GAUSSIAN-Teaching: Difference between revisions

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=== Version ===
=== Version ===
   
   
09
09, 16


=== Author / Distributor ===
=== Author / Distributor ===
Line 21: Line 21:


'''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.
to check if you have permission to use this software.


After you sign the license agreement form and get added to the Gaussian group, please check if there is a directory in /scratch/gtemp with your MyID as its name. If you don't see a directory there for you, please fill out the [https://uga.teamdynamix.com/TDClient/Requests/ServiceDet?ID=25844 GACRC General Support Form] to request that one such directory be created for you.
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'''
Also refer to [[Running Jobs on the teaching cluster]].
 
For more information on Environment Modules on the teaching cluster please see the [[Lmod]] page.


Gaussian09 (g09) is installed in /usr/local/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  
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 Note that in this version of Gaussian, the %NProc directive used in earlier versions is obsolete.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 Note that in this version of Gaussian, the %NProc directive used in earlier versions is obsolete.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 /usr/local/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
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]].


<pre class="gcommand">
For more information on Environment Modules on the teaching cluster please see the [[Lmod]] page.
module load gaussian/09-AMD-SSE4a


. $g09root/g09/bsd/g09.profile
'''GAUSSIAN 16'''
</pre>


'''For Intel processors:'''
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 optimized by Intel processors are installed in /usr/local/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
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/09-Intel-SSE4_2
module load gaussian/16-AVX2


. $g09root/g09/bsd/g09.profile
. $g16root/g16/bsd/g16.profile
</pre>
</pre>




'''Example of a shell script sub.sh to run g09 on the batch queue (Intel processors):'''
'''Example of a shell script sub.sh to run g16 on the batch queue:'''
   
   


Line 63: Line 68:
#SBATCH --partition=batch
#SBATCH --partition=batch
#SBATCH --job-name=testgauss
#SBATCH --job-name=testgauss
#SBATCH --ntasks=4
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --time=20:00:00
#SBATCH --time=20:00:00
#SBATCH --mem=30gb
#SBATCH --mem=30gb
Line 69: Line 75:
cd $SLURM_SUBMIT_DIR
cd $SLURM_SUBMIT_DIR


module load gaussian/09-Intel-SSE4_2
module load gaussian/16-AVX2


. $g09root/g09/bsd/g09.profile
. $g16root/g16/bsd/g16.profile


g09 params.com params.log
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 g09 command will be saved into a file called 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 '''--ntasks=''' 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.  
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 g09 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 g09 job), these files are left in your home directory. Please remove leftover temporary files manually so they do not accumulate in your home directory.
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 97: 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.


The version for Intel processors is installed in /usr/local/apps/eb/gaussian/09-Intel-SSE4_2
Binaries optimized for processors that support AVX2 are installed in /apps/eb/gaussian/16-AVX2
 
The version for AMD processors is installed in /usr/local/apps/eb/gaussian/09-AMD-SSE4a


=== System ===
=== System ===
64-bit Linux
64-bit Linux

Latest revision as of 12:33, 9 May 2024

Category

Chemistry

Program On

Teaching

Version

09, 16

Author / Distributor

See http://www.gaussian.com

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

http://www.gaussian.com

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