[sharp-discuss] problem with SFALL in SHARP

Clemens Vonrhein vonrhein@globalphasing.com
Mon, 2 Dec 2002 13:30:13 +0000


Hi,

remember that when running any CCP4 program through the interface
(Sushi) it will run under Bourne Shell (/bin/sh). Therefore, any
specific setups you have put into your own local
$CCP4/include/ccp4.setup and/or ~/.cshrc and/or ~/.login is not used.

Why might that be important? It looks to me as if the shell limits are
set too low - so even if your machine has 512Mb of memory any process
running under /bin/sh might be restricted to a much lower limit. So
how about doing the following:

  % /bin/sh
  % ulimit -a  # gives limits under /bin/sh

  and then

  % /bin/csh
  % limit -h   # gives limits under /bin/csh
  % unlimit    # removes all limits under /bin/cs
  % limit -h   

(the names don't quite match up, but you might see a difference anyway).

I'm suprised that with my (experimental) ccp4-4.2.1_cv1 patch it seems
to work. After all, this uses rather more memory than the official
version.

Have you tried using the official CCP4 distributed set of binaries?
It's at 4.2.2 at the moment ... so direct cmoparison is a bit
difficult.

Cheers

Clemens

On Sat, Nov 16, 2002 at 11:18:59PM +0800, chernhoe wrote:
> While I was testing the example inputs, I got stuck with SFALL
> complaining about a lack of memory (I got 512MB). This happens everytime
> for all the test cases when I am using ccp4-4.2.1 compiled using gnu
> compilers. The only way I could go around this problem was when I used
> the version compiled using vornhein's ccp4-4.2.1 compiled using ifc and
> gcc. This was even when I used the latest version of sushi/sharp. What
> should I do if I want to use ccp4 compiled using g77? 
> 
> 
> 1###############################################################
>  ###############################################################
>  ###############################################################
>  ### CCP4 4.2: SFALL              version 4.2       : 05/04/02##
>  ###############################################################
>  User:   Run date: 16/11/02  Run time:23:07:34
> 
> 
>  Please reference: Collaborative Computational Project, Number 4. 1994.
>  "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst.
> D50, 760-763.
> 
>  as well as any specific reference in the program write-up.
> 
> 
> 
>  Memory allocation (logical name, type, elements):
>    MEMSIZE R   2000000000
>  Last system error message:
>  Cannot allocate memory
>  SFALL:  CCPALC: can't allocate memory
>  Times: User:       0.0s System:    0.0s Elapsed:    0:00
> 
> 
> 
> 
> 
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss@globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss

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