Overcome Java JNI gdb errors on GNU/Linux

If you happen to try to debug any Java JNI programs using gdb on GNU/Linux you will soon come across error messages.
For example :

$ gdb --args java MyJavaProgramUsingJNI

cannot find user-level thread for LWP nnn: generic error

warning: Cannot initialize thread debugging library: versions of libpthread and libthread_db do not match

The reason for this is that the java program mucks around with LD_LIBRARY_PATH and that prevents gdb from running correctly.

To overcome this, you have to run your Java program and place a pause in the Java code, such as reading a key, and then in another shell, run gdb to attach to the running Java process.

You can then set your breakpoint on your JNI code and debug it.

Here is an example :

Compile your Java program:

$ javac JNITest.java

Generate the JNI header file:

$ javah -jni JNITest.java

Create and compile your C code library:

$ cat jnilib.c
#include "JNITest.h"

JNIEXPORT jint JNICALL Java_JNITest_addValues( JNIEnv *env, jobject jobj, jint a, jint b )
{
   int res = a + b;
   return res;
}

$ gcc -o libjnilib.so -shared -I /opt/jdk1.5.0_16/include -I /opt/jdk1.5.0_16/include/linux jnilib.c

Run it:

$ java JNITest
Result = 75

Run Java program in shell A and attach debugger in session B:

A$ java JNITest

Find running Java process ...

B$ ps -ef
...
user     17809 16492  7 21:28 pts/1    00:00:00 java JNITest
user     17821 14042  4 21:28 pts/2    00:00:00 bash
user     17845 17821  0 21:28 pts/2    00:00:00 ps -ef

Attach debugger:

B$ gdb -p 17809
...
(gdb) break Java_JNITest_addValues
Breakpoint 1 at 0x8ca02402: file jnilib.c, line 5.
(gdb) cont
Continuing.
[Switching to Thread 0xb7e866b0 (LWP 17809)]

Breakpoint 1, Java_JNITest_addValues (env=0x84258b8, jobj=0xbfd2e6d8, a=25,
  b=50) at jnilib.c:5
5  int res = a + b;
(gdb)

(gdb) print a
$1 = 25
(gdb) print b
$2 = 50
(gdb) cont
Continuing.

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