Introduction

An engineering modeling tool installed for Amir Shojaei at S3DF (documentation here)

Have license for 8 cores, may increase up to 36 cores in future.

Abaqus ships with its own MPI, but in principle can be overridden with system mpi.

Quick Start

  • ssh s3dflogin (or use 
  • ssh psana
  • export PATH=/sdf/group/lcls/eng/abaqus/commands:${PATH}
  • to get example: abq2022hf5 fetch -j c2 (fetches c2.inp from local examples)
  • for very quick test of functionality run interactively:
    • export ABA_BATCH_OVERRIDE=1 (we think we have to also "unset ABA_BATCH_OVERRIDE") when we are done with interactive mode
    • abq2022hf5 -j c2 -cpus 8 -inter
  • for production run in the slurm batch queue that has been allocated to LCLS:
    • abq2022hf5 -j c2 -cpus 8 -queue milano (can also add "-verbose 2" for more output (or without the "-", have to use "=")
    • remove memory limits: "abq2022hf5 -j c2 -cpus 8 -queue milano:mem0" (note: no delimiter after "mem" keyword)
  • help for submitting to slurm is in /sdf/group/lcls/eng/abaqus/2022/linux_a64/SMA/site/instructions.txt, for example (from this file):
    • abaqus -job myJob -cpus 6 -queue priority:fslocal:ppn1:em64t
    • sbatch's "account" option may be synonymous with "project" (seems to set an sbatch "wckey" option?)
  • To turn off mpi and use threads:
    • use option "mp_mode=THREADS"

Common Linux Commands/Utilities

You can search the web for more details about these commands.

  • "cd" changes directorires
  • "find" finds files
  • "vi" and "emacs" are common text editors
  • "winscp" can be used as a tool on a windows machine to transfer files between linux and your local machine
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