Ethan Merritt
Thu, 04 Feb 2010 09:01:12 -0800
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 > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > SORTMTZ: Normal termination > Times: User: 13.0s System: 1.2s Elapsed: 0:22 > </pre> > </html> > <!--SUMMARY_END--></FONT></B> > > *************************************************************************** > * 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