Shared libraries - Java 32 bit on 64bit Ubuntu

Question

I am trying to run a Bioinformatics program for MRS spectrosopy analysis called "jMRUI". The executable for this program is a .sh with the following code:

    java -Xss2m -mx1200m -Djava.library.path=lib -jar lib/mrui.jar

I have both the 64bit and 32bit JDK 1.8 installed on my PC at the directory /usr/lib/jvm/.

    64bit found at: /usr/lib/jvm/jdk1.8.0_x64/bin/java
    32bit found at: /usr/lib/jvm/jdk1.8.0_x86/bin/java

The pointer symbolic link at /usr/bin/java points to /etc/alternatives/java which points to /usr/lib/jvm/jdk1.8.0_x64/bin/java if the 64bit version is currently selected or /usr/lib/jvm/jdk1.8.0_x86/bin/java if 32bit is currently selected. Permissions of all three are below.

    lrwxrwxrwx 1 root root 22 Jul  2 17:34 /usr/bin/java -> /etc/alternatives/java
    lrwxrwxrwx 1 root root 34 Jul  2 18:29 /etc/alternatives/java -> /usr/lib/jvm/jdk1.8.0_x(VER#)/bin/java
    -rwxr-xr-x 1 lillian lillian 5730 Mar 18 02:58 /usr/lib/jvm/jdk1.8.0_x64/bin/java
    -rwxr-xr-x 1 lillian lillian 5730 Mar 18 02:58 /usr/lib/jvm/jdk1.8.0_x86/bin/java

I can switch between java versions simply with a bash script that runs the following code: From 32bit java back to 64bit java:

    #!/bin/sh
    #the next 3 commands are only run initially to install the link alternative 
    #associations. I give everything the same priority of 1.
    sudo update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jvm/jdk1.8.0_x64/bin/java" 1
    sudo update-alternatives --install "/usr/bin/javac" "javac" "/usr/lib/jvm/jdk1.8.0_x64/bin/javac" 1
    sudo update-alternatives --install "/usr/bin/javaws" "javaws" "/usr/lib/jvm/jdk1.8.0_x64/bin/javaws" 1

    echo 1 | sudo update-alternatives --config java
    echo 1 | sudo update-alternatives --config javac
    echo 1 | sudo update-alternatives --config javaws

From 64bit to 32bit:

    #!/bin/sh
    #the next 3 commands are only run initially to install the link alternative 
    #associations. I give everything the same priority of 1.
    sudo update-alternatives --install "/usr/bin/java" "java" "/usr/lib/jvm/jdk1.8.0_x86/bin/java" 1
    sudo update-alternatives --install "/usr/bin/javac" "javac" "/usr/lib/jvm/jdk1.8.0_x86/bin/javac" 1
    sudo update-alternatives --install "/usr/bin/javaws" "javaws" "/usr/lib/jvm/jdk1.8.0_x86/bin/javaws" 1

    echo 1 | sudo update-alternatives --config java
    echo 1 | sudo update-alternatives --config javac
    echo 1 | sudo update-alternatives --config javaws

This post told me to also install the following packages for 32bit java. Here is output from all of the suggested test commands.

1. readelf -l /usr/bin/java

   Elf file type is EXEC (Executable file)
   Entry point 0x8048420
   There are 8 program headers, starting at offset 52
   Program Headers:
       Type           Offset   VirtAddr   PhysAddr   FileSiz MemSiz  Flg Align
       PHDR           0x000034 0x08048034 0x08048034 0x00100 0x00100 R E 0x4
       INTERP         0x000134 0x08048134 0x08048134 0x00013 0x00013 R   0x1
          [Requesting program interpreter: /lib/ld-linux.so.2]
       LOAD           0x000000 0x08048000 0x08048000 0x00710 0x00710 R E 0x1000
       LOAD           0x000710 0x08049710 0x08049710 0x00144 0x0014c RW  0x1000
       DYNAMIC        0x00072c 0x0804972c 0x0804972c 0x00108 0x00108 RW  0x4
       NOTE           0x000148 0x08048148 0x08048148 0x00044 0x00044 R   0x4
       GNU_EH_FRAME   0x00069c 0x0804869c 0x0804869c 0x0001c 0x0001c R   0x4
       GNU_STACK      0x000000 0x00000000 0x00000000 0x00000 0x00000 RW  0x4
   
   Section to Segment mapping:
   Segment Sections...
       00     
       01     .interp 
       02     .interp .note.ABI-tag .note.gnu.build-id .hash .gnu.hash .dynsym .dynstr .gnu.version .gnu.version_d .gnu.version_r .rel.dyn .rel.plt .init .plt .text .fini .rodata .eh_frame_hdr .eh_frame 
       03     .ctors .dtors .jcr .data.rel.ro .dynamic .got .got.plt .data .bss 
       04     .dynamic 
       05     .note.ABI-tag .note.gnu.build-id 
       06     .eh_frame_hdr 
       07     
   

2. ls -l /lib/ld-linux.so.2

   lrwxrwxrwx 1 root root 25 Apr 12 05:44 /lib/ld-linux.so.2 -> i386-linux-gnu/ld-2.19.so
   

3. ldd java

   linux-gate.so.1 =>  (0xf775c000)
   libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0xf7728000)
   libjli.so => not found
   libdl.so.2 => /lib/i386-linux-gnu/libdl.so.2 (0xf7722000)
   libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xf7573000)
   /lib/ld-linux.so.2 (0xf775d000) 
   

4. Since libjli.so was not found, I have tried to apt-get at pretty much any recommended package involved with i386. None have changed the "not found" status of libjli.so to found.

When /usr/bin/java points to the 64bit java, jMRUI launches, but crashes when I try to upload an .SDAT file (basically when I open any file). When I try to open a file, I get this error message and then it hangs until you kill the process:

    Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library 
    /home/lillian/Downloads/jMRUI-4.0/lib/libfftw.so which might have disabled stack 
    guard. The VM will try to fix the stack guard now.
    It's highly recommended that you fix the library with 'execstack -c <libfile>', 
    or link it with '-z noexecstack'.
    Exception in thread "Thread-1" java.lang.UnsatisfiedLinkError: 
    /home/lillian/Downloads/jMRUI-4.0/lib/libfftw.so: /home/lillian/Downloads/jMRUI-
    4.0/lib/libfftw.so: 
    wrong ELF class: ELFCLASS32 (Possible cause: architecture word width mismatch)
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1929)
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1847)
        at java.lang.Runtime.loadLibrary0(Runtime.java:870)
        at java.lang.System.loadLibrary(System.java:1119)
        at fft.Fft.<clinit>(Unknown Source)
        at mrui.data.FID.constructSpectrum(Unknown Source)
        at mrui.data.Data.constructSpectrum(Unknown Source)
        at mrui.data.Data.constructSpectrum(Unknown Source)
        at mrui.data.Data.addSignal(Unknown Source)
        at mrui.conversion.philips.FilePhil.loadData(Unknown Source)
        at mrui.plugin.conversion.ConversionManager.loadFile(Unknown Source)
        at mrui.plugin.conversion.FileManagementRead.loadInBackground(Unknown Source)
        at mrui.plugin.conversion.FileManagementRead.run(Unknown Source)
        at java.lang.Thread.run(Thread.java:745)

When /usr/bin/java points to the 32bit java, jMRUI does not launch at all, and I get this error message:

    ./jmrui.sh
    Jul 02, 2014 6:56:04 PM mrui.Launcher main
    INFO: Log properties loaded
    Exception in thread "main" java.lang.UnsatisfiedLinkError: 
    /usr/lib/jvm/jdk1.8.0_x86/jre/lib/i386/libawt_xawt.so: libXrender.so.1: 
    cannot open shared object file: No such file or directory
    at java.lang.ClassLoader$NativeLibrary.load(Native Method)
    at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1929)
    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1814)
    at java.lang.Runtime.load0(Runtime.java:809)
    at java.lang.System.load(System.java:1083)
    at java.lang.ClassLoader$NativeLibrary.load(Native Method)
    at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1929)
    at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1835)
    at java.lang.Runtime.loadLibrary0(Runtime.java:870)
    at java.lang.System.loadLibrary(System.java:1119)
    at java.awt.Toolkit$3.run(Toolkit.java:1651)
    at java.awt.Toolkit$3.run(Toolkit.java:1649)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.Toolkit.loadLibraries(Toolkit.java:1648)
    at java.awt.Toolkit.<clinit>(Toolkit.java:1683)
    at sun.awt.AppContext$2.run(AppContext.java:275)
    at sun.awt.AppContext$2.run(AppContext.java:264)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.awt.AppContext.initMainAppContext(AppContext.java:264)
    at sun.awt.AppContext.access$400(AppContext.java:133)
    at sun.awt.AppContext$3.run(AppContext.java:319)
    at sun.awt.AppContext$3.run(AppContext.java:302)
    at java.security.AccessController.doPrivileged(Native Method)
    at sun.awt.AppContext.getAppContext(AppContext.java:301)
    at javax.swing.SwingUtilities.appContextGet(SwingUtilities.java:1860)
    at javax.swing.UIManager.getLAFState(UIManager.java:243)
    at javax.swing.UIManager.setLookAndFeel(UIManager.java:529)
    at javax.swing.UIManager.setLookAndFeel(UIManager.java:579)
    at mrui.Launcher.main(Unknown Source)

This site told me the 64bit error message is because jMRUI requires 32bit java, so that's why I have both.

Again, this site tells me 32bit java isn't working because I am "trying to run a 64bit system without a 32bit runtime environment".

Lastly, this site told me to add the -d32 option in my jMRUI.sh bash script. It did not change the shared library error message outcome.

What oh what am I missing? I can't imagine I haven't given enough information, but if you need anything else to help debug this, let me know and I'll send the output your way. Thanks a million in advance!

Solution

Having a look at the error messages, I have some conclusions:

• you definitely need to run the 32 bit version, the native library in jMRUI-4.0/lib/libfftw.so is ELF32

• when you run the 32 bit version, the system looks for a missing library: 'libXrender.so.1' (the 32bit version).

Install the package "libxrender1:i386" (libXrender 32bit) and try again with JDK 32 bit.

Comments

[lrthistlethwaite]

YES YES YES. Morgano you are fantastic! I was trying to install the package "libxrender", but that was "invalid" and now I know why! For future reference, how did you know what the package name was called and to put the colon i386, etc? I am still learning about how Ubuntu pulls packages and how one knows the names of the packages they need. You have no idea how grateful I am to have solved this!

[morgano]

I've also had problems with native libraries in the past... As your distro is 64 bit, the packages by default are 64 bit, so they put something to the name of the 32 bit package to diferenciate it from the main one (that's not a standard though), I just searched for the packages which names contained 'xrender' with aptitude search xrender ("aptitute" is a command-line front-end to the apt-get system, nicer to use than the later, you could also use synaptic) that brought me the names of the packages matching with 'xrender', and voila! rest is history

[lrthistlethwaite]

Aptitude is seriously amazing. Thanks for this tip, morgano!