GENESIS: Documentation

Related Documentation:

Frequently Asked Questions

This page provides answers to frequently asked questions (FAQ). The answers to particular questions contain links to more detailed documentation. Questions and their answers are added to the lists as they are received by either the genesis-sim-users mailing list or the GENESIS Development Team.

The categories of FAQ are as listed below. They can be extended as needed or requested.


  1. Why should I subscribe to the GENESIS mailing list?
    Although anyone can email a question or reply to the GENESIS mailing list, if you are not registered, you will only receive a reply if the person answering your question remembers to “reply to all”, something that cannot be guaranteed.
  2. How do I join the genesis-sim-users mailing list?
    Instructions can be found at:

  3. How do I email the genesis-sim-users mailing list?
    Send an email to:

  4. How do I contact the GENESIS Developers Team?
    You can contact us directly at:

  5. How do I generate a FAQ?
    The preferred method of generating a FAQ is to email the genesis-sim-users mailing list. As replies are received a FAQ response will be generated.

    For further information see Workflow User Question.

  6. Who should I be when installing GENESIS on my computer?
    GENESIS should not be installed as superuser/root/administrator or by using the sudo command. However, installation as a regular user will result in a prompt requesting the root password to be entered for each component installed.

    Testing an installation (recommended) as superuser (not recommended) via the command:

       neurospaces_check >/tmp/check.out 2>&1

    generates files that are owned by root. Subsequent use of GENESIS will fail as many files will not be owned by the user. For example, when running Example Script 1 in Tutorial 1, an error message similar to the following will be generated:

       genesis > create cell /n  
       . . .  
       genesis > check /n  
       Can’t locate object method "new" via package "SSP" at /usr/local/glue/swig/perl/ line 1314.  
       at /usr/local/bin/genesis-g3 line 40  
               main::__ANON__(’Can\’t locate object method "new" via package "SSP" at /usr/l...’) called at /usr/local/glue/swig/perl/ line 1314  
               GENESIS3::Commands::run(’/n’, 0) called at /usr/local/glue/swig/perl/ line 224  
               GENESIS3::Commands::check(’/n’) called at (eval 89) line 1  
               eval ’GENESIS3::Commands::check( \’/n\’, )  
       ;’ called at /usr/local/bin/genesis-g3 line 146  
               main::interprete(’check /n’) called at /usr/local/bin/genesis-g3 line 217  
               main::loop() called at /usr/local/bin/genesis-g3 line 279  
               main::main() called at /usr/local/bin/genesis-g3 line 339  
       $Result = undef;  

    If you have this problem a quick fix is to:

    1. Delete all files in /tmp owned by root (find owner with “ls -l”) that were produced by neurospaces_check with a command such as the following:
      root /tmp #  rm -Rf neurospaces/ morphology* file* text_* report_* heccer output* purk_test_soma* readcell_reset.txt  traub91_* text_gshell_1.* singlep.ssp 1.* current_schedule a1 a2  

    2. If the previous step doesn’t fix the problem, remove all _Inline directories from your home directory/folder.
    3. Keep removing files owned by root in /tmp and the _Inline directories in your home directory, until the problem is resolved.

    Although GENESIS is a system-wide install, currently only a single account owner or user should uniquely use a single copy of GENESIS on a machine.

FAQ Acknowledgment: Alexandre Gravier.


  1. How do I find the version numbers of the GENESIS components I have installed ?
    There are several ways to determine the version of the GENESIS components that are currently installed on your machine: