(→%mem vs --mpp)
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Revision as of 10:31, 30 August 2016
|Description: Chemistry, Electronic Structure Programs|
|SHARCNET Package information: see Gaussian software page in web portal|
|Full list of SHARCNET supported software|
- 1 Introduction
- 2 Version Selection
- 3 Job Submission
- 4 Example Job
- 5 General Notes
- 5.1 NBO6
- 5.2 Restart
- 5.3 %mem vs --mpp
- 5.4 Others
- 6 References
Gaussian 09 is the latest in the Gaussian series of electronic structure programs. It can perform density functional theory (including time dependent), Hartree-Fock (including time dependent), Moller-Plesset, coupled-cluster, and configuration interaction calculations. Gaussian is used widely to predict the energies, molecular geometries, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types.
The newest version g09_D.01 has NBO6 added as of Sept. 19, 2013. To use Gaussian, user should load the correct version using 'module load gaussian/version'. For example, to use g09_D.01, user can add the module load line to the end of your .bash_profile file (in your /home directory)
module load gaussian/g09_D.01
save the .bash_profile file, logout and login again. Type 'which g09' should give:
To use the previous g09_C.01, use
module load gaussian/g09_C.01
If you have to use other version such as g09_B.01 (the runscript is 'g09b' instead of 'g09' in g09_C.01 and g09_D.01 in sqsub), you have to replace the above module load line to be
module load gaussian/g09_B.01
To use version g03_D.01 (g03), add the module load line
module load gaussian/g03_D.01
- g09_D.01 or g09_C.01 on orca, saw, brown ("g09"), the general sqsub command for threaded job is
sqsub -q threaded -n cpus -r runtime --mpp=memory(g) -o *.log g09 *.com
cpus (-n cpus) in sqsub should match the %nprocs=cpus specified in the input *.com or *.gjf file (default is 1)
Due to longer waiting time for 8-cpu gaussian jobs, better to run 4-cpu or 6-cpu gaussian jobs instead.
Gaussian output is in *.log. Please use appropriate -r runtime and --mpp=memory in sqsub. Maximum runtime is 7 days, Maximum memory is 15g on saw, 10g (or occasionally 20g) on orca for 8-cpus gaussian jobs
serial job for CI or CC based methods (e.g., 1 cpu, 3 days runtime, 4g memory, inputfile: name.com)
sqsub -r 3.0d --mpp=4g -o name.log g09 name.com
threaded job for MPx and DFT methods (example: 4 cpus, 3 days runtime, 4g memory)
sqsub -q threaded -n 4 -r 3.0d --mpp=4g -o name.log g09 name.com
- g03_D.01 on saw, brown ("g03"), which works for ncpus=4 only, specify %nproc=4 in the input .com file, then the sqsub command will be
sqsub -q threaded -n 4 -r runtime --mpp=memory(g) -o *.log g03 *.com
sqsub -r runtime --mpp=memory(g) -o name.log g03 name.com
- g09_B.01 on orca, saw ("g09b")
To use g09_B.01 instead of g09_C.01, please change the module load line in your .bash_profile file (noticed above)
module load gaussian/g09_B.01
save the file, exit and relogin to saw or orca. The start script for g09_B.01 is g09b
sqsub -q threaded -n cpus -r runtime --mpp=memory(g) -o *.log g09b *.com
sqsub -r runtime --mpp=memory(g) -o name.log g09b name.com
Example input files to start and restart a Gaussian job can be found in
The default NBO in Gaussian is NBO-3.1. There is no update for NBO in G09 because NBO becomes a separate license package. SHARCNET purchased NBO6 site license. We added NBO6 into g09_D.01 on SHARCNET systems.
In g09, the default 'pop=nbo' keyword is for NBO 3, to use NBO 6, replace 'nbo' with 'nbo6', i.e.,
Accordingly, use nbo6read, nbo6del, etc..
For detail NBO6 usage and examples, please check NBO6
You can find some simple g09-NBO6 examples on the clusters under /opt/sharcnet/gaussian/g09_D.01/nbo6/g09tests/
Gaussian usage related to NBO can be found at Gaussian_population
Please note that the license does not include NBOview, a GUI application. If you are interested in NBOview, please contact NBO6 software provider for the separate NBOview license.
Gaussian job can always be restarted.
The geometry optimization job can be restarted from the .chk file as usual.
The one-step computation, such as Analytic frequency calculations, including properties like ROA and VCD with ONIOM; CCSD and EOM-CCSD calculations; NMR; Polar=OptRot; CID, CISD, CCD, QCISD and BD energies, can be restarted from .rwf file. For details please check Gaussian Restart
To restart a job from .chk or .rwf, you need to know where the file is from previous run. By default, .chk is in the directory where you submitted the job but .rwf is in /scratch/yourid/jobid/. You have to move *.rwf file from /scratch/youris/jobid/ to /scratch/yourid/ to restart the previous job from that .rwf file. The following examples specify the .rwf file to your /scratch (/scratch/yourid/*.rwf) for start and restart.
The sample input files to start and restart a 'freq' job could be. Please always leave a blank line at the end of the .com file (you can find real input files in /home/jemmyhu/tests/test_g09/Restart/):
Sample input file (example.com) for a freq job
%rwf=/scratch/yourid/example.rwf %NoSave %chk=example.chk %mem=500mb %nprocs=4 #p freq ... << my example.com >> input continues ...
Restart input file (example_restart.com) to restart the freq job
%rwf=/scratch/yourid/example.rwf %NoSave %chk=example.chk %mem=500mb %nprocs=4 #p restart
The sample input files to start and restart a 'Geom Opt' job could be
Sample input file (example.com) for a Gemo Opt job
%NoSave %chk=example.chk %mem=500mb %nprocs=4 # B3LYP/DGDZVP Opt << my example.com >> input continues ...
Restart input file (example_restart.com) to restart the Geom Opt job
%NoSave %chk=example.chk %mem=500mb %nprocs=4 # B3LYP/DGDZVP Opt Geom=AllCheck Guess=Read
%mem vs --mpp
--mpp in sqsub is to reserve the total memory for a job. %mem is the memory setting in gaussian's input file for a single processor, normally the memory needed for the gaussian job to start. If %mem is not specified gaussian applies a default value of 256mb described here.
The maximum memory in --mpp is 15g on saw for a 8-way gaussian job, it could be 20g for a 8-way job on orca. However, in practice it is not the bigger the better. With --mpp right above the job's total memory needs will give the optimal performance. Please use a portion of the memory for different size gaussian jobs such as use up to half of the max memory for a 4-way gaussian job on saw and orca.
Because a gaussian job will need more memory than what specified via %mem in the input file, --mpp should be larger than %mem. Normally --mpp is roughly double the size used in %mem (it is not %mem times threads). The following guideline is from observation and it should work fine on SHARCNET systems
%mem --mpp <=600MB 2g 600-1500MB 4g 1500-2500MB 6g 2500-3500MB 8g
1. Go to Gaussian 09 Efficiency Considerations page for memory estimate (%mem), etc. for a job. 2. Based on our benchmark results, we recommend -n 8 for MPx and DFT types of jobs, and always 1 cpu (serial) job for CI (CIS, CISD, QCISD, etc) and CC (CCD, CCSD, etc) based methods on SHARCNET systems. 3. Use appropriate -r runtime and --mpp=memory in sqsub. Maximum runtime is 7 days, Maximum memory is 15g on saw, 10g (or occasionally 20g) on orca for 8-cpus gaussian jobs 4. Number of cpus (-n cpus) used in sqsub should match the %nprocs=cpus specified in the input *.com or *.gjf file (default is 1) 5. Run job out of your /scratch or /work directory 6. Delete *.core and the related *.rwf, *.d2e, *.int, and *.scr files manually once your job was terminated abnormally (delete subdirectory 'jobid' from your /scratch when the job with jobid is finished). 7. Gaussian utilities such as formchk, cubegen, etc. can run from command line commands. Please make sure which version is used by typing 'which formchk', if the version is correct, simply do formchk name.chk otherwise, you can type the full path such as for g09_C.01 /opt/sharcnet/gaussian/g09_C.01/formchk name.chk it will generate a file 'name.fchk' in the directory
o Official Gaussian Website
- More detail info, see gaussian software page in web portal