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(Created page with "== Introduction == * [http://www.nwchem-sw.org/index.php/Release61:NWChem_Documentation NWChem 6.1 User Documentation] == Considerations on Carbon == ; [http://www.nwchem-sw....") |
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== Considerations on Carbon == | == Considerations on Carbon == | ||
; [http://www.nwchem-sw.org/index.php/Release61:Top-level#SCRATCH_DIR_.2F_PERMANENT_DIR SCRATCH_DIR]: The *.nw input file is static, which makes it difficult to point to temporary directories that change from call to call. As a solution, I suggest to create a ''symbolic link'' in the job script prior to running NWChem. See <code>$NWCHEM_HOME/sample.job</code> for the full file. | ; [http://www.nwchem-sw.org/index.php/Release61:Top-level#SCRATCH_DIR_.2F_PERMANENT_DIR SCRATCH_DIR]: The *.nw input file is static, which makes it difficult to point to temporary directories that change from call to call. As a solution, I suggest to create a ''symbolic link'' in the job script prior to running NWChem, and use the name of the job script in your *.nw file. See <code>$NWCHEM_HOME/sample.job</code> for the full file. | ||
cat $NWCHEM_HOME/sample.job | |||
<source lang="bash"> | <source lang="bash"> | ||
#!/bin/bash | |||
#PBS ... | |||
# Avoid quota overruns. | # Avoid quota overruns. | ||
# (1) Add the line "scratch_dir ./scratch" to the input file. | # (1) Add the line "scratch_dir ./scratch" to the input file. | ||
| Line 23: | Line 27: | ||
# clean sandbox (won't be reached if job terminates for time) | # clean sandbox (won't be reached if job terminates for time) | ||
[[ $dir =~ $SANDBOX/* ]] && rm -r $dir | [[ $dir =~ $SANDBOX/* ]] && rm -r $dir | ||
</source> | |||
cat job.nw | |||
<source lang="bash"> | |||
title "foo structure" | |||
echo | |||
scratch_dir ./scratch | |||
geometry units angstroms | |||
... | |||
</source> | </source> | ||
; [http://www.nwchem-sw.org/index.php/Release61:Top-level#MEMORY MEMORY]: The default <code>memory</code> allocation is far smaller than useful on Carbon. Raise it using, e.g.: | ; [http://www.nwchem-sw.org/index.php/Release61:Top-level#MEMORY MEMORY]: The default <code>memory</code> allocation is far smaller than useful on Carbon. Raise it using, e.g.: | ||
memory total 3200 mb | memory total 3200 mb | ||
; | ; | ||
Revision as of 13:33, March 15, 2013
Introduction
Considerations on Carbon
- SCRATCH_DIR
- The *.nw input file is static, which makes it difficult to point to temporary directories that change from call to call. As a solution, I suggest to create a symbolic link in the job script prior to running NWChem, and use the name of the job script in your *.nw file. See
$NWCHEM_HOME/sample.jobfor the full file.
cat $NWCHEM_HOME/sample.job
#!/bin/bash
#PBS ...
# Avoid quota overruns.
# (1) Add the line "scratch_dir ./scratch" to the input file.
# (2) Provide this directory as local symlink; choose one of:
# - $SANDBOX: distributed scratch (not auto-cleaned, shared file system)
# - $TMPDIR node-local (auto-cleaned, slower)
dir=$SANDBOX/$PBS_JOBID
#dir=$TMPDIR
link=scratch
mkdir -p $dir
ln -snf $dir $link
mpirun -machinefile $PBS_NODEFILE -np $PBS_NP \
nwchem foo.nw
# clean sandbox (won't be reached if job terminates for time)
[[ $dir =~ $SANDBOX/* ]] && rm -r $dir
cat job.nw
title "foo structure"
echo
scratch_dir ./scratch
geometry units angstroms
...
- MEMORY
- The default
memoryallocation is far smaller than useful on Carbon. Raise it using, e.g.:
memory total 3200 mb