Eiger: Difference between revisions

== Script for generating XDS.INP from master.h5 ==

= Less efficient way of processing Eiger data, using conversion to CBF=  

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, 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 ==

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

INIT:  elapsed wall-clock time      12.0 sec

COLSPOT: elapsed wall-clock time      44.9 sec

INTEGRATE: total elapsed wall-clock time      65.1 sec

 

Total elapsed wall-clock time for XDS      128.3 sec

Total elapsed wall-clock time for XDS      129.3 sec

So a bit of cache-warming helps, but not much. This machine has 64GB RAM. From the output of "top", the highest memory usage occurs during INTEGRATE, when each of the mintegrate_par processes consumes up to 7.4% of the memory. In other words, in this way less than 20GB of total memory are used. "top" shows a CPU consumption around (on average) 4 times 650%.

 

The number of JOBs and PROCESSORs could be optimized. I tried 6 JOBs and get

so there's still some room for improvement.

 

With program versions as of 2016-03-10, eiger2cbf-linux is practically as fast as the H5ToXds binary; hdf2mini-cbf is somewhat slower.

 

When unpacking the .h5 files to .cbf files and processing those, I get on the same machine and with same processing parameters:

Total elapsed wall-clock time for XDS       96.3 sec

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.