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== XDS processing == | == XDS processing == | ||
# use [[generate_XDS.INP]] to obtain a good starting point | |||
# edit [[XDS.INP]] and change the following: | |||
ORGX=3130 ORGY=3040 ! for ADSC, header values are subject to interpretation; better inspect the table in IDXREF.LP! | ORGX=3130 ORGY=3040 ! for ADSC, header values are subject to interpretation; better inspect the table in IDXREF.LP! | ||
TRUSTED_REGION=0 1.5 ! we want the whole detector area | TRUSTED_REGION=0 1.5 ! we want the whole detector area | ||
ROTATION_AXIS=-1 0 0 ! at this beamline the spindle goes backwards! | ROTATION_AXIS=-1 0 0 ! at this beamline the spindle goes backwards! | ||
# for faster processing on a machine with many cores, use (e.g. for 16 cores): | |||
MAXIMUM_NUMBER_OF_PROCESSORS=2 | MAXIMUM_NUMBER_OF_PROCESSORS=2 | ||
MAXIMUM_NUMBER_OF_JOBS=8 | MAXIMUM_NUMBER_OF_JOBS=8 | ||
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and run "xds_par" again. It completes after about 5 minutes on a fast machine, and we may inspect CORRECT.LP . | and run "xds_par" again. It completes after about 5 minutes on a fast machine, and we may inspect CORRECT.LP . | ||
=== Optimization === | |||
The main target of optimization is the asympototic (i.e. best) I/sigma (ISa) (Diederichs (2010) [http://dx.doi.org/10.1107/S0907444910014836 Acta Cryst. D 66, 733-40]) as printed out by CORRECT. A higher ISa means better data. However: ISa also rises if more reflections are thrown out as outliers ("misfits") so it is not considered to be optimization if just WFAC1 is reduced. | |||
The following quantities may be tested for their influence on ISa: | |||
* copying GXPARM.XDS to XPARM.XDS | |||
* including the information from the first integration pass into XDS.INP - just do "grep _E INTEGRATE.LP|tail -2" and get e.g. | |||
BEAM_DIVERGENCE= 0.386 BEAM_DIVERGENCE_E.S.D.= 0.039 | |||
REFLECTING_RANGE= 0.669 REFLECTING_RANGE_E.S.D.= 0.096 | |||
copy these two lines into XDS.INP | |||
== Example: sweep e == | |||
=== [[XDS.INP]]; as generated by [[generate_XDS.INP]] === | |||
=== [[CORRECT.LP]] main table; 1st pass === | |||
=== [[XDS.INP]]; optimized === | |||
=== [[CORRECT.LP]] main table; optimization pass === | |||
=== CORRECT.LP main table; optimization pass === | |||
== XSCALE results == | == XSCALE results == | ||
a few sweeps were optimized by copying the two lines containing mosaicity and beam divergence values from | a few sweeps were optimized by copying the two lines containing mosaicity and beam divergence values from INTEGRATE.LP to XDS.INP | ||
=== main table === | === main table === | ||
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== Comparison of data processing: published (2006) ''vs'' XDS results == | |||
== Comparison of data processing: published ''vs'' XDS results == | |||
<table border = "1"> | <table border = "1"> | ||
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<tr><b> | <tr><b> | ||
<td> published </td> | <td> published(2006) </td> | ||
<td> 30-0.65Å (0.67-0.65Å) </td> | <td> 30-0.65Å (0.67-0.65Å) </td> | ||
<td> 1331953 (12764) </td> | <td> 1331953 (12764) </td> | ||
| Line 165: | Line 123: | ||
</table> | </table> | ||
== timings for processing sweep "e" as a function of MAXIMUM_NUMBER_OF_PROCESSORS and MAXIMUM_NUMBER_OF_JOBS == | |||
The following is going to be rather technical! If you are only interested in crystallography, skip this. | |||
Using | |||
MAXIMUM_NUMBER_OF_PROCESSORS=2 | |||
MAXIMUM_NUMBER_OF_JOBS=8 | |||
we observe for the INTEGRATE step: | |||
total cpu time used 2063.6 sec | |||
total elapsed wall-clock time 296.1 sec | |||
Using | |||
MAXIMUM_NUMBER_OF_PROCESSORS=1 | |||
MAXIMUM_NUMBER_OF_JOBS=16 | |||
the times are | |||
total cpu time used 2077.1 sec | |||
total elapsed wall-clock time 408.2 sec | |||
Using | |||
MAXIMUM_NUMBER_OF_PROCESSORS=4 | |||
MAXIMUM_NUMBER_OF_JOBS=4 | |||
the times are | |||
total cpu time used 2102.8 sec | |||
total elapsed wall-clock time 315.6 sec | |||
Using | |||
MAXIMUM_NUMBER_OF_PROCESSORS=16 ! the default for xds_par on a 16-core machine | |||
MAXIMUM_NUMBER_OF_JOBS=1 ! the default | |||
the times are | |||
total cpu time used 2833.4 sec | |||
total elapsed wall-clock time 566.5 sec | |||
but please note that this actually only uses 10 processors, since the default DELPHI=5 | |||
and the OSCILLATION_RANGE is 0.5°. | |||
Using | |||
MAXIMUM_NUMBER_OF_PROCESSORS=4 | |||
MAXIMUM_NUMBER_OF_JOBS=8 | |||
(thus overcommitting the available cores by a factor of 2) the times are | |||
total cpu time used 2263.5 sec | |||
total elapsed wall-clock time 320.8 sec | |||
Using | |||
MAXIMUM_NUMBER_OF_PROCESSORS=4 | |||
MAXIMUM_NUMBER_OF_JOBS=6 | |||
(thus overcommitting the available cores, but less severely) the times are | |||
total cpu time used 2367.6 sec | |||
total elapsed wall-clock time 267.2 sec | |||
Thus, | |||
MAXIMUM_NUMBER_OF_PROCESSORS=4 | |||
MAXIMUM_NUMBER_OF_JOBS=6 | |||
performs best for a 2-Xeon X5570 (HT enabled, thus 24 cores) machine with 24GB of memory and a RAID1 consisting of 2 1TB SATA disks. It should be noted that the dataset has 27GB, and in 296 seconds this means 92 MB/s continuous reading. The processing time is thus limited by the disk access, not by the CPU. And no, the data are not simply read from RAM (tested by "echo 3 > /proc/sys/vm/drop_caches" before the XDS run). | |||