faq
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faq [2015/03/20 23:49] admin [How do I submit a Gaussian job?] |
faq [2015/03/27 14:05] trombach |
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| A Gaussian SLURM script for a serial (one node) job looks similar to the following tetrafluoromethane example: | A Gaussian SLURM script for a serial (one node) job looks similar to the following tetrafluoromethane example: | ||
| <file bash serial_gauss.slurm> | <file bash serial_gauss.slurm> | ||
| - | #!/bin/bash | + | #!/bin/bash |
| - | ################################## | + | ################################## |
| - | #SBATCH -J CF4 | + | #SBATCH -J CF4 |
| - | #SBATCH -p sgi | + | #SBATCH -p sgi |
| - | #SBATCH -t 0-0:15 | + | #SBATCH -t 0-0:15 |
| - | #SBATCH -N 1 | + | #SBATCH -N 1 |
| - | #SBATCH -n 4 | + | #SBATCH -n 4 |
| - | #SBATCH --mem=4G | + | #SBATCH --mem=4G |
| - | #SBATCH -o CF4.out | + | #SBATCH -o CF4.out |
| - | #SBATCH --mail-type=begin | + | #SBATCH --mail-type=begin |
| - | #SBATCH --mail-type=end | + | #SBATCH --mail-type=end |
| - | #SBATCH --mail-user=you@massey.ac.nz | + | #SBATCH --mail-user=you@massey.ac.nz |
| - | ################################## | + | ################################## |
| - | module load gaussian/sgi | + | module load gaussian/sgi |
| - | source $g09root/g09/bsd/g09.profile | + | source $g09root/g09/bsd/g09.profile |
| | | ||
| - | export GAUSS_SCRDIR=$SCRATCH | + | export GAUSS_SCRDIR=$SCRATCH |
| - | WORKDIR=/home/$USER/<path/ to CF4.inp and CF4.out files> | + | WORKDIR=/home/$USER/<path/ to CF4.inp and CF4.out files> |
| | | ||
| - | echo "This job was submitted from $SLURM_SUBMIT_HOST," | + | echo "This job was submitted from $SLURM_SUBMIT_HOST," |
| - | echo "from the directory $SLURM_SUBMIT_DIR," | + | echo "from the directory $SLURM_SUBMIT_DIR," |
| - | echo "Running on node $HOSTNAME." | + | echo "Running on node $HOSTNAME." |
| - | echo "The local scratch is on $SCRATCH." | + | echo "The local scratch is on $SCRATCH." |
| - | echo START: `date` | + | echo START: `date` |
| - | g09 < $WORKDIR/CF4.inp | + | g09 < $WORKDIR/CF4.inp |
| - | echo FINISH: `date` | + | echo FINISH: `date` |
| </file> | </file> | ||
| **NOTE:** For things you do very often, you can load modules and set environment variable calls within bash startup. For example, in the above script, one might opt to delete the two lines | **NOTE:** For things you do very often, you can load modules and set environment variable calls within bash startup. For example, in the above script, one might opt to delete the two lines | ||
| Line 65: | Line 65: | ||
| ====== III. INTEL Composer XE ====== | ====== III. INTEL Composer XE ====== | ||
| + | -------------------------------------- | ||
| + | ====== IV. VASP ====== | ||
| + | -------------------------------------- | ||
| + | |||
| + | ====== V. Orca ====== | ||
| + | |||
| + | Orca is distributed as binary files only. A sample script could look like this | ||
| + | |||
| + | <code bash> | ||
| + | #!/bin/bash | ||
| + | |||
| + | #SBATCH --job-name=Au12Ih | ||
| + | #SBATCH -t 999:00:00 | ||
| + | #SBATCH -N 1 | ||
| + | #SBATCH -n 4 | ||
| + | #SBATCH --mem=2G | ||
| + | #SBATCH --mail-type=END | ||
| + | #SBATCH --mail-type=FAIL | ||
| + | #SBATCH -o path-to-error-file/orca-%j | ||
| + | #SBATCH --mail-user=you@massey.ac.nz | ||
| + | #SBATCH -p sgi | ||
| + | |||
| + | echo This job was submitted from the computer: | ||
| + | echo $SLURM_SUBMIT_HOST | ||
| + | echo and the directory: | ||
| + | echo $SLURM_SUBMIT_DIR | ||
| + | echo | ||
| + | echo It is running on the compute node: | ||
| + | echo $SLURM_CLUSTER_NAME | ||
| + | echo | ||
| + | | ||
| + | module load intel/compiler/64/15.0/2015.1.133 | ||
| + | module load openmpi/gcc/64/1.8.1 | ||
| + | |||
| + | cd $SLURM_SUBMIT_DIR | ||
| + | echo Current directory: | ||
| + | pwd | ||
| + | echo | ||
| + | |||
| + | |||
| + | echo "---- The Job is executed at "Fri Mar 27 13:36:01 NZDT 2015" on "simurg" ----" | ||
| + | |||
| + | /cm/shared/apps/orca/orca /home/trombach/test-simurg/Au12/Au12Ih.in > /home/trombach/test-simurg/Au12/Au12Ih.out | ||
| + | |||
| + | echo "---- The Job has finished at "Fri Mar 27 13:36:01 NZDT 2015" ----" | ||
| + | </code> | ||
| + | Please note, that if you want run a parallel MPI job, you need to call the binary with its absolute path! | ||
faq.txt · Last modified: 2015/03/27 14:05 by trombach
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