Downloading and Installation of XDS

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

Documentation

To obtain a local copy of the html documentation (and the .INP file templates), download the compressed tar-file named XDS_html_doc.tar.gz to your Desktop. Uncompress and untar the downloaded file. This will create a directory named XDS_html_doc that you can easily access for consultation by a few mouse clicks activating your browser. The downloaded tar-file is no longer needed and can be deleted.

Executables

(Expiration date: Sep 30, 2017)

For downloading select the tar-file appropriate for your computer 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 10.6-10.10, 64 bit

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 32 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 32 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
mcolspot Spot finding program running on a single-processor node of the cluster.
mcolspot_par Spot finding program for parallel execution on a multi-processor node of the cluster.
forkcolspot Program for distributing the spot finding program to the nodes of the cluster.
mintegrate Integration program running on a single-processor node of the cluster.
mintegrate_par Integration program for parallel execution on a multi-processor node of the cluster.
forkintegrate Program for distributing the integration program to the nodes of the cluster.

System or administrator privileges are not required for installation. The XDS package is just a folder containing the executables listed above 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 the XDS-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 check you can open a new terminal window and issue the command which xds or which 2cbf.) 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.

Additional work is only needed for installation of XDS on a cluster system which - unlike the Altix or Xeon - does not have a common address space. Here, each node intended for use by XDS must be explicitly named which makes it necessary to edit the original (downloaded) shell scripts forkcolspot and forkintegrate according to the example forkcolspot, forkintegrate kindly provided by K. Diederichs. Also, to prevent being asked for a password each time by each of the nodes, use of authentication keys for ssh is recommended. Such a key could be generated by the command ssh-keygen -t rsa (see man-pages for ssh-keygen). The resulting public key, ~/.ssh/id_rsa.pub, should then be appended to ~/.ssh/authorized_keys of the cluster nodes.


© 2005-2017, MPI for Medical Research, Heidelberg Imprint.
Wolfgang.Kabsch@mpimf-heidelberg.mpg.de
page last updated: February 15, 2017