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Downloading and Installation of XDS

The XDS package comprises two compressed tar-files containingthe documentation and the executable programs, respectively.

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Documentation

To obtain a local copy of the XDS documentation (and the .INP filetemplates), download the compressed tar-file named XDS_html_doc.tar.gzto your Desktop. Uncompress and untar the downloaded file. This willcreate a directory named XDS_html_doc that you can locally access forconsultation by your browser. Thedownloaded tar-file is no longer needed and can be deleted.

Executables

(Expiration date: Mar 31, 2021)

For downloading select the tar-file appropriate for yourcomputer and operating system.

name of tar-file for downloading	computer	operating system
XDS-INTEL64_Linux_x86_64.tar.gz	Xeon, Intel Core Duo, Opteron	Linux x86_64, 64 bit
XDS-OSX_64.tar.gz	iMac, MacBookPro,Intel processors	Mac OSX version_min,10.10, 64 bit

NOTE Installation of XDS under macOS Catalina.
After downloading the XDS-OSX_64 tarfile un-tar it and run the xattr command:
tar xvf XDS-OSX_64.tar
xattr -dr com.apple.quarantine XDS-OSX_64/*
in order to avoid the message 'quarantine because untrusted software'.

The downloaded file contains the executables as mentioned in the table below.

Executable	Programs that can be called by the user are in bold face.
xds	Program for processing rotation images using a single cpu at each cluster node.
xds_par	Multi-processor version of xds for up to 99 cpu's at each cluster node.
xscale	Scaling program for XDS-produced data sets (single-processor version).
xscale_par	Multi-processor version of xscale for up to 99 cpu's.
xdsconv	Converts reflection intensities determined by XDS to amplitudes in a format suitable for various structure solution program packages.
2cbf	Program to convert various detector image formats to CBF.
merge2cbf	Program to convert (and merge) a series of detector images from their native format to CBF.
cellparm	Computes mean cell constants from a number of XDS-runs.
pix2lab	Helps to find the correct mapping of image pixels to the laboratory frame.
The following programs are called only by XDS
forkxds	Shell script invoked by XDS for distributing computations to the nodes of a cluster.
mcolspot	invoked by forkxds as a main program in single-processor mode for spot finding.
mcolspot_par	invoked by forkxds as a main program running under OpenMP for spot finding.
mintegrate	invoked by forkxds as a main program in single-processor mode for integration.
mintegrate_par	invoked by forkxds as a main program running under OpenMP for integration.

Installation

System or administrator privileges are not required for installation.The XDS package is just a folder containing the executables listedabove and all you have to do for installation is to include this folder in the search path for executables.

Uncompress and untar the downloaded file. This will create a directory named XDS-INTEL64_Linux_x86_64, for example, when you selected theXDS-package for your Intel Core Duo processor running Ubuntu8.1.

Type echo $SHELL to find out which shell you are using. For the bash shell you could append the following lines to your standard personal initialization file ~/.bashrc. (For Mac OS use ~/.bash_login instead).
export PATH=full_path_name_to/XDS-INTEL64_Linux_x86_64:$PATH
export KMP_STACKSIZE=8m
The first line makes the executables of the XDS package accessible, while the second line defines the stack size limit of the Linux POSIX threads libraries used by OpenMP for xds_par. The limit 8m may need to be increased if xds_par collapses with a segmentation fault in the COLSPOT or INTEGRATE step for some of your data sets.

This completes installation of the XDS package for the example case. As a checkyou can open a new terminal window and issue the command which xdsor which 2cbf or which forkxds.Removal of an obsolete XDS package is equally simple and only requires deletion of the folder and of two lines in your ~/.bashrc script. There are no other side effects to worry about.

Installation on a computer cluster

Additional work is only needed for installation of XDS on a cluster system of computer nodes in a networked (NFS) environment where each nodemay in turn consist of several cpu cores sharing a common address space.To prevent being asked for a password each time by each of the nodes,use of authentication keys for ssh is recommended. For each user such a key can be generated by the following procedure.

• Log in to the peer node of the cluster system and type the commandssh-keygen -t rsa -f ~/.ssh/id_rsa.xds.If it asks you for a passphrase, leave it empty.
• The resulting public key, ~/.ssh/id_rsa.xds.pub, should then beappended to your authorized keys by the command
  cat ~/.ssh/id_rsa.xds.pub >> ~/.ssh/authorized_keys
• Set the correct file mode bits by the command
  chmod 400 ~/.ssh/authorized_keys.

Assuming that your home folder

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~

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is mounted on all nodes of thecomputer cluster, you should then be able to ssh to any of them withoutbeing asked for your password. Also, there is no need to specify the names of the nodes of the cluster during program installation. The names of thenodes you want XDS to use for your data processing run are specified in XDS.INP by the parameterCLUSTER_NODES=. Optimaluse of the hardware is made automatically by XDS - depending onthe size of your data set.© 2005-2020, MPI for Medical Research, Heidelberg

Drivers Xds Xtra Datensysteme Laptops & Desktops Download

Drivers Xds Xtra Datensysteme Laptops Walmart

ImprintDatenschutzhinweis.Wolfgang.Kabsch@mpimf-heidelberg.mpg.de
page last updated: July 17, 2020