How to run Gaussian03

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features.。
Please visit the Official Gaussian Web Site: http://www.gaussian.com/.

1. Supercomputer

1-1. Log in
Please use ssh command to log in.
　% ssh -l <user-id> super1
If you did not log in, please try below.
% ssh -l <user-id> super1.imr.edu

1-2. Create input file
Input file (***.com) is necessary to run Gaussian 03. You can specify molecular structure, calculation method, basis set, etc.

You need to set 'nproc=4'. If not, it will be forcelly cancelled.

1-3. Submit jobs
Please use submit command to submit jobs.
Please execute the following command at the working directory.
　　　% submit SC g03 input.com

There are following options for submit command.
　　% submit SC g03 input.com [ output.log ] [ -J Jobname ] [ -B ] [ -N ] [ -u mail_address ]

1-4. Check the job status
Please use statj command to check the job status.
　　% statj super
　（Example）
　　% statj super
　　### Application servers ###
　　JOBID 　　　　　　　　STAT QUEUE WAIT JOB_NAME　　　　 SUBMIT_TIME
　　super25-cx.6425.0 RUN 　qsc 　　　- 　　super25-cx.6425 07/05/30 09:21:06

"statj super" shows only jobs submitted to supercomputer and "statj" shows both jobs submitted to supercomputer and application servers.

Please refer to the this page for others commands.

1-5. Cancel the job
Please use jobdel command to cancel the job.
　　% jobdel Job_ID
　（Example）
　　% statj super
　　### Application servers ###
　　JOBID 　　　　　　　　STAT QUEUE WAIT JOB_NAME　　　　 SUBMIT_TIME
　　super25-cx.6425.0 RUN 　qsc 　　　- 　　super25-cx.6425 07/05/30 09:21:06
　　% jobdel super25-cx.6425.0
　　% statj super
　　### Application servers ###
　　JOBID 　　　　　　　　STAT QUEUE WAIT JOB_NAME　　　　 SUBMIT_TIME

1-6. Check the result
If your job have completed normally, the end of output file says as follows.
---
Normal termination of Gaussian 03 at Fri Apr 6 20:37:05 2007.
---
If your job have finished with error, please check the end of output file. The cause of error may be described.

(1) Not converged
If your job did not converge, the following messages will be appeared in the log file.
---
>>>>>>>>>> Convergence criterion not met.
SCF Done: E(RHF) = -10840.7420210 A.U. after 129 cycles
Convg = .3647D+00 -V/T = 2.0014
S**2 = .0000
Convergence failure -- run terminated.
Error termination via Lnk1e in /opt/g03/g03/l502.exe at Sun Apr 22 07:07:12 2007.
---
The maximum number of SCF cycle is 128 by default. Please try below.
　Increase the maximum number of SCF cycle: SCF=(MaxCycle=N)
　Change the SCF convergence criterion: SCF=(Conver=N)
　Change the basis sets

(2) memory allocation error
If your job exited caused by insufficient memory, the following message will be appeared in the log file.
---
Not enough memory in GToLag:
JobTyp=1 LenV= 1072666082 NeedRS= 441 LenG= 76245 MaxRS= 300
short by 11086689 words.
Error termination via Lnk1e in /app/g03/l1111.exe at Mon Apr 23 16:03:39 2007.
---
Please increase the memory size like %Mem=*GB in the input file.

If there is no message in the log file, it may exit caused by time limitation. The e-time limit is 7 days

1-7. How to run Gaussian utilities
When you run Gaussian utilities, formchk, please make the following script file.
---
#!/bin/csh
formchk test.chk test.fchk
---
After that, please submit as follows.
% submit SB general -exec script.sh

You may get the following messages when you use Gaussian utilities.
---
Out-of-memory error in routine FChkPn-MO (IEnd= 8469235 MxCore= 6291456)
Use %mem=9MW to provide the minimum amount of memory required to complete this step.
---
If you encounter this problem, please add the following statement in the script file.
setenv GAUSS_MEMDEF 9000000

2. Application server C

2-1. Log in
Please use ssh command to log in.
　% ssh -l <user-id> appc
If you did not log in, please try below.
% ssh -l <user-id> appc.imr.edu

2-2. Create input file
Input file (***.com) is necessary to run Gaussian 03. You can specify molecular structure, calculation method, basis set, etc.

2-3. Submit jobs
Please use submit command to submit jobs.

　＊serial calculation
　　Please execute the following command at the working directory.
　　　% submit cg03 input.com

　＊Parallel calculation using 4 cores.
　　Please execure the following command at the working directory.
　　　% submit cg03 input.com -n 4
　　Please change your input file to run 4 parallel job.
　　　NProcShared=4

　There are following options for submit command.
　　% submit cg03 input.com [ output.log ] [ -n num ] [ -J Jobname ] [ -B ] [ -N ] [ -u mail_address ]

The cg03 queue has some limitations. Please check below.

2-4. Check the job status
Please use statj command to check the job status.
　　% statj app
　（Example）
　　% statj app
　　### Application servers ###
　　JOBID STAT QUEUE WAIT EXEC_HOST JOB_NAME SUBMIT_TIME
　　9943　 RUN 　cg03 　　-　　 4*appc　　　　 test　　　　 07/04/24 09:48:06

"statj app" shows only jobs submitted to application servers and "statj" shows both jobs submitted to supercomputer and application servers.

Please refer to the this page for others commands.

2-5. Cancel the job
Please use jobdel command to cancel the job.
　　% jobdel Job_ID
　（Example）
　　% statj app
　　### Application servers ###
　　JOBID STAT QUEUE WAIT EXEC_HOST JOB_NAME SUBMIT_TIME
　　9943　 RUN 　cg03 　　-　　 4*appc　　　　 test　　　　 07/04/24 09:48:06
　　% jobdel 9943
　　% statj app
　　### Application servers ###
　　JOBID STAT QUEUE WAIT EXEC_HOST JOB_NAME SUBMIT_TIME

2-6. Check the result
If your job have completed normally, the end of output file says as follows.
---
Normal termination of Gaussian 03 at Fri Apr 6 20:37:05 2007.
---
If your job have finished with error, please check the end of output file. The cause of error may be described.

(1) Not converged
If your job did not converge, the following messages will be appeared in the log file.
---
>>>>>>>>>> Convergence criterion not met.
SCF Done: E(RHF) = -10840.7420210 A.U. after 129 cycles
Convg = .3647D+00 -V/T = 2.0014
S**2 = .0000
Convergence failure -- run terminated.
Error termination via Lnk1e in /opt/g03/g03/l502.exe at Sun Apr 22 07:07:12 2007.
---
The maximum number of SCF cycle is 128 by default. Please try below.
　Increase the maximum number of SCF cycle: SCF=(MaxCycle=N)
　Change the SCF convergence criterion: SCF=(Conver=N)
　Change the basis sets

(2) memory allocation error
If your job exited caused by insufficient memory, the following message will be appeared in the log file.
---
Not enough memory in GToLag:
JobTyp=1 LenV= 1072666082 NeedRS= 441 LenG= 76245 MaxRS= 300
short by 11086689 words.
Error termination via Lnk1e in /app/g03/l1111.exe at Mon Apr 23 16:03:39 2007.
---
Please increase the memory size like %Mem=*GB in the input file.

If there is no message in the log file, it may exit caused by CPU time limitation. The CPU time limit is 7 days. The standard output and standard error are stored to file named Job_ID.out and Job_ID.err, respectively. Please check the elapsed time and CPU time described in the standard output file. If you put the -N option, it will be sent to the specified address.

2-7. How to run Gaussian utilities
When you run Gaussian utilities, formchk, please make the following script file.
---
#!/bin/csh
formchk test.chk test.fchk
---
After that, please submit as follows.
% submit cm -exec script.sh

You may get the following messages when you use Gaussian utilities.
---
Out-of-memory error in routine FChkPn-MO (IEnd= 8469235 MxCore= 6291456)
Use %mem=9MW to provide the minimum amount of memory required to complete this step.
---
If you encounter this problem, please add the following statement in the script file.
setenv GAUSS_MEMDEF 9000000