I am connected to a supercomputer via SSH and my cluster uses Linux Scientific, I am using the Bash (Unix Shell), I load the modules of Gaussian 09 and Gaussview. I am trying to print orbital densities for a very large tetramer system, but when I try to generate the orbitals on Gaussview, the system crashes because of insufficient memory. On the internet, I found that using the "cubegen" keyword I can generate the cube files of the orbitals. The keyword gives me the power to modify the amount of memory but I do not know how. I go to interactive mode so I can use computational resources directly and on the command shell I do the following: (I try changing Gaussian's memory's environmental variable directly at the folder I am at)



cubegen 16000000 MO=HOMO xxx.fchk xxx.cub 0 h

But it still crashes with the following message,

Out-of-memory error in routine DecCub-RdMO (IEnd=      34279201 MxCore=      33546152)
Use %mem=33MW to provide the minimum amount of memory required to complete this step.
Error termination via Lnk1e at Wed Sep 28 16:41:41 2016.
Segmentation fault (core dumped)

How can I solve this problem? How can I allocate memory to Gaussian from the command window (I do not know where Gaussian folders are located since I just load it as a module, given that the software is already installed on the system)

  • 2
    $\begingroup$ First, you need to know which shell is used. You can type echo $0 to see which shell you are using. $\endgroup$
    – Wildcat
    Sep 28, 2016 at 17:33
  • 3
    $\begingroup$ Anyway, I guess (from the error message), that GAUSS_MEMDEF=33000000 cubegen bla-bla should work fine, at least in Bash shell. IIRC, GAUSS_MEMDEF is set in words, so since the error message says 33MW are needed, use the value 33000000, or a bit more, say, 35000000. $\endgroup$
    – Wildcat
    Sep 28, 2016 at 17:43
  • 1
    $\begingroup$ Note that cubegen nprocs kind fchkfile cubefile npts format cubefile2, so the second number should be the number of processes you'd like to use not the memory. $\endgroup$ Sep 29, 2016 at 3:40
  • 1
    $\begingroup$ Btw. GAUSS_MEMDEF=16gb cubgen [...] should also work fine. It must be set immediately before the command though. As a over the thumb rule you can use 1MW are about 8MB for a 64 bit machine. $\endgroup$ Sep 29, 2016 at 3:48
  • $\begingroup$ For cubegen you want to set GAUSS_UDEF: ``` export GAUSS_UDEF=4GB ``` Then you should be able to run cubegen with nprocs=1 (or whatever). $\endgroup$ Jun 27, 2019 at 20:17

1 Answer 1


By reading the information from Gaussian about cubegen, you would find out, that use of cubegen is like the following:

cubegen nprocs kind fchkfile cubefile npts format cubefile2

They further elaborate about nprocs:


Number of shared memory processors used for electrostatic potential calculations. A value of 0 is equivalent to 1 (it is the default). Note that this parameter must be included if other parameters are specified. Previously this parameter was used to specify the amount of memory to allocate. The GAUSS_MEMDEF environment variable should be used instead.

You can read about setting GAUSS_MEMDEF on the site about the default.route file.

Environment Variables

All of these directives can also be set via environment variables or UNIX command line arguments. The environment variable GAUSS_XDEF provides a line equivalent to -X- in the Default.Route file. Similarly, the command line argument below specifies the same setting:

$ g09 -x="value"

Similarly, all of the following have the equivalent effect:

Default.Route file: -M- 4GB
bash shell: export GAUSS_MDEF=4GB
tcsh shell: setenv GAUSS_MDEF 4GB
command line: g09 -m="4GB"

Based on that, you could try the way by exporting GAUSS_MDEF to the amount that you want, or by using the commandline. But I have no idea if the latter works with cubegen instead of g09. Let me know. :)

  • 3
    $\begingroup$ The latter will not work with cubegen, I tried. Setting (export) the environment variable works very well (it affects the whole session though). It also works immediately specifying it before the command GAUSS_MEMDEF=X cubegen .... $\endgroup$ Oct 11, 2016 at 5:18

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.