Re: [ccp4bb] XDS plugin for efficient reading of HDF5 data

[Kay Diederichs]

Dear all,

unfortunately the very latest BUILT of the XDS package (which fixed a problem 
in XDSCONV) introduced a last-minute bug in the routine that uses the "Neggia" 
plugin. This is documented, together with two workarounds, in the 
Troubleshooting section of the Eiger article in XDSwiki : 
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Eiger#Troubleshooting
 .

The easiest workaround is to just use the 20161205 BUILT of the XDS package 
(replacing the old XDSCONV with the one from the latest BUILT).
 
Sorry about this!

Kay


On Thu, 23 Mar 2017 10:56:54 +0100, Andreas Förster 
 wrote:

>Dear all,
>
>DECTRIS is proud to announce the release of an HDF5 read plugin to take
>advantage of the recently added XDS plugin support (thanks to Wolfgang
>Kabsch and Kay Diederichs) and accelerate the reading of HDF5 files.
>
>EIGER detectors produce data in the large-data format HDF5. Despite
>substantial advantages (few files to handle, excellent compression), HDF5
>data pose some difficulties.  While DIALS and HKL-2000 process HDF5 data
>natively, they are limited in their performance by the lack of parallel
>reading of the HDF library.  Processing of HDF5 data by XDS has thus far
>relied on extraction of temporary CBF images, which adds to the processing
>time.
>
>Neggia, our read plugin for XDS, presents HDF5 data to XDS in a fully
>parallelized way, directly and without interconversion.  Processing of HDF5
>data is now as fast as processing of CBFs.  Refer to the plugin with LIB=
>/path/to/plugin.so in XDS.INP.  The parameter DETECTOR= EIGER should remain.
>
>You can download the plugin from www.dectris.com/neggia.html (registration
>required).  To run it you need a reasonably recent OSX or linux system with
>gcc 4.8 or higher.  We have tested macOS Sierra, CentOS 6, CentOS 7, Mint
>17.3.  Alternatively, you can compile the plugin from the source available
>at https://github.com/dectris/neggia.
>
>The plugin was written to work with recent EIGER data and has been tested
>in house and at a few adventurous beamlines.  If you encounter issues,
>please let me now.  Your problem reports will help make the plugin better,
>to the benefit of the entire community.
>
>All best and happy data processing
>
>
>Andreas
>
>
>
>-- 
>
>Andreas Förster, Ph.D.
>MX Application Scientist, Scientific Sales
>Phone: +41 56 500 2100 | Direct: +41 56 500 2176 | Email:
>andreas.foers...@dectris.com
>DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
>www.dectris.com
>
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>
>
>
>
>
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[ccp4bb] XDS plugin for efficient reading of HDF5 data

[Andreas Förster]

Dear all,

DECTRIS is proud to announce the release of an HDF5 read plugin to take
advantage of the recently added XDS plugin support (thanks to Wolfgang
Kabsch and Kay Diederichs) and accelerate the reading of HDF5 files.

EIGER detectors produce data in the large-data format HDF5. Despite
substantial advantages (few files to handle, excellent compression), HDF5
data pose some difficulties.  While DIALS and HKL-2000 process HDF5 data
natively, they are limited in their performance by the lack of parallel
reading of the HDF library.  Processing of HDF5 data by XDS has thus far
relied on extraction of temporary CBF images, which adds to the processing
time.

Neggia, our read plugin for XDS, presents HDF5 data to XDS in a fully
parallelized way, directly and without interconversion.  Processing of HDF5
data is now as fast as processing of CBFs.  Refer to the plugin with LIB=
/path/to/plugin.so in XDS.INP.  The parameter DETECTOR= EIGER should remain.

You can download the plugin from www.dectris.com/neggia.html (registration
required).  To run it you need a reasonably recent OSX or linux system with
gcc 4.8 or higher.  We have tested macOS Sierra, CentOS 6, CentOS 7, Mint
17.3.  Alternatively, you can compile the plugin from the source available
at https://github.com/dectris/neggia.

The plugin was written to work with recent EIGER data and has been tested
in house and at a few adventurous beamlines.  If you encounter issues,
please let me now.  Your problem reports will help make the plugin better,
to the benefit of the entire community.

All best and happy data processing


Andreas



-- 

Andreas Förster, Ph.D.
MX Application Scientist, Scientific Sales
Phone: +41 56 500 2100 | Direct: +41 56 500 2176 | Email:
andreas.foers...@dectris.com
DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland |
www.dectris.com

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named
recipient(s) and may contain confidential and/or privileged information. If
you
are not the intended recipient, please contact the sender and delete the
message.
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prohibited.