|
|
| Line 630: |
Line 630: |
|
| |
|
| 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). | | 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
| |
| CORRECT: elapsed wall-clock time 2.9 sec
| |
| Total elapsed wall-clock time for XDS 133.6 sec
| |
|
| |
| When I repeat this, I get
| |
| Total elapsed wall-clock time for XDS 128.3 sec
| |
| Repeat once again:
| |
| 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
| |
| Total elapsed wall-clock time for XDS 120.1 sec
| |
| 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.
| |
|
| |
|
| == A script for faster XDS processing of CBF-converted Eiger data (this is only shown out of historic interest) == | | == A script for faster XDS processing of CBF-converted Eiger data (this is only shown out of historic interest) == |