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docs.it4i.cz
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bb15e088
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bb15e088
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8 months ago
by
Jan Siwiec
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Update gaussian.md
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8 months ago
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!!!warning
This page has not been updated yet. The page does not reflect the transition from PBS to Slurm.
# Gaussian
# Gaussian
## Introduction
## Introduction
...
@@ -90,7 +87,7 @@ Include the `%UseSSH` keyword, as well. This enables Linda to spawn parallel wor
...
@@ -90,7 +87,7 @@ Include the `%UseSSH` keyword, as well. This enables Linda to spawn parallel wor
```
```
The number and placement of Linda workers may be controlled by %LindaWorkers keyword or by
The number and placement of Linda workers may be controlled by %LindaWorkers keyword or by
GAUSS_WDEF environment variable. When running multi-node job via the
PBS
batch queue, loading
GAUSS_WDEF environment variable. When running multi-node job via the batch queue, loading
the Linda-enabled module
**automatically sets the `GAUSS_WDEF` variable**
to the correct node-list, using one worker per node.
the Linda-enabled module
**automatically sets the `GAUSS_WDEF` variable**
to the correct node-list, using one worker per node.
In combination with the %CPU keyword, this enables a full-scale multi-node execution.
In combination with the %CPU keyword, this enables a full-scale multi-node execution.
...
@@ -211,12 +208,13 @@ up automatically by the module load.
...
@@ -211,12 +208,13 @@ up automatically by the module load.
```
bash
```
bash
#!/bin/bash
#!/bin/bash
#PBS -A OPEN-0-0
#SBATCH --account=PROJECT_ID
#PBS -q qprod -N MyJobName
#SBATCH --partition=qcpu
#PBS -l select=4
#SBATCH --job-name=MY_JOB
#SBATCH --nodes=4
# change to workdir
# change to workdir
cd
$
PBS_O_WORK
DIR
cd
$
$
SLURM_SUBMIT_
DIR
# load Gaussian Linda enabled module and set up Linda
# load Gaussian Linda enabled module and set up Linda
ml Gaussian/16_rev_c0-binary-Linda
ml Gaussian/16_rev_c0-binary-Linda
...
@@ -225,7 +223,7 @@ ml Gaussian/16_rev_c0-binary-Linda
...
@@ -225,7 +223,7 @@ ml Gaussian/16_rev_c0-binary-Linda
GAUSS_SCRDIR
=
/scratch/work/project/open-0-0/GaussianJob
GAUSS_SCRDIR
=
/scratch/work/project/open-0-0/GaussianJob
mkdir
-p
$GAUSS_SCRDIR
mkdir
-p
$GAUSS_SCRDIR
cd
$GAUSS_SCRDIR
||
exit
cd
$GAUSS_SCRDIR
||
exit
cp
$
PBS_O_WORK
DIR
/
*
.
cp
$
SLURM_SUBMIT_
DIR
/
*
.
# run Gaussian calculation
# run Gaussian calculation
# g16 < input.inp > output.out
# g16 < input.inp > output.out
...
@@ -252,7 +250,7 @@ A 109.471221
...
@@ -252,7 +250,7 @@ A 109.471221
EOF
EOF
# copy output files to home
# copy output files to home
cp
*
$
PBS_O_WORK
DIR
/.
&&
cd
../
cp
*
$
SLURM_SUBMIT_
DIR
/.
&&
cd
../
# delete scratch directory
# delete scratch directory
rm
-rf
$GAUSS_SCRDIR
rm
-rf
$GAUSS_SCRDIR
...
...
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