1
$\begingroup$

I want to launch some kernels on a cluster that uses SGE. The server's operating system is Linux Cent-OS. According to Mathematica documentation, I've added these commands inside my code:

Needs["CLusterIntegration`"]
kernels=LaunchKernels[SGE["mnt-cluster.org"],8]

DistributeDefinitions[F]; (*F is defined in previous lines, and itself cannot be parallelized efficiently.*)
Parallelize[TST = Map[F, {a1, a2, a3, a4}]]; (*An example of what I want to be done on parallel nodes.*)

CloseKernels[kernels]

but once I ran it, these errors were raised:

Java::excptn: A Java exception occurred: java.lang.UnsatisfiedLinkError: no drmaa in java.library.path  
    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1709)  
    at java.lang.Runtime.loadLibrary0(Runtime.java:823)  
    at java.lang.System.loadLibrary(System.java:1030)  
    at com.sun.grid.drmaa.SessionImpl$1.run(SessionImpl.java:58)  
    at java.security.AccessController.doPrivileged(Native Method)  
    at com.sun.grid.drmaa.SessionImpl.<clinit>(SessionImpl.java:56)  
    at com.sun.grid.drmaa.SessionFactoryImpl.getSession(SessionFactoryImpl.java:59).  
SGE::load: Cannot find components required for SGE. >>

and another time I ran it again the list of error has changed to only this one:

Java::excptn: A Java exception occurred: java.lang.NoClassDefFoundError: Could not initialize class com.sun.grid.drmaa.SessionImpl  
    at com.sun.grid.drmaa.SessionFactoryImpl.getSession(SessionFactoryImpl.java:59).
SGE::load: Cannot find components required for SGE. >>  

I can find the file "drmaa" on the server on which I've installed Mathematica8.
I'd appreciate anyone who may help me to find out why these errors raised and how should I resolve them.

$\endgroup$
  • $\begingroup$ A shared library that should be on the path is missing or the path is incorrect. Is the location you found drmaa (is that drmma.so?) in your path (not classpath)? $\endgroup$ – Ymareth Dec 9 '14 at 17:47
  • $\begingroup$ @Ymareth That time I faced the problem, according to this MathGroup archive, I updated my CLASSPATH to where I found drmaa.jar, which was compeletly different with the addresses in the above link. But I didn't found the others: jgdi and juti. $\endgroup$ – Toughee Dec 18 '14 at 4:22
  • $\begingroup$ @Ymareth I also can find drmaa.so and drmaa.so.1.0 inside a folder besides drmaa.jar not exactly in the path. $\endgroup$ – Toughee Dec 18 '14 at 4:25
  • $\begingroup$ What are your values for the PATH and LD_LIBRARY_PATH environment variables? This is to do with loading native shared libraries it is (I believe) nothing to do with CLASSPATH. $\endgroup$ – Ymareth Dec 18 '14 at 9:52

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.