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Submitting a Job on the Grid


Job Submissions

This tutorial will walk you through submitting an application job on the UCR Grid Portal. In this walkthrough, you will set up some sample data in your account on the Collaborative Cluster and use that data in a Q-Chem job.

In our example, Clark Kent, a UCR Researcher, intends to investigate the properties of the amino acid Glutamine. He will use the Qchem computational chemistry software to conduct part of his analysis.

1. Log in to Grid Portal
2. Set up your Input Data
  1. Click on the "Data Manager" tab.
  2. Click on the "HTML Data Manager" subtab.
  3. Select the cluster you want to manage your files on.
  4. You will be presented with a listing of the files in your home directory. We want to create a new input file, so click on "Create New File".
  5. You will be prompted to enter a new file name. Enter
    DFT_glutamine.in
    and click "Create". Copy and paste the following qchem input file into the text box.
    $comment
    glutamine PW91-PW91/6-311G Single point energy
    $end

    $molecule
    0 1
    6 -1.23973536 0.28356377 1.19837231
    6 -2.02294832 -0.05092617 -0.05720877
    6 -1.16425833 0.11331783 -1.30449280
    6 -0.98613533 1.59214578 -1.68594879
    1 -0.90978634 2.20609276 -0.75032580
    7 -2.17109328 2.08999376 -2.42195075
    1 -2.05935234 3.06007974 -2.62592882
    1 -2.29374737 1.58214382 -3.27314382
    6 0.30933064 1.74807278 -2.47708875
    8 0.46060067 1.82271377 -3.68385774
    8 1.43313271 1.82435183 -1.73186779
    1 2.19459659 1.92147581 -2.29499584
    1 -1.62354934 -0.45353122 -2.14053374
    1 -0.17217135 -0.35508116 -1.14187479
    1 -2.92050928 0.59796779 -0.12054282
    1 -2.40883034 -1.08879312 -0.00201583
    7 -0.37904635 -0.70950719 1.73604530
    1 -0.69979234 -1.64213117 1.61126131
    1 -0.04175234 -0.53298124 2.65596718
    8 -1.24084032 1.38053079 1.73902721
    $end

    $rem
    EXCHANGE PW91 GGA91 exchange
    CORRELATION PW91 GGA91 correlation
    BASIS 6-311G Basis Set
    $end

Data-Manager


Editor

3. Set up your Q-Chem Job
  1. Click on the "Job Services" tab.
  2. Click on the "Applications" sub-tab.
  3. On the left side of the screen, you will find a list of the applications available to you. Select Q-chem-Serial by clicking on it.
  4. You may use this screen to customize your job by entering command line arguments, a data file to be redirected as the standard input, and CPU and memory requirements.

    • For our example, we will be running a serial q-chem job on one host. Q-chem accepts the name of the input file as an argument, so you can enter DFT_glutamine.in, the file we just created, in the "arguments" field.
    • Since this is a serial Qchem job, it will only run on 1 processor. One gigabyte of memory should be enough for this program, and one hour of run time should suffice, so we can leave those settings at the default values.
    • To run on the general queue, a queue which includes 40 nodes on the collaborative cluster, enter gen.q in the "Queue Name" field.

  5. When you are done with this form, take a moment to decide if this job is one that you are likely to use many times. If it is, you can check the "Save as your application" box next to the submit button. Jobs you save this way will appear in the "User Applications" subtab under the "Job Services" tab. You can select jobs you have saved from that menu and this form will be pre-filled out with the details from the saved job!

  6. Click on the submit button to send your job into the cluster queue! If everything goes well, you will see a red message at the top of the page reading "Job Submission Successful".




Applications



Job-submission

4. Checking your job's status

Now that you have submitted your job, you will want to check on it's status and get it's output when it is done. We do this from the "Job Status" screen.

  1. Go to the "Job Services" tab.
  2. Go to the "Job Status" subtab.

On this screen you can see the status of all jobs you have submitted from the grid portal. When a job has completed, you can view it's output by clicking on the "stdout" link in the "Output" column. Similarly, you may view the error output from your job by clicking on the "Stderr" link in the Error column. To download a copy of the output or error files to your computer, click the green download arrow.



Job-Status

5. Getting output from your job
  1. Navigate to the job status screen; it is found in the "Job Services" tab and the "Job Status" subtab.
  2. For a completed job, you can view it's output by clicking on the "stdout" link in the "Output" column. Similarly, you may view any error output from your job by clicking on the "Stderr" link in the Error column.
  3. To download a copy of the output or error files to your local computer, click the green download arrow in the appropriate column.


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