I have encountered a very puzzling problems with one of the applications that I use on a regular basis for my research. It involves compiling the current version of the Tinker Molecular Mechanics set of programs and the gui for the applications. The system is the SuSE v 8.1 lixux distribution and using the Intel FORTRAN and C compilers (they give executables with better performance that the GNU FORTRAN and C compilers). My normal practice is to compile new software in /usr/src and then copy it to a working directory once the bugs have been fixed and the program is executing properly. I do this as root on a stand-alone platform and the relog on as a user to use the sortware. Now for the problem. I thought that I would compile the newest version of Tinker in the working directory, rather than root, as this version is 4.1 and the compilation procedures have been well worked out by the author of the program. Everything went well, without even any warning errors, until I went to execute the gui. Oh yes, the gui is written in java and I have the proper java applications installed on my system and working properly. So when I attempt to run the java application I get: abnormal:/usr/local/lib/CompChem/tinker # csh CompChem/tinker# source tinker.csh CompChem/tinker# ffe Exception in thread "main" java.util.zip.ZipException: No such file or directory at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.<init>(ZipFile.java:112) at java.util.jar.JarFile.<init>(JarFile.java:127) at java.util.jar.JarFile.<init>(JarFile.java:65) CompChem/tinker# Which means that java isn't executing. At this point, I said to myself 'Ah Ha! I go back to the old protocol' and compile the software in /usr/scr and then move it to the working directory. Same result. However, if I run the gui in /usr/src it works flawlessly (same compiled software that doesn't work in the working directory.) I am perplexed, and would appreciate any insights that anyone may have. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariant http://web.jadeinc.com/FoundationChem
On Sun, Sep 14, 2003 at 04:11:35PM -0400, Stephen P. Molnar, Ph.D. wrote:
So when I attempt to run the java application I get:
abnormal:/usr/local/lib/CompChem/tinker # csh CompChem/tinker# source tinker.csh CompChem/tinker# ffe Exception in thread "main" java.util.zip.ZipException: No such file or directory at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.<init>(ZipFile.java:112) at java.util.jar.JarFile.<init>(JarFile.java:127) at java.util.jar.JarFile.<init>(JarFile.java:65) CompChem/tinker#
Which means that java isn't executing.
What is your JAVA_HOME environment variable set to? It looks like environment initialization problem in your script.
At this point, I said to myself 'Ah Ha! I go back to the old protocol' and compile the software in /usr/scr and then move it to the working directory. Same result. However, if I run the gui in /usr/src it works flawlessly (same compiled software that doesn't work in the working directory.)
Check if environment variables use relative path (starting from current directory, i.e. ../) If so, change them to be absolute, starting with / Regards, -Kastus
Stephen P. Molnar, Ph.D. wrote:
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Exception in thread "main" java.util.zip.ZipException: No such file or directory at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.<init>(ZipFile.java:112) at java.util.jar.JarFile.<init>(JarFile.java:127) at java.util.jar.JarFile.<init>(JarFile.java:65) CompChem/tinker#
Which means that java isn't executing.
Incorrect. Java is executing and generating an exception for you. It cannot find the file specified. Search for the ZipFile.open() method and plug in the full path of the file you are trying to open. I guess that the ZipFile.open() method has a relative path and not an absolute path.
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expatriate -
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Stephen P. Molnar, Ph.D.