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Frequently Asked Questions

How do I get an account

Go to user accounts section and provide needed information via e-mail to hpchelp@csi.cuny.edu.

How do I login

Use a ssh client to connect into the desired system.


Details on how to login can be found at: http://wiki.csi.cuny.edu/cunyhpc/index.php/Loggingin

Is there a User Manual

Yes, the User Manual can be download on the following webpage: http://www.csi.cuny.edu/cunyhpc/Documentation_and_Help.html
or direct link User Manual Link

I am having problems connecting to one of the systems

  • Are you using the correct username?
  • Are you typing the correct password? (Remember, passwords are case-sensitive.)
  • Which system are you trying to connect to?
    • Only the Chizen and Karle are directly accessible from outside of the College of Staten Island network; you will need to connect to Chizen and then ssh into the desired system
    • Do you have access to the system you are trying to connect to? Be sure that you are typing the full hostname: hostname@csi.cuny.edu

How do I change my password

To change your password, use the following unix command:


The new password must conform to the CUNY password policy, which requires all fours (4) character classes and be at least eight (8) characters long: (1) include at least one capitalized letter, (2) one lowercase latter, (3) one numerical character, and (4) one of the following special characters:

 ! @ # $ % & * = + ) ( 

Passwords are good for 92 days. You will receive a notice two weeks before the end of the 92 day period, requesting that you change your passwords. If you do not change your passwords, your accounts will be locked and the password will need to be reset.

  • Note that users are responsible for protecting their passwords. Passwords are not to be shared.

I forgot my password, how can I reset it

If a user forgets their password they must use our reset form(see user account section). For emergencies please send a password reset request to the Helpline at HPCHelp@csi.cuny.edu.
Be sure to include your username, and a telephone number where you can be reached with the new temporary password.

What is my disk quota

The default disk quota for all users is 50GB or 10000 files on /global/u.
Class accounts have a limited storage of 10GB.
Faculty/research PIs can request additional disk space allocations by sending an email to the helpline at HPCHelp@csi.cuny.edu.

Users must maintain and cleanup their disk storage to ensure they do not exceed their limit.

How do I transfer files

Files can be transferred through the following methods: (1) SFTP/SCP, (2) GlobusOnline, (3) iRods.

  1. SFTP and SCP commands and details can be through the unix manual or through a simple internet search. The following command can be used to transfer directories between 2 machines in HPC domain. (and their respective subdirectories).
    scp -r /location/of/source_file username@hostname:/location/of/endpoint
    scp -r username@hostname:/location/of/source_file username@hostname:/location/of/endpoint
    For transfer of files use cea data transfer node (see section transfer of files). KARLE is accessible externally (from outside the CSI campus) and can be directly connected to.
    *Note: ANDY and KARLE systems share a /home directory; if you intend to use ANDY or KARLE for your jobs, you can directly transfer there (through KARLE).

  2. To use GlobusOnline, create a account (https://www.globus.org/) and set a start/end point to:
    the other end/start point can be designated to your local machine.

  3. iRods file transfer is only available to iRods accounts/groups.

Details on file transfers can be found at: http://wiki.csi.cuny.edu/cunyhpc/index.php/File_transfers

I can't find the application I am looking for

The CUNY HPC Center uses modules to simpify the use of applications. After logging into the desired system, the following command will print out a list of available modules (applications):

module avail

To load a module use:

module load <module_name>

Additional details on modules can be found at: http://wiki.csi.cuny.edu/cunyhpc/index.php/Modules
Details on specific application can be found at: http://wiki.csi.cuny.edu/cunyhpc/index.php/Applications_Environment

How do I write a submission script or compile codes

Example submission scripts can be found at: http://wiki.csi.cuny.edu/cunyhpc/index.php/Applications_Environment
Details on Program Compilation and Compilers: http://wiki.csi.cuny.edu/cunyhpc/index.php/Programcompilation

  • Note, jobs are NEVER to be run on the head node; jobs found running on the head node will be killed and the user account suspended or disabled.

How do I submit a job

Jobs are submitted to the systems with the following unix command:

sbatch submitscript.job

To view jobs running or in queue, use:


How to check if my job is running

To check if your job is running, log into the system where the job was submitted and use:

squeue -u username

the following represents the status of the job:

E - Job is Exiting after having run
H - Job is Held. A job is put into a held state by the server or by a user or administrator. A job stays in a held state until it is released by a user or administrator.
Q - Job is Queued, eligible to run or be routed.
R - Jobs is running
S - Job is Suspended by server. A job is put into the suspended state when a higher priority job needs the resources.
U - Job is User-suspended. A job is put into the user-suspended state workstation occupied by a user.
P - Job is Waiting for its requested execution time to be reached or job specified a staging request which failed for some reason.

How can I delete a job

To delete or kill a job use the following unix command:

scancel jobid

What is /scratch space

/scratch space is temporary system spaced used by jobs queued for or in execution. Output(s) from jobs may temporarily be located in /scratch.
/scratch space is not backed up; if users need to save any files from /scratch they must copy them to long-term storage, ie: their /global/u/username/home directory.

Scratch space is permanently deleted when: (1) usage reaches 70% of available space, or (2) file residence on scratch exceeds two weeks, whichever occurs first.

Additional details can be found at: http://wiki.csi.cuny.edu/cunyhpc/index.php/Dsms

How can I get one-on-one help

The best way to reach the HPC is by sending a detailed email to our helpline at HPCHelp@csi.cuny.edu.
Be sure to send a detailed message, including username, a contact number, hostname, filename/directory, job_id, pertaining to the question you have.

The HPC Center provides Helpdesk hours at the Graduate Center and College of Staten Island (by appointment).

I need a specific software installed

The CUNY HPC will do the best to try and satisfy reasonable software requests. Software requests must be submitted by Supervisors and/or PI's only.
Users can install applications in their own home directory as needed.