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cluster:142 [2015/08/03 18:31] hmeij created |
cluster:142 [2015/09/03 14:49] hmeij [Scratch Spaces] |
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===== Scratch Spaces ===== | ===== Scratch Spaces ===== | ||
- | We have different ... blah, blah, to come | + | We have different |
+ | |||
+ | * **/ | ||
+ | * Local to each node, different sizes roughly around 50-80 GB | ||
+ | * Warning: on nodes n46-n59 there is no hard disk but a SataDOM (usb device pluggedt directly into sysem board, 16 GB in size, holds just the OS). Do not use / | ||
+ | |||
+ | * **/ | ||
+ | * Two 5 TB file systems mounted IpoIB using NFS | ||
+ | * One from greentail' | ||
+ | * One from sharptail' | ||
+ | |||
+ | |||
+ | * **/ | ||
+ | * 5 TB file system provided by local drives (3x2TB, Raid 0) on nodes in the '' | ||
+ | * The list of nodes done: n38 n41 n43 n44 n45 | ||
+ | |||
+ | 48 TB of local scratch space will be made available in 6 TB chunks on the nodes in the queue '' | ||
+ | |||
+ | **Note: Everybody is welcome | ||
+ | |||
+ | |||
+ | You need to change your working directory to the location the scheduler has made for you. Also save your output before the job terminates, the scheduler will remove that working directory. Here is the workflow... | ||
+ | |||
+ | < | ||
+ | |||
+ | # | ||
+ | # submit like so: bsub < run.forked | ||
+ | |||
+ | # if writing large checkpoint files uncomment next lines | ||
+ | #ionice -c 2 -n 7 -p $$ | ||
+ | #ionice -p $$ | ||
+ | |||
+ | #BSUB -q mw256fd | ||
+ | #BSUB -o out | ||
+ | #BSUB -e err | ||
+ | #BSUB -J test | ||
+ | |||
+ | # job slots: match inside gaussian.com | ||
+ | #BSUB -n 4 | ||
+ | # force all onto one host (shared code and data stack) | ||
+ | #BSUB -R " | ||
+ | |||
+ | # unique job scratch dirs | ||
+ | MYSANSCRATCH=/ | ||
+ | MYLOCALSCRATCH=/ | ||
+ | MYLOCALSCRATCH5TB=/ | ||
+ | export MYSANSCRATCH MYLOCALSCRATCH MYLOCALSCRATCH5TB | ||
+ | |||
+ | # cd to remote working directory | ||
+ | cd $MYLOCALSCRATCH5TB | ||
+ | pwd | ||
+ | |||
+ | # environment | ||
+ | export GAUSS_SCRDIR=" | ||
+ | |||
+ | export g09root="/ | ||
+ | . $g09root/ | ||
+ | |||
+ | #export gdvroot="/ | ||
+ | #. $gdvroot/ | ||
+ | |||
+ | # stage input data to localscratch5tb | ||
+ | cp ~/ | ||
+ | touch gaussian.log | ||
+ | |||
+ | # run plain vanilla | ||
+ | g09 < gaussian.com > gaussian.log | ||
+ | |||
+ | # run dev | ||
+ | #gdv < gaussian.com > gaussian.log | ||
+ | |||
+ | # save results back to homedir !!! | ||
+ | cp gaussian.log ~/ | ||
+ | |||
+ | </ | ||