UCVM on Compute Nodes

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Examples of running UCVM Query on compute nodes on Discovery

Running on dedicated compute nodes

Reasons for using compute nodes

  • login (headnode) is shared by all users.
  • compute nodes are dedicated to your job (while in use) and not shared
  • HPC Center's don't like programs running on headnode

Method 1 - Allocation Interactive Compute Nodes

Information To Prepare:

  • salloc - command that will reserve a dedicated compute node for your program.
    • Using dedicated worker nodes should let your program run faster than shared headnode
  • Number of tasks - typically 1 unless running MPI codes
  • Expected max duration of program : Format HH:MM:SS
    • Longer runtimes can
    • HPC systems typically have max runtime (e.g. 24:00:00 or 48:00:00).
    • Must make arrangements with HPC system operates for longer runtimes
  • allocation account - who's allocation will be charged for computing time
    • CARC offers "no-cost" allocations to University researchers that request them
    • Allocation will also include dedicated disk storage on CARC /project filesystem (e.g. /project/maechlin_162 /project/scec_608)
  • CARC Website

Example command for running program on discovery:

  • This reserves a single compute node, for 1 hour, using SCEC allocation
%salloc --ntasks=1 --time=1:00:00 --account=scec_608

Wait until systems assigns you the requested nodes:

  • Your command line prompt will show you when the nodes are assigned.
  • Run your program like you on the command line:
    • Example profile query
  • %ucvm_query -f /project/scec_608/<username>/ucvm_bin/conf/ucvm.conf -m cvmsi < rpv.in > rpv_cvmsi.out
  • %ucvm_query -f /project/maechlin_162/ucvm_bin/conf/ucvm.conf -m cvmsi < rpv.in > rpv_cvmsi.out

Method 2 - Submit job through queue using slurm batch script

This method is best for running large jobs that require many nodes

  • This will put your job into a system queue
  • HPC systems have their own rules for prioritizing jobs in their queues
    • Your queue priority is not necessarily the order submitted
    • short running jobs may have priority
    • jobs requiring few nodes may have priority

Submitting and monitoring your jobs require slurm commands

  • CARC Slurm Examples
  • Commonly used Slurm commands:
    • sbatch <job file name> - Submit job to queue
    • squeue -u <username> - check state of job in queue (waiting, running, completed)
    • Note slurm outputs log file (and possibly an error file) when job completes:
    • These often provide useful information about what happened with your job:


(base) [maechlin@discovery1 test_ucvm]$ sbatch ucvm_query.job
Submitted batch job 4219152
(base) [maechlin@discovery1 test_ucvm]$ squeue -u maechlin
           4219152      main ucvm_que maechlin  R       0:04      1 d05-10 

(base) [maechlin@discovery1 test_ucvm]$ ls -c1 *.out

Information to Prepare:

  • Number of tasks - typically 1 unless running MPI codes
  • Expected max duration of program : Format HH:MM:SS
  • Allocation to charge for computing time
  • Post this information into a slurm "job" file
    • Example in /home1/<username>/test_ucvm

Example Slurm Script:

#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=4GB
#SBATCH --time=0:30:00
#SBATCH --account=scec_608

source /project/maechlin_162/ucvm_bin/conf/ucvm_env.sh
ucvm_query -f /project/maechlin_162/ucvm_bin/conf/ucvm.conf -m cvmsi < rpv.in > rpv_cvmsi.out

Submit job using slurm comments

  • Locate example scripts in /home1/<username>/test_ucvm
    • Confirm the information in the slurm job file
    • %cat ucvm_query.job
  • %sbatch ucvm_query.job
  • %squeue -u maechlin

Check the output results:

  • %cat rpv_cvmsi.out

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