Difference between revisions of "Janus Cheat Sheet"
From PHASTA Wiki
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== Debugging PHASTA == | == Debugging PHASTA == | ||
If you are getting hanging codes or crashing codes, compile with the pgi compilers and try the following flags on C, C++ and Fortran: | If you are getting hanging codes or crashing codes, compile with the pgi compilers and try the following flags on C, C++ and Fortran: | ||
| + | |||
-Ktrap=fp -Mbounds -Kieee | -Ktrap=fp -Mbounds -Kieee | ||
| + | |||
Basically this will make your code crash where you get floating point exceptions, go out of bounds with arrays, or have ieee exceptions. Then if you type | Basically this will make your code crash where you get floating point exceptions, go out of bounds with arrays, or have ieee exceptions. Then if you type | ||
| + | |||
set catchDebugger=1 | set catchDebugger=1 | ||
| + | |||
and then | and then | ||
| + | |||
mpirun <exec> | mpirun <exec> | ||
| + | |||
it will launch debug windows which when you release them will stop at the point of your "foul" which REALLY helps. | it will launch debug windows which when you release them will stop at the point of your "foul" which REALLY helps. | ||
Revision as of 09:33, 6 August 2012
Login
ssh your_identikey_user@login.rc.colorado.edu [pin][token]
Running Jobs
Environment Setup:
use Torque use Moab use Git use .openmpi-1.4.3_intel-12.0_ib use Graphviz use Subversion
available nodes/cores:
pbsnodes -a showbf
Jobscript Template:
#!/bin/bash #PBS -N name_of_job #PBS -l walltime=0:20:00 #PBS -l nodes=1:ppn=12 . /curc/tools/utils/dkinit reuse .openmpi-1.4.3_intel-12.0_ib mpirun /path/to/executable
Submission:
qsub -q janus-debug jobscript.sh
Status
checkjob job_id showq -u $USER
Cancel:
qdel job_id
Large Memory, Interactive:
qsub -I -l nodes=1:ppn=32,walltime=1:00:00 -q himem
Interactive, for debugging (with totalviewer)
qsub -X -I -l nodes=1:ppn=12,walltime=1:00:00 -q janus-debug
Non Default allocation:
qsub -A UCBXXXXXXX job.sh
or in the job script:
#PBS -A UCBXXXXXXX
Debugging PHASTA
If you are getting hanging codes or crashing codes, compile with the pgi compilers and try the following flags on C, C++ and Fortran:
-Ktrap=fp -Mbounds -Kieee
Basically this will make your code crash where you get floating point exceptions, go out of bounds with arrays, or have ieee exceptions. Then if you type
set catchDebugger=1
and then
mpirun <exec>
it will launch debug windows which when you release them will stop at the point of your "foul" which REALLY helps.
Allocation Status
use Crc-allocations check_allocation.py use Moab showstats -u $USER
GridFTP
export MYPROXY_SERVER_DN=$MYPROXY_SERVER_DN"/C=US/O=Globus Consortium/OU=Globus Connect Service/CN=842a610a-4de7-11e1-9674-123138151443" myproxy-logon -T -b -s gridftp-00.rc.colorado.edu -v -l bema1643
globus-url-copy -v -r -cd -rst -rst-retries 0 -fast -vb -p 64 -stripe -tcp-bs 4M -g2 -ss '/C=US/O=Globus Consortium/OU=Globus Connect Service/CN=842a610a-4de7-11e1-9674-123138151443' gsiftp://gridftp-00.rc.colorado.edu/lustre/janus_scratch/bema1643/test.img sshftp://matthb2@jumpgate-phasta.colorado.edu/scratch/matthb2/foo/
globus-url-copy -v -r -cd -rst -rst-retries 0 -fast -vb -p 64 -stripe -tcp-bs 4M -g2 -ds '/C=US/O=Globus Consortium/OU=Globus Connect Service/CN=842a610a-4de7-11e1-9674-123138151443' sshftp://matthb2@jumpgate-phasta.colorado.edu/scratch/mrasquin/416M/ gsiftp://gridftp-00.rc.colorado.edu/lustre/janus_scratch/bema1643/
(note: -ss to specify that the source server has a non-standard DN, -ds for the destination)
Queues/Policy
https://www.rc.colorado.edu/crcdocs/queues https://www.rc.colorado.edu/policies/janus-jobs
