Getting Started with Bridges-2 Cluster - ISC24 SCC

Owned by Ophir Maor
Last updated: Dec 06, 2023
10 min read

 

Follow the following procedures to setup an account for PSC Bridges-2

 

Setting up the account

 

Start by creating one account per team on the Access portal:

https://identity.access-ci.org/new-user - Two way authentication is needed via DUO mobile app

Login here: https://cilogon.org/

 

Later on, we will need your team username to be able to apply the allocation to the team.

 

Check your username here: https://allocations.access-ci.org/profile

You will see the “Pittsburgh Supercomputing Center” username.

 

To reset the password, see here: https://apr.psc.edu/enter_info

And follow the steps.

 

Login to Bridges2

 

Login using your psc username and password:

bash-4.1$ ssh maor@bridges2.psc.edu maor@bridges2.psc.edu's password: Warning: No xauth data; using fake authentication data for X11 forwarding. ********************************* W A R N I N G ******************************** You have connected to br014.ib.bridges2.psc.edu, a login node of Bridges 2. This computing resource is the property of the Pittsburgh Supercomputing Center. It is for authorized use only. By using this system, all users acknowledge notice of, and agree to comply with, PSC polices including the Resource Use Policy, available at http://www.psc.edu/index.php/policies. Unauthorized or improper use of this system may result in administrative disciplinary action, civil charges/criminal penalties, and/or other sanctions as set forth in PSC policies. By continuing to use this system you indicate your awareness of and consent to these terms and conditions of use. LOG OFF IMMEDIATELY if you do not agree to the conditions stated in this warning ********************************* W A R N I N G ******************************** For documentation on Bridges 2, please see www.psc.edu/resources/bridges-2/user-guide/ Please contact help@psc.edu with any comments/concerns. Last login: Mon Nov 15 19:58:05 2021 from 149.165.168.51 Projects --------------------------------------------------------------------------------------------------------------------------------------- Project: bio220064p [Default charging account] PI: Ophir Maor Regular Memory 999,979 SU remain of 1,000,000 SU Active: Yes Ocean /ocean/projects/bio220064p 16k used of 4.883T

 

Get the project ID:

$ projects | grep ID Charge ID: cis230088p Charge ID: cis230088p Charge ID: cis230088p

 

Use slurm to allocate a node

[maor@bridges2-login014 ~]$ sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST RM* up infinite 1 down* r059 RM* up infinite 1 drng r384 RM* up infinite 1 drain r191 RM* up infinite 2 resv r[099,174] RM* up infinite 34 mix r[053-055,057-058,063,068,071,073-075,077,080-081,084-085,090,092,094,109,126-127,129,135,137,143,151,157,161,172-173,175,190,282] RM* up infinite 393 alloc r[050-052,056,060-062,064-067,069-070,072,076,078-079,082-083,086-089,091,093,095-098,100-108,110-125,128,130-134,136,138-142,144-150,152-156,158-160,162-171,176-189,192-246,248-251,253-272,274-281,283-360,362-376,378-383,386-446,448-488] RM* up infinite 2 idle r[247,377] RM* up infinite 5 down r[252,273,361,385,447] RM-512 up infinite 16 alloc l[001-016] RM-shared up infinite 1 down* r059 RM-shared up infinite 2 resv r[099,174] RM-shared up infinite 70 mix r[005-008,010-013,018,020-025,027-029,031-037,039-049,053-055,057-058,063,068,071,073-075,077,080-081,084-085,090,092,094,109,126-127,129,135,137,143,151,157,161,172-173,175,190,282] RM-shared up infinite 158 alloc r[009,014-017,019,026,030,038,050-052,056,060-062,064-067,069-070,072,076,078-079,082-083,086-089,091,093,095-098,100-108,110-125,128,130-134,136,138-142,144-150,152-156,158-160,162-171,176,180-181,192-196,199-204,208,223,227-229,245-246,250,257-258,260,263-264,285,289-291,293,295,301,310,319,323-325,328-330,332-333,336-337,342,344-345,347,353-354,356-360,367] RM-small up infinite 2 mix r[001-002] RM-small up infinite 2 idle r[003-004] GPU up infinite 18 mix v[003-006,008-012,015-016,018,025,027-030,033] GPU up infinite 13 alloc v[007,013-014,017,019-024,026,031-032] GPU up infinite 1 idle v034 GPU-shared up infinite 18 mix v[003-006,008-012,015-016,018,025,027-030,033] GPU-shared up infinite 13 alloc v[007,013-014,017,019-024,026,031-032] GPU-small up infinite 1 alloc v002 GPU-small up infinite 1 idle v001 EM up infinite 1 mix e001 EM up infinite 3 alloc e[002-004] BatComputer up infinite 1 mix dv001 BatComputer up infinite 3 alloc dv[002-004]

 

7. Allocate a node.

 

Note: For ISC24 use only RM partition with up to 4 nodes allocation, or the GPU partition with single GPU allocation.

Here is an example to allocate single node. use -A with the project ID

Installing and using HPC-X (Example)

 

  1. Download the above file.

  2. tar xjfp hpcx-2.13.1.tbz

  3. module use <path to hpcx-2.13.1>/modulefiles

  4. module load hpcx

  5. which mpirun

 

Help

We will have one account per team (the team captain will manage it). All teams should refer to Bridges-2 User Guide when running on Bridges-2 clusters. For any connectivity questions, email help@psc.edu .