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If the "xds_par" binary crashed, try "xds". xds_par uses OpenMP for parallelization, which adds complexity. If it works with xds, but not with xds_par, then there is a chance that some environment variable needs to be set/changed. In any case the XDS developers would like to learn about this.
 
If the "xds_par" binary crashed, try "xds". xds_par uses OpenMP for parallelization, which adds complexity. If it works with xds, but not with xds_par, then there is a chance that some environment variable needs to be set/changed. In any case the XDS developers would like to learn about this.
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As of March 2021, Thomas Hauß (HZB) reported an OpenMP-related problem that is due to a bug in a library that the ifort compiler links into xds_par. It is unknown to us which version of the compiler has or does not have this bug. The bug has been seen with xds_par (VERSION Jan 31, 2020  BUILT=20200417) and is a crash with error message containing:
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<pre>
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OMP: Error #13: Assertion failure at z_Linux_util.cpp(2361).
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OMP: Hint Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.
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forrtl: error (76): Abort trap signal
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Image              PC                Routine            Line        Source           
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xds_par            00000000005620C4  Unknown              Unknown  Unknown
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libpthread-2.17.s  00002ADC08AAA630  Unknown              Unknown  Unknown
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libc-2.17.so      00002ADC08EF1387  gsignal              Unknown  Unknown
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libc-2.17.so      00002ADC08EF2A78  abort                Unknown  Unknown
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xds_par            000000000063FB83  Unknown              Unknown  Unknown
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xds_par            000000000062BDFF  Unknown              Unknown  Unknown
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xds_par            000000000060748C  Unknown              Unknown  Unknown
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xds_par            000000000067980E  Unknown              Unknown  Unknown
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xds_par            000000000063D737  Unknown              Unknown  Unknown
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xds_par            000000000063EC58  Unknown              Unknown  Unknown
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xds_par            0000000000629A0E  Unknown              Unknown  Unknown
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xds_par            0000000000419056  xds_                    21586  MAIN_XDS.f90
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xds_par            0000000000418951  MAIN__                      1  MAIN_XDS.f90
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xds_par            0000000000415862  Unknown              Unknown  Unknown
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libc-2.17.so      00002ADC08EDD555  __libc_start_main    Unknown  Unknown
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xds_par            0000000000415769  Unknown              Unknown  Unknown
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</pre>
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The bug is not related to the xds_par source code, but also happens with other software. The workaround is to set the environment variable
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    bash: export KMP_INIT_AT_FORK=FALSE
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    tcsh: setenv KMP_INIT_AT_FORK FALSE
    
=== 64bit binary on a 32bit operating system ===
 
=== 64bit binary on a 32bit operating system ===
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  THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN.
 
  THE "DATA_RANGE=" IN FILE "XDS.INP" AND START ALL OVER AGAIN.
   −
This is printed out for you to actually read, and take action accordingly. In most cases you just change the JOBS - line in XDS.INP to read
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This is printed out for you to actually read, and take action accordingly. In most cases you just change the JOB= line in XDS.INP to read
 
  JOB= DEFPIX INTEGRATE CORRECT
 
  JOB= DEFPIX INTEGRATE CORRECT
 
and then continue to run XDS. In other cases you may want to change SPOT.XDS, or other keywords in [[XDS.INP]] (see also below). But in any case this is an important alert that should make you check the correctness of the parameters that describe the data collection (X-RAY_WAVELENGTH, DETECTOR_DISTANCE, ORGX, ORGY, OSCILLATION_RANGE, NAME_TEMPLATE_OF_DATA_FRAMES).
 
and then continue to run XDS. In other cases you may want to change SPOT.XDS, or other keywords in [[XDS.INP]] (see also below). But in any case this is an important alert that should make you check the correctness of the parameters that describe the data collection (X-RAY_WAVELENGTH, DETECTOR_DISTANCE, ORGX, ORGY, OSCILLATION_RANGE, NAME_TEMPLATE_OF_DATA_FRAMES).
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If this does not help, try to refine even less items, e.g. leave out AXIS.
 
If this does not help, try to refine even less items, e.g. leave out AXIS.
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=== IDXREF prints ERROR IN REFINE !!! RETURN CODE IS IER= 0 ===
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This is due to either wrong inputs in XDS.INP, or due to bad data, e.g. spots from many crystals whose diffraction patterns overlap. The first possibility applies if the diffraction pattern is clean. The second applies if the diffraction pattern is ugly, and unsuitable for indexing. In that case, maybe try a different SPOT_RANGE.
    
=== IDXREF.LP does not show the expected lattice ===
 
=== IDXREF.LP does not show the expected lattice ===
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               BEAM_DIVERGENCE=    BEAM_DIVERGENCE_E.S.D.=  
 
               BEAM_DIVERGENCE=    BEAM_DIVERGENCE_E.S.D.=  
   −
then you should reduce the upper limit of the DATA_RANGE, to stop before the problematic frames, and re-run INTEGRATE. In this example, you would modify XDS.INP to have
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then there are two ways to resolve this:
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* you could insert a line DELPHI=10 (or DELPHI=20, for 10 or 20 degrees batches; the default is 5 degree batches) into XDS.INP and re-run INTEGRATE
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* as the error message suggests, you should reduce the upper limit of the DATA_RANGE, to stop before the problematic frames, and re-run INTEGRATE. In this example, you would modify XDS.INP to have
 
  DATA_RANGE=1 135
 
  DATA_RANGE=1 135
  JOB=INTEGRATE CORRECT
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  JOB=INTEGRATE CORRECT  
 
Save XDS.INP, run XDS and inspect INTEGRATE.LP, to find the lines (e.g.)
 
Save XDS.INP, run XDS and inspect INTEGRATE.LP, to find the lines (e.g.)
 
  BEAM_DIVERGENCE=  0.478  BEAM_DIVERGENCE_E.S.D.=  0.048
 
  BEAM_DIVERGENCE=  0.478  BEAM_DIVERGENCE_E.S.D.=  0.048
 
  REFLECTING_RANGE=  1.100  REFLECTING_RANGE_E.S.D.=  0.157
 
  REFLECTING_RANGE=  1.100  REFLECTING_RANGE_E.S.D.=  0.157
 
Copy them to XDS.INP. Restore the original DATA_RANGE and continue.
 
Copy them to XDS.INP. Restore the original DATA_RANGE and continue.
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If this problem happens with multiple XDS jobs working on the same data set, you might also get a message like
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.../bin1_02.tmp
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Image              PC                Routine            Line        Source           
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xds_par            0000000000592B91  Unknown              Unknown  Unknown
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xds_par            00000000004BEF21  joinintegrate_          8995  MAIN_XDS.f90
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xds_par            0000000000410A5B  xds_                    21690  MAIN_XDS.f90
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xds_par            000000000040B3A4  MAIN__                      1  MAIN_XDS.f90
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xds_par            00000000004083F6  Unknown              Unknown  Unknown
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libc.so.6          00007FB40222E830  Unknown              Unknown  Unknown
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xds_par            00000000004082E9  Unknown              Unknown  Unknown
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which looks like a real crash of the program, but in this case with a known reason.
    
Another error mode of INTEGRATE (in processing of small-molecule data) is ...
 
Another error mode of INTEGRATE (in processing of small-molecule data) is ...
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The error message is misleading in this case: there are too few reflections to build the average profile. The fix is: restart INTEGRATE after inserting e.g.
 
The error message is misleading in this case: there are too few reflections to build the average profile. The fix is: restart INTEGRATE after inserting e.g.
 
  DELPHI=20 ! default is 5, so try with e.g. 10, 20, 45, 90, 180  
 
  DELPHI=20 ! default is 5, so try with e.g. 10, 20, 45, 90, 180  
and re-run INTEGRATE.
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in XDS.INP and re-run INTEGRATE.
    
=== INTEGRATE cell and/or distance run away; xds crashes or has to be killed ===
 
=== INTEGRATE cell and/or distance run away; xds crashes or has to be killed ===
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