The nXDS package comprises two compressed tar-files containing the documentation and the executable programs, respectively.
To obtain a local copy of the html documentation (and the .INP file templates), download the compressed tar-file named nXDS_html_doc.tar.gz to your Desktop. Uncompress and untar the downloaded file. This will create a directory named nXDS_html_doc that you can locally access for consultation by your browser. The downloaded tar-file is no longer needed and can be deleted.
(Expiration date: Mar 30, 2022)
For downloading select the tar-file appropriate for your computer and operating system.
name of tar-file for downloading | computer | operating system |
---|---|---|
nXDS-INTEL64_Linux_x86_64.tar.gz | Xeon, Intel Core Duo, Opteron | Linux x86_64, 64 bit |
nXDS-OSX_64.tar.gz | iMac, MacBookPro,Intel processors | Mac OSX version_min,10.10, 64 bit |
The downloaded file contains the executables mentioned in the table below.
Executable | Programs that can be called by the user are in bold face. |
nxds | Program for processing snapshots by a single cpu at each cluster node. |
nxds_par | Multi-processor version of nxds for up to 99 cpu's at each cluster node. |
nxscale | Scaling and postrefinement program for data sets from the INTEGRATE step of nXDS (single-processor version). |
nxscale_par | Multi-processor version of nxscale for up to 99 cpu's. |
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. |
pix2lab | Helps to find the correct mapping of image pixels to the laboratory frame. |
The following programs are called only by nXDS | |
forknxds | Shell script invoked by nXDS for distributing computations to the nodes of a cluster. |
nfilter | invoked by forknxds as a main program in single-processor mode for recognizing useless snapshots. |
nfilter_par | invoked by forknxds as a main program running under OpenMP for recognizing useless snapshots. |
ncolspot | invoked by forknxds as a main program in single-processor mode for spot finding. |
ncolspot_par | invoked by forknxds as a main program running under OpenMP for spot finding. |
nidxref | invoked by forknxds as a main program in single-processor mode for indexing. |
nidxref_par | invoked by forknxds as a main program running under OpenMP for indexing. |
nintegrate | invoked by forknxds as a main program in single-processor mode used for integration. |
nintegrate_par | invoked by forknxds as a main program running under OpenMP used for integration. |
System or administrator privileges are not required for installation. The nXDS 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 nXDS-INTEL64_Linux_x86_64, for example, when you selected the nXDS-package for your Intel Core Duo processor running Ubuntu8.1.
Type echo $SHELL to find out which shell you are using. For the bash
shell you could append the following lines to your standard personal
initialization file ~/.bashrc. (For Mac OS use ~/.bash_login instead).
export PATH=full_path_name_to/nXDS-INTEL64_Linux_x86_64:$PATH
export KMP_STACKSIZE=8m
The first line makes the executables of the nXDS package accessible, while
the second line defines the stack size limit of the Linux POSIX threads
libraries used by OpenMP for nxds_par. (The limit 8m may need to
be increased if nxds_par collapses with a segmentation fault in the COLSPOT
or INTEGRATE step for some of your data sets.)
This completes installation of the nXDS package. As a check open
a new terminal window and issue the command which nxds
or which forknxds. In fact, all executables from the downloaded tar-file
mentioned in the table above should be tested in this way. Furthermore,
you should verify using the 'ls -l' command whether the reported file names
refer indeed to the executables just installed.
Removal of an obsolete nXDS 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 nXDS on a cluster system of computer nodes in a networked (NFS) environment where each node may 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.
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