I am using Gaussian 09 to calculate molecular charges. However, I encoutered an error which I never met before. It would really nice if someone can help me out. Thanks a lot!
I am using qsub job submitting system. The system error message is as following:
--------------------------------------------- System error information ---------------------------------------------------------------
Problem with file /home/software/gaussian/g09/l1.exe omode 33261 compare 7.
Error: segmentation violation
rax 0000000000000000, rbx 0000000000000203, rcx ffffffffffffffff
rdx 0000000000002767, rsp 00007fffb1aec208, rbp 00007fffb1af2f75
rsi 000000000000000b, rdi 0000000000002767, r8 00002b18c422b160
r9 0000000000000000, r10 00007fffb1aebf90, r11 0000000000000202
r12 00007fffb1af2f90, r13 00007fffb1af2690, r14 00007fffb1af2f90
r15 00007fffb1af0380
--- traceback not available
-------------------------------------------- System error information ----------------------------------------------------------------
Gaussian Output is :
-------------------------------------- Gaussian output error information --------------------------------------
Entering Gaussian System, Link 0=/home/software/gaussian/g09/g09
Files in the Gaussian directory are world accessible.
This must be fixed.
-------------------------------------- Gaussian output error information --------------------------------------
Gaussian Input file is：
-------------------------------------- Gaussian input file --------------------------------------
%NProcShared=32
%Chk=checkpoint.chk
#P AM1/STO-3G pop=chelpg scf=(direct)
L0617 Gaussian AM1
-10 1
O
H 1 B1
C 1 B2 2 A2
H 3 B3 1 A3 2 D3
balabala
-------------------------------------- Gaussian input file --------------------------------------
Job submitting script is:
-------------------------------------- job submitting script --------------------------------------
#!/bin/bash
#$ -pe mpi 32 #no. of processors going to using, can assign up to 128
#$ -N LAM1 #job name
#$ -cwd #change to working directory
#$ -e output2.err #specify file name for standard error
#$ -o output2.out #specify file name for standard output
# setting up Guassian environment
export g09root=/home/software/gaussian
# $HOME/tmp folder already been changed by chmod -R 777 $HOME/tmp
export GAUSS_SCRDIR=$HOME/tmp
source $g09root/g09/bsd/g09.profile
export MACHINEFILE=$TMPDIR/machines
filename=myjob
$g09root/g09/g09 < ${filename}.com > ${filename}.out
-------------------------------------- job submitting script --------------------------------------
Dear Liangzhen,
my wild guess is that you are permitting all the users to use Gaussian executables. According to the previous version of Gaussian:
"Making the Gaussian 03 directories world accessible (i.e. by all users) is a security problem, is prohibited by the license, and the program will now refuse to run if there is world access."
http://www.gaussian.com/g_misc/g03/g03_rel.htm
So you probably need to take care of the users/groups who can access the G09 executables - possibly by definition of new group. Maybe simply removing the executable permission to Others may be enough.
Hope this helps,
Martin
As Martin said, gaussian requires that the access to g09 directory (in your case it's apparently /home/software/gaussian/g09/g09) is restricted to you. The simplest way to do it is to change the permissions: e.g. chmod -R 700 /home/software/gaussian/g09 which will restrict the access to the entire directory (recursively) only to you, as long as you're the owner of the directory.
If not, do first chown -R your_username:your_username /home/software/gaussian/g09 (you man need to be superuser to perform it).
Hi Martin,
Thanks for your explanation. It helps.
I tried to tar the "/home/software/gaussian/g09" folder and copy the compressed file to my own folder "/home/liangzhen/software/" and unzip it, then I could have the g09 package copied to my own software folder. Therefore the g09 package in my own folder is only accessible to me. And I tried to run calculation using g09, it worked fine this time.
And, also thanks a lot, Bartosz. I am not the owner of the original Gaussian 09 directory. Since I am not the systAdd your answerem administrator, therefore I cannot chmod -R or chown -R. The problem is, the g09 was installed to be used by our whole lab, so I may ask the administrator to chmod -R 700 the folder. Besides, I was told that if chmod -R 755 may also solve the problem, however, I am not sure about this. I will ask the administrator to change the permission to have a try.
If anyone is still searching the easiest way is
chmod u+x *.exe
chmod u+x g09
Dear Devashish,
unfortunately your solution is not going to work in this case. The original problem stated by Liangzhen is that the files were "world accessible". Your suggestion would only give the user "executable permissions". Since the program was run by the OP, he already has the permissions to execute G09. The only workaround to avoid this kind of error is to tighten the permissions from world accessible as stated in the license.
Best regards,
Martin
Use this Worked for me...
chmod -R 700 /home/username/path_to_Gaussian/g09
*replace username & path_to_Gaussian accordingly.
The chmod command changes the permissions of the file/folder. The 700 means that the owner has full access, and no one else. The -r means to apply the rules recursively (through subfolders).
Thank You.
Dear Elaprolu and Bakary,
the critical error message is:
Search path GAUSS_EXEDIR is ""
: No such file or directory
That means "g09" command is looking in the directory "GAUSS_EXEDIR" which needs to be set as an environmental variable to the directory of your binaries, for example in bash:
GAUSS_EXEDIR="/home/user/path/to/gaussian/binaries/"
prior to running the g09 command.
Best,
Martin
Thank you Martin for your reply.
My problem was solved. I was setting the wrong path for GAUSS_SCRDIR.
I was directing as: GAUSS_SCRDIR=$WORKING_DIR/$PBS_JOBID
Now I'm using
GAUSS_SCRDIR=$WORKING_DIR
and it is working.
$WORKING_DIR being the working directory.
Best,
Ajay Khanna Sir,
My problem is solved through your way.
Thanks
I am also facing the same problem. I am trying to run g09 job in my own laptop (Linux OS). Unfortunately, My job gets terminated without any error message! I have followed the recommended answers, but can not get rid off the issue. The input and output files are attached herewith
Dear, Ajay Khanna
This: (without sudo permissions)
chmod -R 700 /home/username/path_to_Gaussian/g09
worked really well for me.
Thank you.
Best regards.
Dear Ajay Khanna
chmod -R 700 /home/username/path_to_Gaussian/g09
worked well for me too. Thanks
Ajay Khanna Martin Novak
Please can you help me to solve this problem error message #2070
# opt b3lyp/6-311++g(d,p) geom=connectivity
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
Unrecognized atomic symbol: ?d
Symbol not recognized in MSubst.
Error termination via Lnk1e in C:\G09W\l101.exe at Sun Mar 13 20:46:46 2022.
Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds.
File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1
thank you very much
Ayoub Chahid , it seems like Gaussian can't recognize an atomic symbol. Is it possible for you to share the list of atomic symbols from Z-matrix?
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