Re: [ccp4bb] Strange problem running cpp4i over nx - job reported as failed even though it succeeds-log file has nx errors

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Melanie Adams-Cioaba maa23 {- at -} PSU {- dot -} EDU
Date: 2010-02-04

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Subject: Re: Strange problem running cpp4i over nx - job reported as failed even though it succeeds-log file has nx errors
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2010-02-04

On Thursday 04 February 2010 05:14:24 hari jayaram wrote:
> Hi I just installed a fresh ccp4-6.1.3 installation on my 64 bit ubuntu box.
> After the install my first job was a regular ccp4 sortmtz job using
> ccp4i gui .
>
> The sortmtz job "fails" with the following NX - related errors in the
> log file ( see below and snapshot above).
> Also the GUI says the job failed , even though the output files seems
> well in order.
> mtzdump also gives an error popup saying problem in mtzdump and then
> goes ahead and displays the mtzdump information just fine.
>
> sortmtz and mtzdump work just fine from the command line so the error
> seems NX client / ccp4i related.
>
> I will try and run it directly on the machine without NX once I get
> in. But thought I would report this rather strange non ccp4 related
> error in the ccp4 log file.
>
> Thanks
> Hari
>
> * Resolution Range :
>
> 0.00019 0.13717 ( 73.369 - 2.700 A )
>
> * Sort Order :
>
> 1 2 3 0 0
>
> * Space group = 'P3' (number 143)
>
> 3179776 records output
>
> SORTMTZ: Normal termination
> Times: User: 13.0s System: 1.2s Elapsed: 0:22
>
>
>
>
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> The program run with command: /mega/ccp4-6.1.3/ccp4-6.1.3/bin/sortmtz
> HKLOUT "/mega/hj-8-2-1/hjbr5-1/hjbr5-1_sorted_mosflm.mtz"
> has failed with error message
> ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD
> cannot be preloaded: ignored.

My guess is that your machine configuration includes a file that
initializes LD_PRELOAD for NX on login. But it should not do this.

The LD_PRELOAD setting applies to all programs, so it should not
be set blindly to include program-specific libraries.
What you see, I think, is that ccp4 is trying to load the NX
initialization libraries because they are present in LD_PRELOAD.
If you clear LD_PRELOAD from your environment (actually from
ccp4's environment, which may not be the same thing if run by
script from ccp4i) I think this problem will go away.

Ethan

> ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from LD_PRELOAD cannot
> be preloaded: ignored.
> ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD
> cannot be preloaded: ignored.
> ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from LD_PRELOAD cannot
> be preloaded: ignored.
> ***************************************************************************
>
>
> #CCP4I TERMINATION STATUS 0 "ERROR: ld.so: object
> '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded:
> ignored. ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from
> LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object
> '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded:
> ignored. ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from
> LD_PRELOAD cannot be preloaded: ignored."
> #CCP4I TERMINATION TIME 04 Feb 2010 07:59:30
> #CCP4I MESSAGE Task failed
>
>
> #CCP4I TERMINATION STATUS 0 ERROR: ld.so: object
> '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded:
> ignored. ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from
> LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object
> '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded:
> ignored. ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from
> LD_PRELOAD cannot be preloaded: ignored.Error from script
> /mega/ccp4-6.1.3/ccp4-6.1.3/ccp4i/scripts/sortmtz.script: invalid
> command name "CreateAnnotatedLogfile"
> #CCP4I TERMINATION TIME 04 Feb 2010 07:59:30
> #CCP4I MESSAGE Task failed
>

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Dynamics Software for DynaPro DLS?
From: Melanie Adams-Cioaba maa23 {- at -} PSU {- dot -} EDU
Date: 2010-02-04

Next message:
Subject: DLS installation Files Found
From: Melanie Adams-Cioaba maa23 {- at -} PSU {- dot -} EDU
Date: 2010-02-04