IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

sgifaceserver with big databases

Ed Griffiths edgrif at sanger.ac.uk
Mon Nov 11 12:35:04 EST 2002


> My ACEDB database is now rather large and I'm experiencing a problem
> with sgifaceserver 4.9f crashing as it trys to grab more memory than the
> user process datasize. I tried to up the datasize limit as root but I
> guess that only lasts as long as the current environment? As soon as the
> server crashes and restarts it inherits the (inadequate) hard limits
> that came with the system.
> Is there any way around this apart from rebuilding the kernel :-(

First, I don't know what operating system you are using so can't give exact

but.....the below is a start....

Process limits come in two flavours: "hard" and "soft", only root can increase
the "hard" limits and then only as high as the kernel build will allow. The soft
limit can be adjusted by a user for themselves up to the hard limit. The command
that adjusts the limit is built into the shell since if must execute within the
current shell to take effect, in csh the command is "limit" and you can see a
description by typing "man csh" and paging down to the "limit" section.

Display the process hard limits using   limit -h

If the limits for datasize and stacksize are big enough then you can adjust them
without needing to be root using:

limit datasize <insert_size_from_above>
limit stacksize <insert_size_from_above>

If you always want these limits then put them in your .cshrc file and all shells
will have this limit.

Try this and let me know how you get on.

cheers Ed
| Ed Griffiths, Acedb development, Informatics Group,                    |
|        Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,  |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif at sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |

More information about the Acedb mailing list

Send comments to us at biosci-help [At] net.bio.net