

Create a Job Script

  • You must first create a TORQUE job script file in order to tell TORQUE how and what to execute on the nodes.
  • Type the following into a text editor and save the file test.sh ( Linux text editing )
#!/bin/bash
#PBS -j oe

sleep 20
echo "Test Script" 
  • Change the permissionson on the script to allow execution.
chmod 775 test.sh
  • You just created a simple PBS TORQUE Job Script.
  • Line by line explanation
    • #!/bin/bash - tells linux this is a bash program and it should use a bash interpreter to execute it.
    • #PBS - are PBS parameters, for explanations of these please scroll down to PBS Parameters Explanations section.
    • sleep 20 - Sleep 20 seconds (only used to simulate processing time for this example)
    • echo "Test Script" - Output some text to the screen when job completes ( simulate output for this example)
  • For example if you would like to run a blast job you may simply replace the last two line with the following
module load blast
blastall -p blastn -d nt -i input.fasta -e 10 -o output.result -v 10 -b 5 -a 5
  • Note: the module commands are explained under the Environment Modules section.

TORQUE PBS Parameters Explanations:

These are just a few parameter options, for more type man qsub while logged into the cluster.

Command Description
#PBS -S /bin/bash The program will be using bash for its interpreter. Required.
#PBS -q QUEUENAME Run the job on a specific queue. This defaults to the "default" queue
#PBS -d /tmp/working_dir Run the script from the /tmp/working_dir directory. This defaults to your home directory (/home/a-m/username, /home/n-z/username).
#PBS -N ExampleJobName Name of the job will be ExampleJobName
#PBS -j oe Join the standard out and standard error streams together into one file. This file will be created in the working directory and will be named in this case test.sh.o# where # is the job number assigned by Torque.
#PBS -M username@illinois.edu Send an e-mail to username@igb.illinois.edu to receive job information.
#PBS -m abe Send email when job aborts, job begins, and job ends
#PBS -l Reserves resources such as number of processors, memory, wallclock.
#PBS -l nodes=X:ppn=Y Reserve X number of nodes with Y processors per node.
#PBS -l mem=XGB Reserve X gigabytes of RAM for the job.
#PBS -l nodes=1:ppn=5,mem=4GB To combine multiple resources, separate them with a comma

Create a Job Array Script

Making a new copy of the script and then submitting each one for every input data file is time consuming. An alternative is to make a job array using the -t option in your submission script. The -t option allows many copies of the same script to be queued all at once. You can use the PBS_ARRAYID to differentiate between the different jobs in the array. A brief example on how to do this is available at Job Array Example

Submit Serial Job

  • To submit the serial job you will use the qsub program. For example to submit test.sh TORQUE Job you would type:
qsub test.sh
  • You may also define the TORQUE parameters from the section above as qsub parameters instead of defining them in the script file. Example:
qsub -j oe -S /bin/bash test.sh

Submit Parallel Job

  • To submit the parallel job you will use the qsub program.
  • For more information please refer to this page Submitting TORQUE Jobs

Start An Interactive Login Session On A Compute Node

  • Use interactive qsub if you would like to run a job interactively such as running a quick perl script or run a quick test interactively on your data.
qsub -I
  • This will automatically reserve you a slot on one of the compute nodes and will start a terminal session on it.
  • Closing your terminal window will also kill your processes running in your interactive qsub session, therefor it's better to submit large jobs via non-interactive qsub.
  • To run an application with a user interface run
qsub -I -X
  • For this to work you will need to setup xserver on your computer Xserver Setup

View/Delete Submitted Jobs

Viewing Job Status

  • To get a simple view of your current running jobs you may type:
qstat
  • This command brings up a list of your current running jobs.
  • The first number represents the job's ID number.
  • Jobs may have different status flags:
    • R = job is currently running
    • W = job is waiting to be submitted (this may take a few seconds even when there are slots available so be patient)
    • Eqw = There was an error running the job.
    • S = Job is suspended (job overused the resources subscribed to it in the qsub command)
  • For more detailed view type:
 qstat -f 
  • This will return a list of all nodes, their slot availability, and your current jobs.

List Queues

  • Simple view
qstat -q
  • Advance view (Ex: where queue name is budget)
    • max_user_queuable - max number of jobs allowed to be in the queue
    • max_user_run - max number of jobs the queue will run at same time
qstat -Qf budget 

List All Jobs on Cluster With Nodes

qstat -a -n

Deleting Jobs

  • Note: You can only delete jobs which are owned by you.
  • To delete a job by job-ID number:
  • You will need to use qdel, for example to delete a job with ID number 5523 you would type:
qdel 5523
  • Delete all of your jobs
qdel all

Troubleshooting job errors

  • To view job errors in case job status shows Eqw or any other error in the status column use qstat -j, for example if job # 23451 failed you would type:
qstat -j 23451

View Job Details

  • To view job details, you can use the qstat -f JOB_NUMBER, checkjob JOBNUMBER, tracejob JOBNUMBER to monitor your job.
qstat -f 12345
checkjob 12345
tracejob 12345

Applications

  • All Applications are installed in
/home/apps/

Environment Modules

  • To automatically load the proper environment for some programs you may use the module command
  • To list all available environments run module avail (please e-mail help@igb.illinois.edu for special requests):
bash-4.1$ module avail


  • To load a particular environment for example qiime/1.5.0 simply run this command:
module load qiime/1/5.0
  • If you would like to simply load the latest version, run the the command without the /1.50 (version number):
module load qiime
  • To view which environments you have loaded simply run module list:
bash-4.1$ module list
Currently Loaded Modulefiles:
  1) qiime
  • When submitting a job using a qsub script you will have to add the module load qiime/1.5.0 line before running qiime in the script.
  • To unload a module simply run module unload:
module unload qiime
  • Unload all modules
module purge

Transferring data files

Transferring from personal machine

  • In order to transfer files to the cluster from a personal Desktop/Laptop you may use WinSCP the same way you would use it to transfer files to the File Server.

Transferring from file server (Very Fast)

  • To transfer files to the cluster form the file-server you will need to first setup Xserver on your machine. Please follow this guide to do so Xserver Setup.
  • Once Xserver is setup on your personal machine you will need to SSH into the cluster using putty as mentioned above.
  • Then start gFTP by typing in the terminal:
gftp
  • This will launch a graphical interface for gFTP on your computer, it should look like this

Gftp ui.png

  • Enter the following into the gFTP user interface:
    • Host: file-server.igb.illinois.edu
    • Port: leave this box blank
    • User: Your IGB username
    • Pass: Your IGB password
    • Select SSH2 from the drop down menu
  • Hit enter and you should now be connected to the file-server from the cluster.
  • You may now select files and folders from your home directories and click the arrows pointing in each direction to transfer files both ways.
  • Please move files back to the file-server or your personal machine once you are done working with them on the cluster in order to allow others to use the space on the cluster for their jobs.
  • Note: You may also use the standard command line tool "sftp" to transfer files if you do not want to use gFTP.


References