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Eiger: Difference between revisions
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# It is advisable to use the most recent 64bit version of XDS (since version Oct 15, 2015 the 32bit versions are no longer distributed anyway). The idea of the new framecache in XDS is that RAM is used to save on I/O. To this end, XDS tries to store NUMBER_OF_IMAGES_IN_CACHE=DELPHI/OSCILLATION_RANGE images in memory. Each frame is stored as (number of pixels)*(4 bytes) which means 72 MB in case of the Eiger. As an example: if DELPHI=20 and OSCILLATION_RANGE=0.05 your computer has to have 400*72MB = 29GB of memory (plus some more for the program and the operating system). If it has not, the fallback is to the old behaviour of reading each frame three times. | # It is advisable to use the most recent 64bit version of XDS (since version Oct 15, 2015 the 32bit versions are no longer distributed anyway). The idea of the new framecache in XDS is that RAM is used to save on I/O. To this end, XDS tries to store NUMBER_OF_IMAGES_IN_CACHE=DELPHI/OSCILLATION_RANGE images in memory. Each frame is stored as (number of pixels)*(4 bytes) which means 72 MB in case of the Eiger. As an example: if DELPHI=20 and OSCILLATION_RANGE=0.05 your computer has to have 400*72MB = 29GB of memory (plus some more for the program and the operating system). If it has not, the fallback is to the old behaviour of reading each frame three times. | ||
# Dectris provides [https://www.dectris.com/tl_files/root/download/H5ToXds_x86_64.zip H5ToXds] which is needed by XDS. H5ToXds should be copied to e.g. /usr/local/bin/H5ToXds.bin . | # Dectris provides [https://www.dectris.com/tl_files/root/download/H5ToXds_x86_64.zip H5ToXds] which is needed by XDS. H5ToXds should be copied to e.g. /usr/local/bin/H5ToXds.bin - note the .bin filename extension! | ||
# For faster processing, the shell script below should be copied to /usr/local/bin/H5ToXds and made executable (<code>chmod a+rx /usr/local/bin/H5ToXds*</code>). This script ''also'' uses RAM to speed up processing; it uses it for fast storage of the temporary file that Dectris' H5ToXds writes, and that each parallel thread ("processor") of XDS reads. | # For faster processing, the shell script below should be copied to /usr/local/bin/H5ToXds and made executable (<code>chmod a+rx /usr/local/bin/H5ToXds*</code>). This script ''also'' uses RAM to speed up processing; it uses it for fast storage of the temporary file that Dectris' H5ToXds writes, and that each parallel thread ("processor") of XDS reads. The amount of additional RAM this requires is modest (about (number of pixels)*(number of threads) bytes). | ||
A suitable XDS.INP should normally be written by the beamline software; [[generate_XDS.INP]] does not (yet) write it. The XDS_from_H5.py script can be used if XDS.INP is not available. | A suitable XDS.INP should normally be written by the beamline software; [[generate_XDS.INP]] does not (yet) write it. The XDS_from_H5.py script can be used if XDS.INP is not available. | ||
The number of pixels of the Eiger 16M is 3 times higher than that of the Pilatus 6M. However, with the Eiger firmware installed in October 2015, the amount of data from a Eiger 16M experiment at SLS X06SA is 4-6 times larger for most users than the equivalent experiment on a Pilatus 6M (a future version of the Eiger firmware should produce better compression). It is therefore advisable to compress the .h5 files on-site, before transferring them home using disk or internet. | |||
The fastest (parallel) program with the best compression that I found is [http://lbzip2.org lbzip2] (available from the EPEL repository for RHEL clones). It is supposedly fully compatible with bzip2. | |||