JNI applications fail because shared libraries cannot be found

Hi Nikolaus,

Sorry you're having troubles. Can you explain how you installed mdsplus? I am unable to reproduce this using Ubuntu 10.04 LTS and following the instructions for Ubuntu11 and stable in http://www.mdsplus.org/index.php/Latest_Ubuntu_Packages. Also, attempts to do simpler things with JNI didn't show anything like this.

Can you strace the open() calls to see what path it's looking for for libhpi.so, like so:

  strace -o /tmp/jScope.strace -f -e trace=open jScope

That will put the output of the strace in /tmp/jScope.strace.

Another possibility path for debugging would by to modify the jScope shell script to add '-verbose:jni' to the $java invocation, and capturing the output. That said, if I did not have libsybdb.so.5 installed, I got a similar error for libsybdb.so.5, and the verbose jni information did not give anything additionally relevant to it.

I also note that the path of libhpi.so did not change between the two versions of openjdk-6-jre-headless.

That said, I note that http://h1svr.anu.edu.au/wiki/Hardware/Computers/prl45 reports a similar error finding libhpi.so on Ubuntu 12.04 LTS. Due to multiarch changes in the distribution, I wonder if the patch that was added to openjdk-6 to fix https://bugs.launchpad.net/ubuntu/+source/openjdk-6/+bug/737603 is causing problems here.

Thanks.

Hi Steve,

Thanks for your efforts! Our MDSplus installation has been compiled from source. I have attached the strace output as well as the debugging output.

I tried running NativeTest.java from bug 737603 with the same environment variables that are used for the jScope invocation (exept the classtpath):

Before the upgrade:

$ LD_LIBRARY_PATH=:/opt/hbt/valen/lib/i686/:/opt/mdsplus//lib SHLIB_PATH=:/opt/mdsplus//lib DYLD_LIBRARY_PATH=:/opt/mdsplus//lib /usr/bin/java -Xmx128M NativeTest JavaMds
java.library.path: /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64::/opt/hbt/valen/lib/i686/:/opt/mdsplus//lib:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
sun.boot.library.path: /usr/lib/jvm/java-6-openjdk/jre/lib/amd64
System.mapLibraryName(): libJavaMds.so

After the upgrade:

$ LD_LIBRARY_PATH=:/opt/hbt/valen/lib/i686/:/opt/mdsplus//lib SHLIB_PATH=:/opt/mdsplus//lib DYLD_LIBRARY_PATH=:/opt/mdsplus//lib /usr/bin/java -Xmx128M NativeTest JavaMds
java.library.path: /usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server:/usr/lib/jvm/java-6-openjdk/jre/lib/amd64:/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64::/opt/hbt/valen/lib/i686/:/opt/mdsplus//lib:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
sun.boot.library.path: /usr/lib/jvm/java-6-openjdk/jre/lib/amd64
System.mapLibraryName(): libJavaMds.so
Exception in thread "main" java.lang.UnsatisfiedLinkError: /opt/mdsplus/lib/libJavaMds.so: libhpi.so: cannot open shared object file: No such file or directory
 at java.lang.ClassLoader$NativeLibrary.load(Native Method)
 at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1750)
 at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1675)
 at java.lang.Runtime.loadLibrary0(Runtime.java:840)
 at java.lang.System.loadLibrary(System.java:1047)
 at NativeTest.main(NativeTest.java:6)

Hi Nikolaus,

Sorry, I've been unable to reproduce this issue. Can you tell me specifically what version of MDSplus version you're running, as well as any specific configure options that you built it with, so I can further attempt to reproduce what you're seeing? I also tried running NativeTest.java from bug 737603 as you did and it loaded the JavaMDS library just fine; however, I noticed when strace'ing it that it never attempted to open libhpi.so in doing so, and I'm not sure why (hence my asking for configure options that may affect this).

I should also point out that bug 737603 is a bit of a red herring; I re-examined the openjdk-6 packaging and the patch for bug 737603 is included in the package but is not actually applied during the build (I was going to prepare a test package for you with that patch disabled...).

A couple more things to look at to diagnose this:

* can you run 'ldd /opt/mdsplus/lib/libJavaMds.so' to confirm that it's the library itself that has the dependency on libhpi.so?

* can you re-run the NativeTest.java test, both with the older version of java installed where it succeeds and the failing versions, with the addition of the LD_DEBUG environment variable set to 'all' (i.e. add 'LD_DEBUG=all' to the command line)? I'd like to see what symbols are causing libhpi.so to get pulled in and how the resolution is happening.

Thanks, and my apologies for the difficulties this upgrade has caused.

Hi Steve,

I can give you a shell account on a server affected by the problem.
Would that help?

If so, please send me an ssh key.

Best,

   -Nikolaus

--
 »Time flies like an arrow, fruit flies like a Banana.«

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Closing that outdated report as EOL has been reached long time ago