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Performance: Difference between revisions
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# XDS scales well (i.e. the wallclock time for data processing goes down when the number of available cores is increased) in the COLSPOT, IDXREF, INTEGRATE and CORRECT steps when using the [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_PROCESSORS= MAXIMUM_NUMBER_OF_PROCESSORS] keyword. This triggers program-level parallelization, using [http://www.openmp.org OpenMP] threads. | # XDS scales well (i.e. the wallclock time for data processing goes down when the number of available cores is increased) in the COLSPOT, IDXREF, INTEGRATE and CORRECT steps when using the [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_PROCESSORS= MAXIMUM_NUMBER_OF_PROCESSORS] keyword. This triggers program-level parallelization, using [http://www.openmp.org OpenMP] threads. | ||
# the program scales very well in the COLSPOT and INTEGRATE steps when using the [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_JOBS= MAXIMUM_NUMBER_OF_JOBS] keyword. This triggers a shell-level parallelization. There is a slight penalty associated with high values of MAXIMUM_NUMBER_OF_JOBS= : | # the program scales very well in the COLSPOT and INTEGRATE steps when using the [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_NUMBER_OF_JOBS= MAXIMUM_NUMBER_OF_JOBS] keyword. This triggers a shell-level parallelization. There is a slight penalty associated with high values of MAXIMUM_NUMBER_OF_JOBS= : | ||
##in INTEGRATE, geometry refinement results are not transferred between JOBs: see [[Pathologies]]; | |||
##in COLSPOT, the phi values at the borders between JOBs are less accurate (in particular if the mosaicity is high), and the same reflection may be listed twice in SPOT.XDS if it extends over the border between JOBs. The latter effect may be mitigated by having as many SPOT_RANGEs as JOBs, and leaving gaps between the SPOT_RANGEs. | |||
# combining these two keywords gives the highest performance in my experience (see [[2VB1#XDS_processing]] for an example). As a rough guide, I'd choose them to be approximately equal; an even number for MAXIMUM_NUMBER_OF_PROCESSORS should be chosen because that fits better with usual hardware. If in doubt, use a lower number for MAXIMUM_NUMBER_OF_JOBS than for MAXIMUM_NUMBER_OF_PROCESSORS. | # combining these two keywords gives the highest performance in my experience (see [[2VB1#XDS_processing]] for an example). As a rough guide, I'd choose them to be approximately equal; an even number for MAXIMUM_NUMBER_OF_PROCESSORS should be chosen because that fits better with usual hardware. If in doubt, use a lower number for MAXIMUM_NUMBER_OF_JOBS than for MAXIMUM_NUMBER_OF_PROCESSORS. | ||
# some overcommitting of resources (i.e. MAXIMUM_NUMBER_OF_PROCESSORS * MAXIMUM_NUMBER_OF_JOBS > number of cores) is beneficial; you'll have to play with these two parameters. | # some overcommitting of resources (i.e. MAXIMUM_NUMBER_OF_PROCESSORS * MAXIMUM_NUMBER_OF_JOBS > number of cores) is beneficial; you'll have to play with these two parameters. | ||