GAUSSIAN-Teaching: Difference between revisions
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=== Version === | === Version === | ||
09 | 09, 16 | ||
=== Author / Distributor === | === Author / Distributor === | ||
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'''NOTE''': Users are required to sign a license agreement form before being allowed to run this software. Please fill out the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25844 GACRC General Support Form] | '''NOTE''': Users are required to sign a license agreement form before being allowed to run this software. Please fill out the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25844 GACRC General Support Form] | ||
to check if you have permission to use this software. | |||
After you sign the license agreement form and | After you sign the license agreement form and send the signed form to us (or after the course instructor sends your signed form to us) you will be added to the Gaussian group. Then you should be able to run gaussian on this cluster. | ||
=== Running Program === | === Running Program === | ||
'''GAUSSIAN 09''' | |||
Gaussian09 (g09) is installed in | Gaussian09 (g09) is installed in /apps/eb/gaussian and it was installed without TCP-Linda, so it can only use cores within a single node (and you cannot specify %LindaWorkers larger than one). The number of threads is not specified by default. Please use the %NProcShared keyword to specify the number of threads to use. Note that in this version of Gaussian, the %NProc directive used in earlier versions is obsolete. | ||
of threads is not specified by default. Please use the %NProcShared keyword to specify the number of threads to use. Note that in this version of Gaussian, the %NProc directive used in earlier versions is obsolete. | |||
'''For AMD processors:''' | '''For AMD processors:''' | ||
Gaussian binaries optimized by AMD processors are installed in | Gaussian binaries optimized by AMD processors are installed in /apps/eb/gaussian/09-AMD-SSE4a. To use this version of Gaussian, please first load the gaussian/09-AMD-SSE4a module and source g09.profile with | ||
module load gaussian/09-AMD-SSE4a | |||
. $g09root/g09/bsd/g09.profile | |||
'''For Intel processors:''' | |||
Gaussian binaries optimized by Intel processors are installed in /apps/eb/gaussian/09-Intel-SSE4_2. To use this version of Gaussian, please first load the gaussian/09-Intel-SSE4_2 module and source g09.profile with | |||
module load gaussian/09-Intel-SSE4_2 | |||
. $g09root/g09/bsd/g09.profile | |||
Also refer to [[Running Jobs on the teaching cluster]]. | |||
For more information on Environment Modules on the teaching cluster please see the [[Lmod]] page. | |||
'''GAUSSIAN 16''' | |||
''' | Gaussian16 (g16) is installed in /apps/eb/gaussian and it was installed without TCP-Linda, so it can only use cores within a single node (and you cannot specify %LindaWorkers larger than one). The number | ||
of threads is not specified by default. Please use the %NProcShared keyword to specify the number of threads to use. Note that in this version of Gaussian, the %NProc directive used in earlier versions is obsolete. | |||
'''With AVX2 optimization''' | |||
Gaussian binaries | Gaussian binaries that have AVX2 optimization are installed in /apps/eb/gaussian/16-AVX2. To use this version of Gaussian16, please first load the gaussian/16-AVX2 module and source g16.profile with | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
module load gaussian/ | module load gaussian/16-AVX2 | ||
. $ | . $g16root/g16/bsd/g16.profile | ||
</pre> | </pre> | ||
'''Example of a shell script sub.sh to run | '''Example of a shell script sub.sh to run g16 on the batch queue:''' | ||
| Line 62: | Line 67: | ||
#!/bin/bash | #!/bin/bash | ||
#SBATCH --partition=batch | #SBATCH --partition=batch | ||
#SBATCH --ntasks=4 | #SBATCH --job-name=testgauss | ||
#SBATCH --ntasks=1 | |||
#SBATCH --cpus-per-task=4 | |||
#SBATCH --time=20:00:00 | #SBATCH --time=20:00:00 | ||
#SBATCH --mem=30gb | #SBATCH --mem=30gb | ||
cd $ | cd $SLURM_SUBMIT_DIR | ||
module load gaussian/ | module load gaussian/16-AVX2 | ||
. $ | . $g16root/g16/bsd/g16.profile | ||
g16 params.com params.log | |||
</pre> | </pre> | ||
where params.com is a sample input parameter file that needs to be replaced by the name of the file you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well. In this example, the standard output of the | where params.com is a sample input parameter file that needs to be replaced by the name of the file you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well. In this example, the standard output of the g16 command will be saved into a file called params.log. | ||
Please set the '''-- | Please set the '''--cpus-per-task=''' variable to be the same number as the number of threads specified in your parameter file (params.com) with the variable %NProcShared, e.g. %NProcShared=4. Please also request as much memory for the job as you set the %Mem keyword in your parameter file. | ||
Submit the job to the queue with | Submit the job to the queue with | ||
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'''Gaussian scratch files''': | '''Gaussian scratch files''': | ||
By default | By default g16 jobs generate temporary files called Gau-* in the user's home directory, /home/username. The job automatically deletes these files when it completes successfully. However, if the job crashes (or if you delete a running g16 job), these files are left in your home directory. Please remove leftover temporary files manually so they do not accumulate in your home directory. | ||
=== Documentation === | === Documentation === | ||
| Line 96: | Line 103: | ||
Built without TCP-Linda, therefore it can only run within one node. | Built without TCP-Linda, therefore it can only run within one node. | ||
Binaries optimized for processors that support AVX2 are installed in /apps/eb/gaussian/16-AVX2 | |||
=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
Latest revision as of 11:33, 9 May 2024
Category
Chemistry
Program On
Teaching
Version
09, 16
Author / Distributor
Description
Gaussian is a set of programs for performing semi-empirical, density functional theory and ab initio molecular orbital calculations.
NOTE: Users are required to sign a license agreement form before being allowed to run this software. Please fill out the GACRC General Support Form to check if you have permission to use this software.
After you sign the license agreement form and send the signed form to us (or after the course instructor sends your signed form to us) you will be added to the Gaussian group. Then you should be able to run gaussian on this cluster.
Running Program
GAUSSIAN 09
Gaussian09 (g09) is installed in /apps/eb/gaussian and it was installed without TCP-Linda, so it can only use cores within a single node (and you cannot specify %LindaWorkers larger than one). The number of threads is not specified by default. Please use the %NProcShared keyword to specify the number of threads to use. Note that in this version of Gaussian, the %NProc directive used in earlier versions is obsolete.
For AMD processors:
Gaussian binaries optimized by AMD processors are installed in /apps/eb/gaussian/09-AMD-SSE4a. To use this version of Gaussian, please first load the gaussian/09-AMD-SSE4a module and source g09.profile with
module load gaussian/09-AMD-SSE4a . $g09root/g09/bsd/g09.profile
For Intel processors:
Gaussian binaries optimized by Intel processors are installed in /apps/eb/gaussian/09-Intel-SSE4_2. To use this version of Gaussian, please first load the gaussian/09-Intel-SSE4_2 module and source g09.profile with
module load gaussian/09-Intel-SSE4_2 . $g09root/g09/bsd/g09.profile
Also refer to Running Jobs on the teaching cluster.
For more information on Environment Modules on the teaching cluster please see the Lmod page.
GAUSSIAN 16
Gaussian16 (g16) is installed in /apps/eb/gaussian and it was installed without TCP-Linda, so it can only use cores within a single node (and you cannot specify %LindaWorkers larger than one). The number of threads is not specified by default. Please use the %NProcShared keyword to specify the number of threads to use. Note that in this version of Gaussian, the %NProc directive used in earlier versions is obsolete. With AVX2 optimization
Gaussian binaries that have AVX2 optimization are installed in /apps/eb/gaussian/16-AVX2. To use this version of Gaussian16, please first load the gaussian/16-AVX2 module and source g16.profile with
module load gaussian/16-AVX2 . $g16root/g16/bsd/g16.profile
Example of a shell script sub.sh to run g16 on the batch queue:
#!/bin/bash #SBATCH --partition=batch #SBATCH --job-name=testgauss #SBATCH --ntasks=1 #SBATCH --cpus-per-task=4 #SBATCH --time=20:00:00 #SBATCH --mem=30gb cd $SLURM_SUBMIT_DIR module load gaussian/16-AVX2 . $g16root/g16/bsd/g16.profile g16 params.com params.log
where params.com is a sample input parameter file that needs to be replaced by the name of the file you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well. In this example, the standard output of the g16 command will be saved into a file called params.log.
Please set the --cpus-per-task= variable to be the same number as the number of threads specified in your parameter file (params.com) with the variable %NProcShared, e.g. %NProcShared=4. Please also request as much memory for the job as you set the %Mem keyword in your parameter file.
Submit the job to the queue with
sbatch sub.sh
Gaussian scratch files:
By default g16 jobs generate temporary files called Gau-* in the user's home directory, /home/username. The job automatically deletes these files when it completes successfully. However, if the job crashes (or if you delete a running g16 job), these files are left in your home directory. Please remove leftover temporary files manually so they do not accumulate in your home directory.
Documentation
Installation
Built without TCP-Linda, therefore it can only run within one node.
Binaries optimized for processors that support AVX2 are installed in /apps/eb/gaussian/16-AVX2
System
64-bit Linux