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