2VB1

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!
TRUSTED_REGION=0 1.5 ! we want the whole detector area
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_JOBS=8

For all the sweeps, processing stopped with the usual error message after the IDXREF step.

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

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 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).