[sharp-discuss] Problem with ARP/wARP autobuild

[Derek Logan]

Hi Clemens,

Thanks for this useful tip. It may take some time to report on whether or not it works, as I am still not sure what I or the system does to trip the problem.

On to the next question! I seem to be getting an ARP/wARP bug almost identical to the one described by Narayanan Ramasubbu in December 2009:

http://www.globalphasing.com/pipermail/sharp-discuss/2009-December/001983.html

i.e. the autobuilding script fails (see attached HTML) and directs me to look in the attached .log file, which says:

 Data line--- LABIN  E1=FBshasol E2
MtzParseLabin: run out of labels trying to match "E2"
 CAD:  Error in label assignments in LKYSET

When I Googled using this text I found the discussion from last December. However that issue was resolved by upgrading from 7.0.0 to 7.0.1, and I am already using 7.1. Can my problem be due to something else?

Thanks
Derek

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___________________________________________________________________
Derek Logan                                    tel: +46 46 222 1443
Associate Professor                            fax: +46 46 222 4692
Dept. of Biochemistry and Structural Biology   mob: +46 76 8585 707
Centre for Molecular Protein Science           www.cmps.lu.se
Lund University, Box 124, 221 00 Lund, Sweden  www.saromics.com

On Nov 19, 2010, at 12:53, Clemens Vonrhein wrote:

> Hi Derek,
> 
> On Fri, Nov 19, 2010 at 09:55:30AM +0100, Derek Logan wrote:
>>> as URL (assuming it is runnong on part 8080)? What does the
>>> $BDG_home/sushi/logs/error_log file has to say?
>> 
>> Yes, I also get it when logged onto the computer itself and using localhost. Looking in the SUSHI file the most relevant-looking lines I can find are:
> ...
>> perl: no user 503
>> perl: no user 503
>> 
>> The last 4 lines are then repeated at least 10 times.
>> 
>> Does this give you any further ideas?
> 
> Yes - this is most likely something we've seen before happening with
> Apples perl on Snow Leopard. We're still trying to convince Apple that
> this is a bug, but this proves slightly tricky.
> 
> I _think_ we have a workaround, that I wanted to test before sending a
> reply. But funnily enough, another user reports the same problem it
> seems just this morning. So if you're up to some testing yourself:
> 
>  1. install a different Perl distribution. The easiests would be
>     ActivePerl from
> 
>       http://www.activestate.com/activeperl/downloads
> 
>     This should install a new perl distribution into
>     /usr/local/ActivePerl-5.12.
> 
>  2. if you are still installing SHARP/autoSHARP: start again using
>     the command
> 
>     a) if you are using sh/bash/ksh/zsh:
> 
>        BDG_perl=/usr/local/ActivePerl-5.12/bin/perl
>        export BDG_perl
>        ./GPhL_SHARP_production-academic_install.sh
> 
>     b) for tcsh/csh
> 
>        setenv BDG_perl /usr/local/ActivePerl-5.12/bin/perl
>        ./GPhL_SHARP_production-academic_install.sh
> 
>  3. if you have already an installation: modify all
> 
>       machines/*/host.setup
> 
>     files (there should be only one) so that the BDG_perl parameter
>     in there points to
> 
>       /usr/local/ActivePerl-5.12/bin/perl
> 
> As I said, I haven't tested this (yet) in the context of a
> SHARP/autoSHARP server ... but it sounds right. If you try this and it
> works (even after loggin out again), please let us know.
> 
> If it doesn't work I'm sure you'll let us know anyway ;-)
> 
> Cheers
> 
> Clemens
> 
> 
> -- 
> 
> ***************************************************************
> * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
> *
> *  Global Phasing Ltd.
> *  Sheraton House, Castle Park 
> *  Cambridge CB3 0AX, UK
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