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blog:use_crc_clusters

Best (my) way to use CRC clusters

Software needed

If you are using a Mac, use the following similar software

  • Terminal (already installed) to replace PuTTY.
  • TextWrangler to replace Notepad++
  • FileZilla can be equally used on a Mac.

Upload files using FileZilla

See the screen below:

ftp.jpg

  • Host: newcell.crc.nd.edu
  • Username: your netid
  • Password: your password
  • Port: 22
  • Click Quickconnect
  • On the remote site (right panel), browse to the Private folder. Typically create folders and files under the Private folder.
  • On the Local site (left panel), choose the files/folders to upload and drag them to the remote site folder.

Use PuTTY

See the screen below:

putty.jpg

Steps

  • Host name: crcfe01.crc.nd.edu
  • Port: 22
  • Connection type: ssh
  • You might save the information by clicking “Save” button.
  • Click on Open button
  • In the new window
    • log in as: Your netid
    • password: your password (note that you will not say anything when typing. just finish typing your password).
    • Then you should login.

Most useful commands

  • pwd : print the current directory
  • ls : list the file and folders
    • ls -alh: list all the information
  • cd dir : change to a new directory (dir)
    • cd .. : go to last level of directory
    • cd : go the the initial directory you log in
  • mkdir dir : create a new directory called dir
  • rm file1 : delete a file
  • rm -r dir : delete a directory
  • nano : a text editor.
  • chmod g+s dirname: file created belongs to the group.
  • setfacl -d -m g::rwx mathfeud : set the permission for the group

Use Notepad++

  • Use the ftp of Notepad++ to edit files directly.
  • Show the ftp windows by the menu: Plugins – nppFTP – show NppFTP window (see the screen below)

notepadpp.jpg

  • On the ftp window, click the settings button and then Profile settings (see the screen below)

notepadpp3.jpg

  • Then in the new window
    • Click “Add new” on the bottom left corner
    • Give a name, e.g., CRC
    • Then input the information required
      • Hostname: newcell.crc.nd.edu
      • Connection type: SFTP
      • Port: 22
      • Username: your netid
      • Password: leave empty and check “Ask for password”
      • Initial remote directory: the output of pwd commend in putty.
      • close the window

notepadpp2.jpg

  • Connect to ftp. Click the connection button and choose CRC as shown below.
    • Input your password when asked.
    • Your files will be listed.
    • To edit a file, click on it and it will open in Notepad++.
    • You can also right click to create/delete a directory, create/delete a file.
    • After editing, save the file directly using Notepad++.

notepadpp4.jpg

notepadpp5.jpg

Submit a job (SGE)

For more information, go to http://wiki.crc.nd.edu/wiki/index.php/Submitting_Batch/SGE_jobs

  • Log in using Putty
  • Create a new folder -test- within Putty using command
    mkdir test

    or do that within Notepad++ using the FTP plugin

  • Go the new folder test.
  • Create a test R file with the following content. You can use Notepad++. If using Putty, you can use the
    nano test.R

    The content of the R file is

    rnorm(100)
    • When using nano, Ctrl+O saves the file and Ctrl+X quits the edits.
  • Create another file (a submission file) called test.sh. In the file, include the following information (change the email address to yours)
    #!/bin/csh
    #$ -M xxxx@nd.edu
    #$ -m abe
    #$ -r y
    
    module load R
    
    R CMD BATCH test.R
    
  • To submit a job, in Putty (has to use Putty or other SSH client), type the command
    qsub test.sh

    Your job should be submitted now.

  • To check the status of your job, use
    qstat -u netid

    Your job should already finished by now, so you won't see anything for this simply example.

  • You can list all the files using command ls. You will see a file called test.Rout. Any error can also be found in it.
  • There will also be a file called test.sh.oxxxx (xxxx is a number). If no error, the size of it should be 0 typically.
  • If there is error in your job, you will see a file like test.sh.exxxx.
  • To use SAS, change module load R to module load sas. All available module can be found using module avail
  • If the test job works fine, you can start your regular jobs!

Submit an array job (SGE)

Sometimes, it might be convenient to split a big jobs to smaller ones. Preferably, each small job runs within its own folder. For example, one might have a sas job in the following folders

  • sasjob1
  • sasjob2
  • sasjob3
  • sasjob4

Within each folder, there is a sas file called runsas.sas. To submit such jobs, use the batch file with contents below

#!/bin/csh
#$ -M zzhang4@nd.edu
#$ -m abe
#$ -r y
#$ -t 1-4

module load sas
cd sasjob$SGE_TASK_ID

sas runsas.sas

If one prefers to put all small jobs in one folder like

  • sasjob1.sas
  • sasjob2.sas
  • sasjob3.sas
  • sasjob4.sas

Then the following script file can be used

#!/bin/csh
#$ -M zzhang4@nd.edu
#$ -m abe
#$ -r y
#$ -t 1-4

module load sas

sas sasjob$SGE_TASK_ID.sas

Debug

To reset the CRC environment, use

/opt/crc/usr/local/bin/crc_setup
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