[sharp-discuss] error calculating maps

[Clemens Vonrhein]

Hi,

On Mon, Jul 30, 2007 at 12:53:18PM -0400, Alba Guarne wrote:
> Hi,
> 
> We have installed sharp and run our first jobs but we are unable to  
> see the maps. the problem is due to
> 
>   Variable "$BDG_mapman" is not imported at
>   /usr/local/sharp/sushi/cgi-bin/map.pl
>   line 532.
> 
> We've run mapman-setup and set it up to either xdlmapman or mapman,  

Hmmm - this should have been done automatically when you've run the

  % ./installSHARP -F

command. It seems you did the complicated 'installing every component
by hand' routine - see

  http://www.globalphasing.com/sharp/installation/scenarios.html

for some suggestions.

However, the 'mapman-setup' is the correct thing to do. Don't set it
to xdsmapman - this is an ANCIENT version of mapman once ported to
CCP4. Nothing you ever want to use these days. If you set the
parameter, you need to use the full path (so /usr/local/bin/mapman and
not just mapman).

> but when we try to generate O maps we get
> 
> child error=256
> OS error= bad file descriptor
> eval error=
> 
> Program "/usr/local/ccp4/bin/mapmask mapin $BDG_scr/20854.dir/EDEN. 
> 1.map"
> 
> and the logfile says that /tmp/20854.dir/EDEN.1.map cannot be opened

??? that is odd ... have you got the directory /tmp/20854.dir/? What
does $BDG_home/sushi/logs/error_log say?

> If we try to save the scripts to generate the map as a ccp4 tar file  
> we get a different error but also due to not finding a /tmp/20963.dir
> 
> child error=0
> OS error=bad file descriptor
> 
> What are we missing?

Something is wrong with your setup ... if you had to run mapman-setup
by hand (i.e. you did the installation by hand): have you run the
'newmachine' command at all? How did you install the SERVER and
MASTER, i.e. which instructions did you follow?

Cheers

Clemens


> 
> Thanks
> 
> Alba
> 
> 
> Alba Guarné, PhD
> Department of Biochemistry and Biomedical Sciences
> Health Sciences Centre, Room 4N57A
> McMaster University
> 1200 Main Street West. Hamilton, ON L8N 3Z5
> Phone: (905) 525-9140 ext. 26394
> FAX: (905) 522-9033
> 

> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/sharp-discuss


-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************