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Introduction to Using Picotte

Overview

Picotte is a Drexel URCF's High Performance Computing (HPC) cluster1. A "cluster" is a group of servers (computers).

Nodes

In a cluster, servers are called "nodes". Picotte has:

  • One management node
  • One login node (this is the computer you connect to use the system)
  • 88 compute nodes:
    • 74 standard compute nodes in the def partition
    • 2 big memory compute nodes in the bm partition
    • 12 GPU compute nodes in the gpu partition

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Using Picotte

The only interface to Picotte is the command line in a terminal program. For an introduction to using the command line, try these tutorials:

Although these links all say "Linux", the content more-or-less applies to macOS as well. You can even get a Linux command line on Windows using Windows Subsystem for Linux.

For other resources, see: List of Online Resources

terminal login session.png

Visual Studio Code can be used for a more convenient interface, with some familiar graphical elements. See:

Usage Pattern

  1. SSH into picottelogin.urcf.drexel.edu (a.k.a. picotte001).
  2. Create your program (or Python script, or R script, or Stata script, or Matlab script, etc.) or use one already installed on Picotte.
  3. Create a job script (or use one previously uploaded).
  4. Submit the job script with sbatch.
    1. Jobs are not guaranteed to start within any specific time period. Jobs start running when there are resources available, and when the job's position in the pending list (queue) allows.
  5. Wait for job to complete. Use squeue to view status during run.
    1. Optionally, in the previous steps, set the “--mail-type” option in the job script to send email.
  6. View the output.
    1. Optionally, check usage statistics with sacct.

In short:

while project not complete
    write job_script
    sbatch job_script
    while curious
        squeue and/or scontrol
    sacct
    sreport

Search this wiki for the commands referred to above for details, and the official Slurm documentation.

See also: Monitoring#Job Monitoring on Picotte

Logging In

Use Drexel's Virtual Private Network (VPN) to be able to connect to Picotte.

Access is via SSH (Secure Shell), via a text-based terminal application. For an appropriate app for your PC, see:

IMPORTANT you must specify your URCF username to SSH, which is likely not the same as the username on your personal computer.

Changing Passwords

IMPORTANT Never ever give your password out to anyone. URCF sysadmins will not ask for it. Drexel IT will not ask for it. It is never needed by any IT staff for any reason.

We strongly recommend the use of a password-saving application or smartphone app. KeePassXC is one open source, free option. Microsoft Authenticator, currently used at Drexel, now has a password saving feature; but, it has one downside in that the font it uses does not distinguish between certain characters. There are multiple commercial password-saving apps and/or desktop applications.

URCF login info has no connection at all to Drexel Connect, except that we try to use the same username for convenience. Passwords must be at least 12 characters long, and have letters, numbers, and punctuation. The apg command line below will produce a legal password. After 3 failed attempts at login, your IP address will be blocked for 90 minutes. So, if your password does not work twice, double check it before trying a third time. Note that many characters look almost indistinguishable: O, 0, I, l, |, 1.

To change passwords, use the passwd command on the login node (picottelogin):

[juser@picotte001]$ passwd
Changing password for user juser.
Enter login(LDAP) password: ********
New password:
Retype new password:
LDAP password information changed for juser
passwd: all authentication tokens updated successfully.

NOTE If the "all authentication tokens updated successfully" message does not appear, your password was not successfully changed. Try again.

To generate a random pronounceable password, use the apg command:

[juser@picotte001]$ apg -M NCS -m 12
IvEcHigg1oj\
Bockog_Swaj1
<quettowCaw3
RuAk5odciOn/
Es9flelchof~
AtAm2Grolet+

or use the pwgen command (this generates 18 passwords of length 12):

[juser@picotte001]$ pwgen -c -n -y 12 18
Ohb8eec1uxi! gu7raipee!M4 ohohB@iiB8en phool@oe5aiX uy5wai[Mo1Qu EvuaYoo=Tee0
eop1Na}i;di2 ouFo1ue@n0ka vo2da/e4Kai6 veeHu0ae&qui aeQu6Yie}Nie eeF9mieQu\ah
wae=c&ee0Ta6 aiwaewae#S4u Ke0Coo=th}ie Gae`thuy4paf Uu9zie6cohm< Ieb3zah"ghai

NOTE If the "all authentication tokens updated successfully" message does not appear, your password was not successfully changed. Try again.

To generate a random pronounceable password, use the apg command: 

[juser@picotte001]$ apg -M NCS -m 12
IvEcHigg1oj\
Bockog_Swaj1
<quettowCaw3
RuAk5odciOn/
Es9flelchof~
AtAm2Grolet+

or use the pwgen command (this generates 18 passwords of length 12):

[juser@picotte001]$ pwgen -c -n -y 12 18
Ohb8eec1uxi! gu7raipee!M4 ohohB@iiB8en phool@oe5aiX uy5wai[Mo1Qu EvuaYoo=Tee0
eop1Na}i;di2 ouFo1ue@n0ka vo2da/e4Kai6 veeHu0ae&qui aeQu6Yie}Nie eeF9mieQu\ah
wae=c&ee0Ta6 aiwaewae#S4u Ke0Coo=th}ie Gae`thuy4paf Uu9zie6cohm< Ieb3zah"ghai

Multi-Factor Authentication

Please see: Multi-Factor Authentication

Getting Help/Technical Support

All issues, questions should be emailed to urcf-support@drexel.edu. This will add your issue to our tracking system, which ensures that all URCF administrators can see it and helps us get back to you in a timely manner.

Hardware

See: Picotte Hardware and Software

Job Scheduler and Resource Manager

Picotte uses the Slurm job scheduler.

Storage

  • Home directories -- there is a quota of 64 GiB on home directories:

/home/juser

  • Groups directories:

/ifs/groups/somethingGrp

  • BeeGFS fast parallel scratch:

/scratch  (symbolic link to /beegfs/scratch)

  • Node-local scratch:

/local/scratch

See also: Managing Your Group Directory

See Also

References

  1. The National Institute for Computational Sciences - What is HPC? ↩