2,652
edits
Problems: Difference between revisions
Jump to navigation
Jump to search
→Problems with OpenMP
(→Integration failure: INTEGRATE run-away) |
|||
| (6 intermediate revisions by the same user not shown) | |||
| Line 3: | Line 3: | ||
== XDS crashes == | == XDS crashes == | ||
XDS should never crash (if it terminates with an error message, this does not count as crash). If it does, it is either a bug in the program which should be brought to the attention of Wolfgang Kabsch or Kay Diederichs, and will be fixed, or it is a problem with your computer. | XDS should never crash (if it terminates with an error message, this does not count as crash). If it does, it is either a bug in the program which should be brought to the attention of Wolfgang Kabsch or Kay Diederichs, and will be fixed, or it is a problem with your computer, or (rarely) it is due to improper inputs ([[Problems#INTEGRATE_cell_and.2For_distance_run_away.3B_xds_crashes_or_has_to_be_killed|this]] is the only example I know of). | ||
If it crashes for the second reason, these are the things to try/consider: | If it crashes for the second reason, these are the things to try/consider: | ||
| Line 30: | Line 30: | ||
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. | ||
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: | |||
<pre> | |||
OMP: Error #13: Assertion failure at z_Linux_util.cpp(2361). | |||
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/. | |||
forrtl: error (76): Abort trap signal | |||
Image PC Routine Line Source | |||
xds_par 00000000005620C4 Unknown Unknown Unknown | |||
libpthread-2.17.s 00002ADC08AAA630 Unknown Unknown Unknown | |||
libc-2.17.so 00002ADC08EF1387 gsignal Unknown Unknown | |||
libc-2.17.so 00002ADC08EF2A78 abort Unknown Unknown | |||
xds_par 000000000063FB83 Unknown Unknown Unknown | |||
xds_par 000000000062BDFF Unknown Unknown Unknown | |||
xds_par 000000000060748C Unknown Unknown Unknown | |||
xds_par 000000000067980E Unknown Unknown Unknown | |||
xds_par 000000000063D737 Unknown Unknown Unknown | |||
xds_par 000000000063EC58 Unknown Unknown Unknown | |||
xds_par 0000000000629A0E Unknown Unknown Unknown | |||
xds_par 0000000000419056 xds_ 21586 MAIN_XDS.f90 | |||
xds_par 0000000000418951 MAIN__ 1 MAIN_XDS.f90 | |||
xds_par 0000000000415862 Unknown Unknown Unknown | |||
libc-2.17.so 00002ADC08EDD555 __libc_start_main Unknown Unknown | |||
xds_par 0000000000415769 Unknown Unknown Unknown | |||
</pre> | |||
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 | |||
bash: export KMP_INIT_AT_FORK=FALSE | |||
tcsh: setenv KMP_INIT_AT_FORK FALSE | |||
=== 64bit binary on a 32bit operating system === | === 64bit binary on a 32bit operating system === | ||
| Line 111: | Line 138: | ||
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 | 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). | ||
| Line 206: | Line 233: | ||
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. | ||
=== IDXREF prints ERROR IN REFINE !!! RETURN CODE IS IER= 0 === | |||
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 === | ||
| Line 244: | Line 275: | ||
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 | then there are two ways to resolve this: | ||
* 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 | |||
* 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 | 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. | ||
If this problem happens with multiple XDS jobs working on the same data set, you might also get a message like | |||
.../bin1_02.tmp | |||
Image PC Routine Line Source | |||
xds_par 0000000000592B91 Unknown Unknown Unknown | |||
xds_par 00000000004BEF21 joinintegrate_ 8995 MAIN_XDS.f90 | |||
xds_par 0000000000410A5B xds_ 21690 MAIN_XDS.f90 | |||
xds_par 000000000040B3A4 MAIN__ 1 MAIN_XDS.f90 | |||
xds_par 00000000004083F6 Unknown Unknown Unknown | |||
libc.so.6 00007FB40222E830 Unknown Unknown Unknown | |||
xds_par 00000000004082E9 Unknown Unknown Unknown | |||
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 ... | ||
| Line 263: | Line 308: | ||
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. | 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 === | ||