Last Update: May 26, 2022 description about g16c02 added.
Aim of this page is to show how to run Gaussian jobs with g16sub command on RCCS.
Following conditions must be satisfied beforehand.
Please visit quickstartguide page if ssh, scp, sftp settings are not yet complete.
In the following, we use ch3cl.gjf file (.gjf is one of the common file extensions of Gaussian input file) as an example. We need to send this file to RCCS first, and then run Gaussian.
%chk=ch3cl.chk
# HF/6-31G(d,p) Optmethyl chloride
0,1
C -0.000004 1.127470 0.000000
H -0.511417 1.468491 0.885898
H -0.511417 1.468491 -0.885898
H 1.022922 1.468527 0.000000
Cl -0.000004 -0.657078 0.0000
Please note that %mem, %nprocshared, %cpu are usually overwritten by g16sub/g09sub. Number of CPU cores can be specified by -np option of g16sub/g09sub. For the memory amount, you don't need to set it manually. This is because reasonable value will be automatically assigned according to the jobtype and number of CPU cores.
We employ WinSCP in this example.
Connect to ccfep.ims.ac.jp, and move to the folder (your PC side) where the Gaussian input file exists. (Note: on RCCS system, /lustre/home/users/(username) and /home/users/(username) are the same path.)
You can create a directory on RCCS side for this job. In this example, we created CH3Cl directory under the home directory (/home/users/(username)/CH3Cl).
Send input file (e.g. ch3cl.gjf) to RCCS. Once the file transfer finished, you then need to login to RCCS using SSH.
Login to ccfep.ims.ac.jp (using PuTTY or something). Then, go to the directory where you placed input file (CH3Cl directory in this example) using "cd" command. You can see file list of directories using "ls" command.
Last login: Thu May 23 17:26:40 2019 from ******.****.**.**
[user@ccfep8 ~]$ ls CH3Cl/
ch3cl.gjf
[user@ccfep8 ~]$ cd CH3Cl/
[user@ccfep8 CH3Cl]$ ls
ch3cl.gjf
[user@ccfep8 CH3Cl]$
In the target directory (CH3Cl here), submit a Gaussian job with g16sub command.
[user@ccfep8 CH3Cl]$ g16sub ch3cl.gjf
If you submit a job without any arguments other than input file name like above, this job will use 6 CPU cores on a node of "core" jobtype. The walltime limitation of the job is set to 72 hours. If the job won't finish within the time, the job will be killed by the system.
Some lengthy information like below will be shown when you run the command.
[user@ccfep8 CH3Cl]$ g16sub ch3cl.gjf
QUEUE detail
------------------------------------------------------------------------------
QUEUE(MACH) Jobtype MaxMem DefMem TimLim DefCPUs(Min-Max)
------------------------------------------------------------------------------
PN( lx) core 4.8GB 4.0GB 72:00:00 6(1-36)
------------------------------------------------------------------------------
Job detail
======================================================================
MOL name(s) : ch3cl
INP file(s) : ch3cl.gjf.lx
OUT file(s) : ch3cl.out
Current dir : /lustre/home/users/***/CH3Cl
SCRATCH dir : /work/users/${USER}/${PBS_JOBID}QUEUE : PN
Memory : 24.0GB
Time limit : 72:00:00
Job script : /lustre/home/users/***/CH3Cl/PN_28524.sh
Input modified : y
======================================================================/usr/local/bin/jsub –q PN /lustre/home/users/***/CH3Cl/PN_28254.sh
4529602.cccms1
[user@ccfep8 CH3Cl]$
You can see the status of the job with "jobinfo" command. (Job might not be shown immediately after the job submission. Please wait a while in this case.)
[user@ccfep8 CH3Cl]$ jobinfo –q PN –c –l
-------------------------------------------------------------------------------
Queue Job ID Name Status CPUs User/Grp Elaps Node/(Reason)
-------------------------------------------------------------------------------
PN 4529602 PN_28254.sh Run 6 ***/--- 00:00:00 cccc120
-------------------------------------------------------------------------------
[user@ccfep8 CH3Cl]$
Once the job is succefully accepted by the queue, the job exists (and will run eventually) even after you closed the SSH connection.
Once the job finished, you may see new files in the directory. Among them, PN_*** (PN_28254.sh, PN_28254.sh.e4529602, PN_28254.sh.o4529602) and ***.lx (ch3cl.gjf.lx) are the files created by g16sub/g09sub. They are not necessary if the job finished successfully.
[user@ccfep8 CH3Cl]$ ls
PN_28254.sh PN_28254.sh.o4529602 ch3cl.gjf ch3cl.out
PN_28254.sh.e4529602 ch3cl.chk ch3cl.gjf.lx
[user@ccfep8 CH3Cl]$
Gaussian output file (ch3cl.out here) can be checked during job execution using "less" or "tail" command. Checkpoint file (if requested) will also be found in the same directory.
You can run formchk on RCCS frontend. But you need to run the following command before running formchk.
In case your loginf shell is /bin/bash or /bin/zsh:
[user@ccfep8 CH3Cl]$ source /local/apl/lx/g16/g16/bsd/g16.profile
In case your login shell is /bin/csh:
[user@ccfep8 CH3Cl]$ source /local/apl/lx/g16/g16/bsd/g16.login
This command won't output anything. But the setting will be modified. Now you can run formchk.
[user@ccfep8 CH3Cl]$ formchk ch3cl.chk ch3cl.fchk
Read checkpoint file ch3cl.chk
Write formatted file ch3cl.fchk
FChkPn: Coordinates translated and rotated
FChkPn: Coordintesmatch /B/ after translation and rotation
[user@ccfep8 CH3Cl]$
If you are not sure what your login shell is, please run "echo $SHELL" command like below.
[user@ccfep8 CH3Cl]$ echo $SHELL
These two lines below are equivalent.
[user@ccfep8 CH3Cl]$ g16sub ch3cl.gjf
[user@ccfep8 CH3Cl]$ g16sub -j core -rev g16c01 -np 6 -walltime 72:00:00 ch3cl.gjf
You can change settings by these options. For example, if you specify -np 4 in the command line, the submitted job will use 4 CPU cores.
Following versions and revisons of Gaussian are available on RCCS system.
Workding (scrtach) directory of the job is determined using the unique job ID.
SCRATCH dir: /work/users/****/${PBS_JOBID}
"${PBS_JOBID}" will be replaced by jobid (4529602.cccms1 for the example above). This directory name can be found at the beginning of the output file (ch3cl.out for the example in this page). But please note that the working directory will be automatically removed when the job is finished within the specified walltime.
If you want to change this behaviour, please see the section below.
You need to prepare input file template. Once the job script is prepared, you just need to run that job with "jsub" command instead of g16sub.
In either of cases, please submit the job with "jsub" command instead of g16sub/g09sub.