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Eiger: Difference between revisions
→Slower way of processing Eiger data with XDS i.e. using H5ToXds/eiger2cbf to convert to CBF
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</pre> | </pre> | ||
= | = Less efficient way of processing Eiger data, using conversion to CBF= | ||
Since the release of NEGGIA, a plugin for XDS that parallelizes the reading of images from HDF5 data, conversion to H5ToXds | Since the release of NEGGIA, a plugin for XDS that parallelizes the reading of images from HDF5 data, conversion to H5ToXds should no longer required in most usage scenarios. The sections below nevertheless describe this possibility, since preliminary experience with some less common network file systems (apparently GPFS, but not NFS) seems to indicate low performance of NEGGIA. | ||
Dectris provides | Conversion program options: Dectris provides [https://www.dectris.com/news.html?page=2 H5ToXds] (Linux only!). That program converts (as the name indicates) the HDF5 files to CBF files; however, it does not write the geometry and other information into the CBF header (therefore, [[generate_XDS.INP]] or MOSFLM does not work with these files). Alternatives are GlobalPhasing's hdf2mini-cbf program (needs autoPROC license) or, from http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/downloads, the eiger2cbf-osx or eiger2cbf-linux program written by T. Nakane. The latter programs do write a useful CBF header. | ||
For faster processing | For faster processing, the [[Eiger#A_script_for_faster_XDS_processing_of_CBF-converted Eiger data|shell script]] below should be copied to /usr/local/bin/H5ToXds and made executable (<code>chmod a+rx /usr/local/bin/H5ToXds*</code>). The binary H5ToXds then should be named e.g. /usr/local/bin/H5ToXds.bin - note the .bin filename extension! The script ''also'' uses RAM to speed up processing; it uses it for fast storage of the temporary CBF file that H5ToXds/eiger2cbf/hdf2mini-cbf 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). | ||
== Benchmark using H5ToXds == | == Benchmark using H5ToXds == | ||
The numbers below refer to the H5ToXds binary as used in the script below. | This was run on a single unloaded CentOS7.2 64bit machine with dual Intel(R) Xeon(R) CPU E5-2667 v2 @ 3.30GHz , HT enabled (showing 32 processors in /proc/cpuinfo), on a local XFS filesystem (all defaults), with four JOBs and 12 PROCESSORS. The numbers below refer to the H5ToXds binary as used in the script below. | ||
The timing, using the XDS (BUILT=20151231), is on the first run | The timing, using the XDS (BUILT=20151231), is on the first run | ||
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which indicates a 24% overhead due to the HDF5-to-CBF conversion. However, one has to add to this the time for the HDF5-to-CBF conversion, which is (with 18 parallel H5ToXds jobs each converting 50 frames) 34.2 sec, so overall the "on-the-fly" route using the script below is faster than the "pre-conversion" route, at least on this machine. | which indicates a 24% overhead due to the HDF5-to-CBF conversion. However, one has to add to this the time for the HDF5-to-CBF conversion, which is (with 18 parallel H5ToXds jobs each converting 50 frames) 34.2 sec, so overall the "on-the-fly" route using the script below is faster than the "pre-conversion" route, at least on this machine. | ||
== A script for faster XDS processing of Eiger data == | == A script for faster XDS processing of CBF-converted Eiger data == | ||
<pre> | <pre> | ||
#!/bin/bash | #!/bin/bash | ||
# Kay Diederichs 10/2015 | # Kay Diederichs 10/2015 | ||
# 3/2016 adapt for eiger2cbf | # 3/2017 include RAMdisk creation for MacOS: attention, this is untested! | ||
# 3/2016 adapt for eiger2cbf and hdf2mini-cbf | |||
# for the latter see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;58a4ee1.1603 and | # for the latter see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;58a4ee1.1603 and | ||
# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;a048b4e8.1603 | # https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;a048b4e8.1603 | ||
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# Recommendation: | # Recommendation: | ||
# - for the fast local directory one should use a RAMdisk (one GB size at most) | # - for the fast local directory one should use a RAMdisk (one GB size at most) | ||
# - /dev/shm seems to be set up for that purpose on most Linux distributions | # - /dev/shm seems to be already set up for that purpose on most Linux distributions | ||
# - on MacOS you can set this up as | # - on MacOS you can easily set this up as described at http://stackoverflow.com/questions/2033362/does-os-x-have-an-equivalent-to-dev-shm | ||
# example on MacOS for 1GB RAMdisk (needs to be repeated after booting): | |||
# diskutil eraseVolume HFS+ RAMdisk $(hdiutil attach -nomount ram://$((2 * 1024 * 1000))) | |||
# | # | ||
# on MacOS the next line should then be: | |||
# tempfile=/Volumes/RAMdisk/H5ToXds${PWD//\//_}.$3" | |||
# and on Linux: | |||
tempfile="/dev/shm/H5ToXds${PWD//\//_}.$3" | tempfile="/dev/shm/H5ToXds${PWD//\//_}.$3" | ||
# | # | ||
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/usr/local/bin/H5ToXds.bin $1 $2 "$tempfile" || rm "$tempfile" | /usr/local/bin/H5ToXds.bin $1 $2 "$tempfile" || rm "$tempfile" | ||
#/usr/local/bin/eiger2cbf-linux $1 $2 "$tempfile" >& /dev/null || rm "$tempfile" | #/usr/local/bin/eiger2cbf-linux $1 $2 "$tempfile" >& /dev/null || rm "$tempfile" | ||
#/usr/local/bin/eiger2cbf-osx $1 $2 "$tempfile" >& /dev/null || rm "$tempfile" | |||
#/usr/local/bin/hdf2mini-cbf $1 $2 "$tempfile" || rm "$tempfile" | #/usr/local/bin/hdf2mini-cbf $1 $2 "$tempfile" || rm "$tempfile" | ||
ln -sf "$tempfile" $3 2>/dev/null | ln -sf "$tempfile" $3 2>/dev/null | ||
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= See also = | |||
[[Performance]] | [[Performance]] | ||