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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 16M. 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 16M. 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/news.html?page=2 H5ToXds] (Linux only!) which is needed by XDS. H5ToXds should be copied to e.g. /usr/local/bin/H5ToXds.bin - note the .bin filename extension! | # Dectris provides [https://www.dectris.com/news.html?page=2 H5ToXds] (Linux only!) which is needed by XDS. H5ToXds should be copied to e.g. /usr/local/bin/H5ToXds.bin - note the .bin filename extension! As an alternative, one could use GlobalPhasing's hdf2min-cbf program or, from http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/downloads, the miniCBF-OSX or miniCBF-Linux program. | ||
# 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). | # 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). | ||
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# Installation: This script should reside in $PATH, e.g. /usr/local/bin/H5ToXds | # Installation: This script should reside in $PATH, e.g. /usr/local/bin/H5ToXds | ||
# Dectris' H5ToXds should be /usr/local/bin/H5ToXds.bin | # Dectris' H5ToXds should be /usr/local/bin/H5ToXds.bin | ||
# Alternatively, miniCBF-Linux or miniCBF-OSX or hdf2mini-cbf could be installed | |||
# | # | ||
# Recommendation: | # Recommendation: | ||
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# | # | ||
/usr/local/bin/H5ToXds.bin $1 $2 "$tempfile" | /usr/local/bin/H5ToXds.bin $1 $2 "$tempfile" | ||
# | |||
# if miniCBF-Linux/miniCBF-OSX or Globalphasing's hdf2min-cbf are used, the above line needs to be adapted | |||
# | |||
ln -sf "$tempfile" $3 2>/dev/null | ln -sf "$tempfile" $3 2>/dev/null | ||
</pre> | </pre> | ||