NPK set-up

Getting NPK

To obtain the program, simply send a mail to Marc A. Delsuc. The program is free for academic use.

For a commercial use, please contact the NMRtec company

Program set-up

NPK permits to process 1D, 2D and 3D NMR data-sets very efficiently. Either you use pre-programmed actions, or realize your own processing in python, and a complete processing modelisation is available.

NPK appears as a python program, you can either use NPK with standard procedures, or write you own python program.

NPK is really a java program, so you will need Java installed. Starting NPK is thus lauching a java program. However the NPK user interface is based on python. This is done thanks to the jython development : www.jython.org. Jython magically implements python within Java. You program in python, yet it is the Java machine that does the work. Additionnaly, the whole Java environment is available.

Thanks to java, NPK is available for MacOsX, Linux and Windows. The archive contains all the binary necessary for 4 different plateforms : Windows/X86 - Linux/X86 - MacOsX/X86 - MacOsX/PPC.

WARNING, NPK is only 32bit for the moment. So if you are running on a 64bit Linux distribution with a Java Machine 1.5, which runs in 64bit, you will be in trouble. On my cluster, java -d32 does not work, so I had to downgrade to Java 1.4 to have NPK working.

The mathematics are done through the use of an external library, linked into java as a JNI library. This library is a rewrite of the Gifa program.

NMRnotebook, a commercial program developed by NMRtec SA, is based on NPK and permit to graphically display the NMR data-sets.

Directories and files

The program is composed of the following files/directory :

• Java - a directory with java code as well as the binary code. Java is plateform independent
• NPK.jar and jython.jar - these files contain the java code
• Linux set-up
• libnpk_core.so : is the library code for Linux, compiled on RedHat enterprise
• libnpk_core_glibc2.4.so : the same as the previous, compiled on a Ubuntu 7 system, using GLibC 2.4
• Widows set-up
  libnpk_core.dll : : is the library code for Windows, should work on Windows XP and Vista.
• MacOsX setup
  • MAC_10.3.9 : this folder contains the files required for MacOsX v10.3.9
  • MAC_10.4 : this folder contains the files required for MacOsX v10.4; both x86 and ppc
  depending on the system you're using, you should copy the content of one of these folder down to the Java folder (thus having a Java/ppc folder (e.g.))
• python - a directory that contains all the python code
• Lib is the standard jython distribution
• NPK is the set of python code implementing NPK
• NPK/Param contains the default processing parameters
  these files can be recomputed with the do_default.py program
• NPK.sh - the shell script that launch NPK itself, you will have to modify this file to adapt the content to your set-up

The first time NPK is started, several files are created.

Installation

First be sure that the SUN Java JRE is installed on your machine. The 1.4 version or higher is required.
If you unsure on which version is installed on your machine type :

java -version

in a terminal

After having unzipped the NPK.zip archive, you will have the file set-up described above. Depending on the system you are using, you have to copy the needed library into the Java directory.

Then you will have to adapt the NPK.sh shell script (Linux and MacOsX) or npk.bat (Windows) by setting the variable values to the correct ones.

Finally, running the program consists simply in typing in a terminal

NPK.sh

(on MacOsX and Linux)
or

npk.bat

on Windows

The first time the program is run, several files are created : first jython creates cache files for all the java set-up. These files are located in NPK/python/cachedir directory.

Then the python code is compiled as *$py.class files in the NPK/python/NPK directory.

Possibles difficulties

• If your java cache files are recomputed each time you start NPK, and you have the following message:
  *sys-package-mgr*: can't write cache file for ...
  then try to remove the NPK/python/cachedir directory

NPK is an NMR processing program developped by