Performance: Difference between revisions

Performance (view source)

Revision as of 07:51, 5 April 2018

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→‎Single-machine considerations

Kay

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 In the order of effect:
-# XDS scales well (i.e. the wallclock time for data processing goes down when the number of available cores is increased) in the INIT, 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 INIT, 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. IDXREF and CORRECT have a significant serial part, for example due to I/O.
-# 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 parallelisation and results in individual processes run by the operating system. 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; see [[Problems#IDXREF_produces_too_long_axes]].
-# 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 (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. Since 2017, XDS has an automatic feature that divides up the available cores into JOBS (operating system processes) running with multiple cores each. You use this automatic feature when you run <code>xds_par</code>, and don't specify MAXIMUM_NUMBER_OF_JOBS.
-# NUMBER_OF_IMAGES_IN_CACHE avoids repeated (3-fold) reading of data frames in the INTEGRATE task during processing of a batch of frames. This comes at the expense of memory (RAM) and is discussed in [[Eiger]]. The default is DELPHI/OSCILLATION_RANGE+1 and is usually adequate. Only on low-memory systems (e.g a 8GB RAM machine for processing Eiger 16M data collected with 0.1° oscillation range, at DELPHI=5 and MAXIMUM_NUMBER_OF_JOBS=1) should this be set to 0, to conserve memory and avoid slow processing due to thrashing, or even killed XDS processes. If the cache size of a process exceeds 8GB, XDS will print a warning, and in that case the user has to explicitly include a NUMBER_OF_IMAGES_IN_CACHE=<desired number> line in XDS.INP, to confirm that actually so much memory should be used.
+# NUMBER_OF_IMAGES_IN_CACHE avoids repeated (3-fold) reading of data frames in the INTEGRATE task during processing of a batch of frames. This comes at the expense of memory (RAM) and is discussed in [[Eiger]]. The default is DELPHI/OSCILLATION_RANGE+1 and is usually adequate. Only on low-memory systems (e.g a 8GB RAM machine for processing Eiger 16M data collected with 0.1° oscillation range, at DELPHI=5 and MAXIMUM_NUMBER_OF_JOBS=1) should this be set to 0, to conserve memory and avoid slow processing due to thrashing, or even killed XDS processes. If the cache size of a process exceeds 8GB, XDS will print a warning, and in that case the user has to explicitly include a NUMBER_OF_IMAGES_IN_CACHE=<desired number> line in XDS.INP, to confirm that actually so much memory should be used. '''Typically, you don't specify NUMBER_OF_IMAGES_IN_CACHE'''.
 # 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. 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.
 # performance-wise, I/O also plays a role because as soon as you run 24 or so processes then a single GB 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.
-# XDS with the MAXIMUM_NUMBER_OF_JOBS keyword 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].
 # Hyperthreading (SMT), if available, is often beneficial. A "virtual" core has only about 20% performance of a "physical" core but it comes at no cost - you just have to switch it on in the BIOS of the machine.