Gaussian16
Gaussian16 is available on the following servers.
important
Intermediate files created by Gaussian16 are tend to be very large and your home directory size is limited to 500 GB.We recommend that when you use Gaussian16 you create a directory in /work area and run it in the directory.
Input file example
The following input file calculates geometry optimization for hexacarbonyl.
It specifies Hartree-Fock method and 3-21G basis set.
(Example）
$ ls -l /work/app/Gaussian/example.com -rw-r--r-- 1 root root 420 Jul 12 16:33 /work/app/Gaussian/example.com
Large-Scale Parallel Computing Server
Please submit job from the front end node of Large-Scale Parallel Computing Server(super.sc.imr.tohoku.ac.jp)
The following applications are available on the supercomputer.
| Version | Settings command |
|---|---|
| B.01 | source /work/app/Gaussian/g16.profile |
| C.01 | source /work/app/Gaussian/C.01/g16.profile |
The number of threads
Specify 'CPU=0-35' in the input file for parallelization. In the case of 'NProc=36' is specified,
the job cannot run in parallel normally.
Following is an example using 36 cores.
Specification example in the input file
%CPU=0-35
The directory for temporary files
Create a directory on /work/scratch area for outputting Gaussian temporary files.
(例)
%Chk=example_app.chk
Job submission script
Create a script file in advance.
Set '-d parallel number' to the same value as 'CPU' in the input file.
#!/bin/sh #PBS -l select=1 #PBS -q queue #PBS -N jobname source /work/app/Gaussian/g16.profile DIRNAME=`basename $PBS_O_WORKDIR` WORKDIR=/work/$USER/$PBS_JOBID mkdir -p $WORKDIR cp -raf $PBS_O_WORKDIR $WORKDIR cd $WORKDIR/$DIRNAME aprun -j 1 -d parallel number g16 input file 2> error file cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi
(Example)
#!/bin/sh #PBS -l select=1 #PBS -q P_016 #PBS -N g16 source /work/app/Gaussian/g16.profile DIRNAME=`basename $PBS_O_WORKDIR` WORKDIR=/work/$USER/$PBS_JOBID mkdir -p $WORKDIR cp -raf $PBS_O_WORKDIR $WORKDIR cd $WORKDIR/$DIRNAME aprun -j 1 -d 36 g16 test0000.com 2> g16.err cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi
Accelerator Server
Please submit job from the front end node of Accelerator Server(gpu.sc.imr.tohoku.ac.jp).
Available executables
| Version | Path | Queue |
|---|---|---|
| C.01 | source /usr/local/app/Gaussian/g16.profile | A_004 |
The number of threads
Specify ‘CPU=0-35’ in the input file for parallelization. In the case of ‘NProc=36’ is specified, the
job cannot run in parallel normally.
Using GPU
In order to use GPU, it is necessary to specify the number of cores and GPUs.
Below is an example using 36 cores and 10 GPUs.
Specification example in input file
%CPU=0-35 %GPUCPU=0-9=0-4,18-22
Example of environment variable specification
export GAUSS_CDEF="0-35" export GAUSS_GDEF="0-9=0-4,18-22"
Not valid for all calculations.
Consider setting the upper limit of elapsed time.
See also the following page.
http://gaussian.com/gpu/
The directory for temporary files
Create a directory on /work/scratch area for outputting Gaussian temporary files.
(Example)
%Chk=example_app.chk
Create a script file in advance.
#!/bin/sh #PBS -l select=1 #PBS -q queue #PBS -N jobname source /usr/local/app/Gaussian/g16.profile DIRNAME=`basename $PBS_O_WORKDIR` WORKDIR=/work/$USER/$PBS_JOBID mkdir -p $WORKDIR cp -raf $PBS_O_WORKDIR $WORKDIR cd $WORKDIR/$DIRNAME g16 input file 2> error file cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi
(Example)Accelerator Server
#!/bin/sh #PBS -l select=1 #PBS -q A_004 #PBS -N g16 source /usr/local/app/Gaussian/g16.profile DIRNAME=`basename $PBS_O_WORKDIR` WORKDIR=/work/$USER/$PBS_JOBID mkdir -p $WORKDIR cp -raf $PBS_O_WORKDIR $WORKDIR cd $WORKDIR/$DIRNAME g16 test0000.com 2> g16.err cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi
Parallel Computing and Informatics Server
Please submit job from the front end node of Accelerator Server(gpu.sc.imr.tohoku.ac.jp).
Available executables
| Version | Path | Queue |
|---|---|---|
| B.01 | source /work/app/Gaussian/g16.profile | C_002 |
| C_004 | ||
| C.01 | source /work/app/Gaussian/C.01/g16.profile | C_002 |
| C_004 |
The number of threads
Specify‘CPU=0-35’ in the input file for parallelization.
In the case of ‘NProc=36’ is specified, the job cannot run in parallel normally.
Below is an example using 36 cores.
Specification example in input file
%CPU=0-35
The directory for temporary files
Create a directory on /work/scratch area for outputting Gaussian temporary files.
(Example)
%Chk=example_app.chk
Job script
Create a script file in advance.
#!/bin/sh #PBS -l select=1 #PBS -q queue #PBS -N jobname source /usr/local/app/Gaussian/g16.profile DIRNAME=`basename $PBS_O_WORKDIR` WORKDIR=/work/$USER/$PBS_JOBID mkdir -p $WORKDIR cp -raf $PBS_O_WORKDIR $WORKDIR cd $WORKDIR/$DIRNAME g16 input file 2> error file cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi
(Example)
#!/bin/sh #PBS -l select=1 #PBS -q C_002 #PBS -N g16 source /usr/local/app/Gaussian/g16.profile DIRNAME=`basename $PBS_O_WORKDIR` WORKDIR=/work/$USER/$PBS_JOBID mkdir -p $WORKDIR cp -raf $PBS_O_WORKDIR $WORKDIR cd $WORKDIR/$DIRNAME g16 test0000.com 2> g16.err cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi
Virtual Server
Available executables
| Version | Settings |
|---|---|
| B.01 | source /work/app/Gaussian/g16.profile |
| C.01 | source /work/app/Gaussian/C.01/g16.profile |
Prepare input files of Gaussian 16(***.com) in the working directory.
The following input file calculates geometry optimization for hexacarbonyl. It specifies Hartree-Fock method and 3-21G basis set.
(Example)
$ ls -l /usr/local/app/Gaussian/example.com -rw-r--r--1 root root 420 Jul 12 16:33 /usr/local/app/Gaussian/example.com
・The number of threads
Specify 'CPU=0-N'in the input file for parallelization.
In the case of 'NProc=N' is specified, the job cannot run in parallel normally.
Execute the commands as follows.
source /usr/local/app/Gaussian/g16.profile g16 input file
(Example)
source /usr/local/app/Gaussian/g16.profile g16 test0000.com