Automated Submission Script Creation & Submission
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- | Example script for automation of submission script creation and submission to qsub of multiple jobs. | + | Example script for automation of submission script creation and submission to qsub of multiple jobs or to submit directly from a program such as Gaussview. |
Using example for gaussian calculation: [[Gaussian]] | Using example for gaussian calculation: [[Gaussian]] | ||
Line 6: | Line 6: | ||
qsubl <JobFile(s).com><br> | qsubl <JobFile(s).com><br> | ||
- | < | + | <source lang=sh>#!/bin/bash |
- | #Replaces com with script for all JobFile(s) | + | # Replaces com with script for all JobFile(s) |
script_files=`echo "$*" | sed -e "s/\.com/.script /g"` | script_files=`echo "$*" | sed -e "s/\.com/.script /g"` | ||
- | #Loops through all script file(s) to create submission script submits to cluter | + | # Loops through all script file(s) to create submission script & submits to cluter |
for file in $script_files; do | for file in $script_files; do | ||
- | + | echo "#!/bin/bash" > $file.script | |
- | + | echo "#$ -N $file" >> $file.script | |
- | + | echo "#$ -cwd" >> $file.script | |
- | + | echo "#$ -pe fah 4" >> $file.script | |
- | + | echo '/usr/sweet/bin/g09 $JOB_NAME.com $JOB_NAME.log' >> $file.script | |
qsub $file.script | qsub $file.script | ||
- | done</ | + | done |
- | <br> | + | </source> |
+ | <br> | ||
+ | |||
+ | To setup Gaussview to work with this script and submit jobs to Barley | ||
+ | |||
+ | <br> | ||
+ | |||
+ | File --> Preferences --> Gaussian Setup | ||
+ | |||
+ | Click Calculation | ||
+ | |||
+ | On Link 0 Tab | ||
+ | |||
+ | Memory Limit Specify = 8 GB | ||
+ | |||
+ | Shared Processors Specify = 4 | ||
+ | |||
+ | Click Retain | ||
+ | |||
+ | <br> | ||
+ | |||
+ | File --> Preferences --> Job Setup | ||
+ | |||
+ | Select Application: Gaussian | ||
+ | |||
+ | Command Line: qsubl @INFILE | ||
+ | |||
+ | <br> | ||
+ | |||
+ | Gaussian Calculation Setup | ||
+ | |||
+ | Setup Calculation and Click Submit | ||
+ | |||
+ | Save file as .com | ||
+ | |||
+ | Job will be submitted to Barley | ||
+ | |||
+ | Will get error that log file is not found. Just ignore. |
Latest revision as of 10:51, 1 August 2012
Example script for automation of submission script creation and submission to qsub of multiple jobs or to submit directly from a program such as Gaussview.
Using example for gaussian calculation: Gaussian
qsubl <JobFile(s).com>
#!/bin/bash # Replaces com with script for all JobFile(s) script_files=`echo "$*" | sed -e "s/\.com/.script /g"` # Loops through all script file(s) to create submission script & submits to cluter for file in $script_files; do echo "#!/bin/bash" > $file.script echo "#$ -N $file" >> $file.script echo "#$ -cwd" >> $file.script echo "#$ -pe fah 4" >> $file.script echo '/usr/sweet/bin/g09 $JOB_NAME.com $JOB_NAME.log' >> $file.script qsub $file.script done
To setup Gaussview to work with this script and submit jobs to Barley
File --> Preferences --> Gaussian Setup
Click Calculation
On Link 0 Tab
Memory Limit Specify = 8 GB
Shared Processors Specify = 4
Click Retain
File --> Preferences --> Job Setup
Select Application: Gaussian
Command Line: qsubl @INFILE
Gaussian Calculation Setup
Setup Calculation and Click Submit
Save file as .com
Job will be submitted to Barley
Will get error that log file is not found. Just ignore.