2,684
edits
Performance: Difference between revisions
Jump to navigation
Jump to search
→Single-machine considerations
| Line 11: | Line 11: | ||
# some overcommitting of resources (i.e. MAXIMUM_NUMBER_OF_PROCESSORS * MAXIMUM_NUMBER_OF_JOBS > number of cores) may be beneficial; you'll have to play with these two parameters since this depends on the actual hardware. If MAXIMUM_NUMBER_OF_PROCESSORS * MAXIMUM_NUMBER_OF_JOBS is >4096 (the default in RHEL), you may have to adjust the maxproc limit of your shell; in bash: <code>ulimit -u unlimited</code>. | # some overcommitting of resources (i.e. MAXIMUM_NUMBER_OF_PROCESSORS * MAXIMUM_NUMBER_OF_JOBS > number of cores) may be beneficial; you'll have to play with these two parameters since this depends on the actual hardware. If MAXIMUM_NUMBER_OF_PROCESSORS * MAXIMUM_NUMBER_OF_JOBS is >4096 (the default in RHEL), you may have to adjust the maxproc limit of your shell; in bash: <code>ulimit -u unlimited</code>. | ||
# the next thing to consider is [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DELPHI= DELPHI] together with [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#OSCILLATION_RANGE= OSCILLATION_RANGE]: if DELPHI (the rotation range of a ''batch'' of frames) is an integer multiple of MAXIMUM_NUMBER_OF_PROCESSORS * OSCILLATION_RANGE that would be good because it nicely balances the usage of the threads. For this purpose, you may want to change (if possible, raise) the value of DELPHI (default is 5 degrees). If you are doing fine-slicing then mis-balancing of threads is not an issue - but for those users who want to collect 1° frames (which I think is not the best way nowadays ...) it should be a consideration. Additional consideration: the total number of frames should be an integer multiple of the intended number of frames in a batch. Example: 360 frames of 0.5° can be processed on a 8-core machine optimally by specifying DELPHI=4, since then there are 8 frames in a batch and the complete dataset has 45 batches. For weak data one should consider raising DELPHI to 12; that would give 15 batches. A trick: if you want to use DELPHI=8 in this situation then just specify DATA_RANGE=1 368 (pretending 23 batches of 8°) instead of DATA_RANGE=1 360 . XDS will complain about the missing 8 frames, but that has no adverse effects except that no FRAME.cbf will be produced. All of this doesn't matter for a single dataset, but for mass processing of datasets it does make a difference. | # the next thing to consider is [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DELPHI= DELPHI] together with [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#OSCILLATION_RANGE= OSCILLATION_RANGE]: if DELPHI (the rotation range of a ''batch'' of frames) is an integer multiple of MAXIMUM_NUMBER_OF_PROCESSORS * OSCILLATION_RANGE that would be good because it nicely balances the usage of the threads. For this purpose, you may want to change (if possible, raise) the value of DELPHI (default is 5 degrees). If you are doing fine-slicing then mis-balancing of threads is not an issue - but for those users who want to collect 1° frames (which I think is not the best way nowadays ...) it should be a consideration. Additional consideration: the total number of frames should be an integer multiple of the intended number of frames in a batch. Example: 360 frames of 0.5° can be processed on a 8-core machine optimally by specifying DELPHI=4, since then there are 8 frames in a batch and the complete dataset has 45 batches. For weak data one should consider raising DELPHI to 12; that would give 15 batches. A trick: if you want to use DELPHI=8 in this situation then just specify DATA_RANGE=1 368 (pretending 23 batches of 8°) instead of DATA_RANGE=1 360 . XDS will complain about the missing 8 frames, but that has no adverse effects except that no FRAME.cbf will be produced. All of this doesn't matter for a single dataset, but for mass processing of datasets it does make a difference. | ||
# performance-wise, I/O also plays a role because as soon as you run 24 or so processes | # performance-wise, I/O also plays a role because as soon as you run 24 or so processes, a single Gigabit ethernet connection may be limiting. OTOH shell-level parallelization smoothes the load. | ||
# REFINE(INTEGRATE)= ! (empty list) makes INTEGRATE go much faster through the frames, since frames are processed less often when analyzing a batch of frames, and no geometry refinement takes place. | # REFINE(INTEGRATE)= ! (empty list) makes INTEGRATE go much faster through the frames, since frames are processed less often when analyzing a batch of frames, and no geometry refinement takes place. | ||
# XDS with the MAXIMUM_NUMBER_OF_JOBS and CLUSTER_NODES keywords can use [[Performance#Cluster|several machines]]. This requires some setup as explained at the bottom of [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/downloading.html]. | # XDS with the MAXIMUM_NUMBER_OF_JOBS and CLUSTER_NODES keywords can use [[Performance#Cluster|several machines]]. This requires some setup as explained at the bottom of [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/downloading.html]. | ||