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howto:gaussian [2015/02/24 13:25]
alopis [Example PBSPro job script for Single Node Jobs (multiple CPU's)] 		howto:gaussian [2025/10/17 09:51] (current)
alopis [Easy Gaussian09 and Gaussian16 PBS creation and submission]
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 ====== Gaussian at CHPC ====== ====== Gaussian at CHPC ======
  
-  * **NOTE : You should always run your jobs from ''scratch5''**+This license can only be used by CHPC registered users, which are associated with either **South African** or **SKA partner** higher education institutions
  
 +Gaussian can be run over 1 or 2 nodes (see example below) 
  
-There are two modules of Gaussian 09 at CHPC which can be used. +====Easy Gaussian09 and Gaussian16 PBS creation and submission====
-Here is an example on how to access them:+
  
-  embele@login01:~/scratch5 $ module avail                   ### list available modules +In order to see all available Easy Scripts, first include/load this module - even better if your add this line to your .bashrc:
-  embele@login01:~/scratch5 $ module add gaussian/g09.D01    ### load g09 version D01 (previous) or +
-  embele@login01:~/scratch5 $ module add gaussian/g09.anton  ### load g09 version anton (new, Recommended) +
-  +
-  +
-====Example PBSPro job script for Single Node Jobs (multiple CPU's)====+
  
 +  module load chpc/easy_scripts
  
- #! /bin/sh+Execute **qg09_E01** or **qg16_A03** or **qg16_B01** or **qg16_C01**
  
- # (1) These are standard type lines for PBS job specification. Modify them for your own requirements - choice of nodes; walltime;  +This script handles PBS setup and submission. 
- # your directory on scratch for standard out and error files ; email of job starting, ending and errors+Also takes care of jobs running over more than one node with LINDA and does cleanup of temporary GAU files when job is completed/killed. Examples of these scripts are provided below.
  
- #PBS -N C60.job +              EXAMPLE1 
- #PBS -l select=1:ncpus=12:jobtype=westmere,place=free:group=nodetype +  Enter project name/shortname 
- #PBS -l walltime=2:31:00 +  CHEM0100 
- #PBS -q workq      +  Enter input file (with .com or .gjf extension) 
- #PBS -o /export/home/aslopis/scratch5/Gaussian_Support/C60_4/C60.out +  test.gjf 
- #PBS -e /export/home/aslopis/scratch5/Gaussian_Support/C60_4/C60.err +  Enter number of nodes on which to run job 
- #PBS -m abe +  1 
- #PBS -M aslopis@gmail.com+  Enter total walltime (hour:minute) 
 +  2:00 
 +  Enter email address 
 +  testing@gmail.com 
 +  Generated pbs file for test 
 +  Do you wish to submit job to cluster (y/n) 
 +  y
  
- # End of comments (1)  Make changes above. 
  
 +    EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
 +  Enter project name/shortname
 +  CHEM0100
 +  Enter input file (with .com or .gjf extension)
 +  test.gjf
 +  Enter number of nodes on which to run job
 +  
 +  Enter total walltime (hour:minute)
 +  
 +  Enter email address
 +  testing@gmail.com
 +  Generated pbs file for test
 +  Do you wish to submit job to cluster (y/n)
 +  y
 +  
 +  
 +If you wish to use the utility **formchk** (to create readable format files for visualisers) please do the following.
 +  
 +  module load chpc/gaussian16/C01
 +  source $g16root/g16/bsd/g16.profile
 +  
 +Then the command **formcheck** should be available for use. Other Gaussian commands should also be available, such as **freqchk** and **chkchk**.
  
  
- # (2) This is to clean up temporary files which are left behind if Gaussian crashes. No changes required below.    
- cleanup_scratch() { 
-     echo "Deleting inside signal handler, meaning I probably either hit the walltime, or deleted the job using qdel" 
-  
-     cd "$PBS_O_WORKDIR" 
-     rm -rfv "$GAUSS_SCRDIR" 
-    echo "---" 
-    echo "Signal handler ending time:" 
-    date 
-    exit 0 
- } 
  
- # Associate the function "cleanup_scratch" with the TERM signal (and others), which is usually how jobs get killed +You can use a **checkpoint file (.chk)** which will allow you to continue with a 2nd (or subsequent) calculation from close to where the initial/previous calculation ended. This is especially helpful for jobs which exceed walltime limits or have stopped for another reason. There is info online including from Gaussian website, these links may be helpful too:
- trap 'cleanup_scratch' SIGTERM SIGHUP SIGINT SIGQUIT SIGFPE SIGKILL SIGALRM +
-  +
- # End of comments (2) No changes required above. +
-  +
-  +
- # (3) You can remove this first line below once you've run the script once, but won't cause a problem if remains.   +
- mkdir  /lustre/SCRATCH5/gau/$USER +
-  +
-  +
- # (4) Please leave this line unchanged. Creating a subdirectory with your jobid for temporary Gaussian files - these are removed after job. +
- # Previously everone's Gaussian temporary files were written in /SCRATCH5/gau +
- mkdir  /lustre/SCRATCH5/gau/$USER/$PBS_JOBID +
-  +
-  +
- # (5) Change to your work directory. Specify if explictly if you find issues. +
- cd $PBS_O_WORKDIR +
-  +
- echo "My job starts here" +
- date +
-  +
-  +
- # (6) Please leave unchanged. This new module specifies the new directory for Gaussian variable GAUSS_SCRDIR for temporary files directory. +
- source /etc/profile.d/modules.sh +
- module add gaussian/g09.anton +
- source /opt/gridware/applications/gaussian/g09/bsd/g09.profile +
-====Example PBSPro job script for g09.D01====+
  
-  #! /bin/sh +https://gaussian.com/faq2/
-  #PBS -N molecule.job +
-  #PBS -l select=1:ncpus=12:jobtype=dell,place=free:group=nodetype +
-  #PBS -l walltime=1:00:00 +
-  #PBS -q workq +
-  #PBS -m abe +
-  #PBS -o /export/home/username/scratch/gaussian.out +
-  #PBS -e /export/home/username/scratch/gaussian.err +
-  #PBS -M username@email +
-   +
-  cd $PBS_O_WORKDIR +
-  source /etc/profile.d/modules.sh +
-  module add gaussian/g09.D01 +
-  source /opt/gridware/applications/gaussian/g09/bsd/g09.profile +
-   +
-  g09 < molecule.com > molecule.log+
  
 +https://gaussian.com/restart/
  
 +https://gaussian.com/tip4/
  
-Example of a gaussian input file, note the blank lines within the file: +https://www.researchgate.net/post/How-can-I-res... 
-   + 
-  %nprocshared=12 +Very occassionally  a checkpoint file may be corrupted, so keeping the most recent backup copy of a good checkpoint (.chk) file can be helpful. Otherwise in these circumstances the calculation may need to be started from scratch - or the most recent molecular geometry (the coordinated of all the atoms) could be used from the Gaussian output (.log) file. 
-  %nprocl=1 +
-  #P HF/6-31G*  IOP(6/33=2,6/41=10,6/42=17) SCF=Tight Pop=MK +
-          +
-  Title Card Required +
-   +
-  0 1 +
-   C                 -3.19550100    0.11344600   -0.18511100 +
-   O                 -3.05859100    0.83554400   -1.15941100 +
-   N                 -2.14200500   -0.25446800    0.60848900 +
-   H                 -2.32841200   -0.78506500    1.44398900 +
-   C                 -0.75900100    0.12341400    0.36048900 +
-   C                  0.14379200   -0.42259800    1.48678900 +
-   C                  0.59047400   -1.84630300    1.03238900 +
-   C                  1.59689900    0.10938400    1.28248900 +
-   C                  0.08697100   -2.05959700   -0.42431100 +
-   C                  2.05278100   -1.31402200    0.82788900 +
-   C                 -0.14011000   -0.59319400   -0.87441100 +
-   C                  1.35866600   -2.48501300   -1.17731100 +
-   C                  1.32989700   -0.05621300   -1.07501100 +
-   C                  1.66721100    0.99508300    0.02128900 +
-   C                  2.20428100   -1.28752400   -0.71551100 +
-   C                  0.60162500    2.08159700    0.02358900 +
-   N                 -0.63668200    1.58111300    0.28218900 +
-   O                  0.86964000    3.24909300   -0.21751100 +
-   H                 -1.43757500    2.10622300   -0.04521100 +
-   O                  2.93691800    1.56466600   -0.15981100 +
-   H                  2.76333000    2.51016900   -0.30861100 +
-   H                 -0.28050600   -0.28619200    2.48278900 +
-   H                  0.43696300   -2.68340100    1.71298900 +
-   H                  2.07960500    0.56667700    2.14378900 +
-   H                 -0.78403700   -2.70728500   -0.52611100 +
-   H                  2.86017500   -1.79913300    1.37408900 +
-   H                 -0.75990800   -0.47138600   -1.76101100 +
-   H                  1.22276500   -2.52601100   -2.26181100 +
-   H                  1.75375300   -3.44771800   -0.83891100 +
-   H                  1.50280200    0.34398500   -2.07391100 +
-   H                  3.22968200   -1.22473700   -1.07621100 +
-   C                 -4.55170800   -0.42883700    0.22928900 +
-   H                 -5.23089700    0.41157200    0.38338900 +
-   H                 -4.52881600   -1.04383700    1.13088900 +
-   H                 -4.94951500   -1.02253200   -0.59631100 +
-          +
-         +
  
 +Please **recheck** your molecular **geometry very carefully** to ensure there are no issues - this will result in calculations which take much longer than necessary.
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