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cluster:142 [2015/08/03 18:36] hmeij |
cluster:142 [2015/09/11 19:23] hmeij |
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===== Scratch Spaces ===== | ===== Scratch Spaces ===== | ||
- | We have different ... blah, blah, to come | + | We have different |
* **/ | * **/ | ||
- | * local to each node, off different sizes | + | * 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 | + | * 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-n45, all are done (10sep15) | ||
- | 48 TB of local scratch space will be available in 6 TB chunks on the nodes in the queue '' | + | 48 TB of local scratch space will be made available in 6 TB chunks on the nodes in the queue '' |
+ | |||
+ | **Note: Everybody is welcome to store content in ''/ | ||
+ | |||
+ | |||
+ | 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... | ||
< | < | ||
+ | |||
#!/bin/bash | #!/bin/bash | ||
# submit like so: bsub < run.forked | # submit like so: bsub < run.forked | ||
- | # if writing large checkpoint files uncommnet | + | # if writing large checkpoint files uncomment |
#ionice -c 2 -n 7 -p $$ | #ionice -c 2 -n 7 -p $$ | ||
#ionice -p $$ | #ionice -p $$ | ||
- | |||
- | rm -rf err* out* output.* | ||
#BSUB -q mw256fd | #BSUB -q mw256fd | ||
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MYSANSCRATCH=/ | MYSANSCRATCH=/ | ||
MYLOCALSCRATCH=/ | MYLOCALSCRATCH=/ | ||
- | export MYSANSCRATCH MYLOCALSCRATCH | + | MYLOCALSCRATCH5TB=/ |
+ | export MYSANSCRATCH MYLOCALSCRATCH | ||
- | # cd to remote working | + | # cd to remote working |
- | cd $MYSANSCRATCH | + | cd $MYLOCALSCRATCH5TB |
pwd | pwd | ||
# environment | # environment | ||
- | export GAUSS_SCRDIR=" | + | export GAUSS_SCRDIR=" |
export g09root="/ | export g09root="/ | ||
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#. $gdvroot/ | #. $gdvroot/ | ||
- | # copy input data to fast disk | + | # stage input data to localscratch5tb |
cp ~/ | cp ~/ | ||
touch gaussian.log | touch gaussian.log | ||
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#gdv < gaussian.com > gaussian.log | #gdv < gaussian.com > gaussian.log | ||
- | # save results back to homedir | + | # save results back to homedir |
cp gaussian.log ~/ | cp gaussian.log ~/ | ||
+ | |||
</ | </ | ||