Re: [OMPI users] Segfault in mpi-java

Sun, 1 Feb 2015 17:09:07 -0500 (EST) 

Hi,

I created an issue with a simplified example:

https://github.com/open-mpi/ompi/issues/369

Regards,
Oscar


El 25/01/15 a las 19:36, Oscar Vega-Gisbert escribió:

Hi,
I also reproduce this behaviour. But I think this crash is not related with garbage collector. Java is much better than you think. 

May be MPI corrupts the Java runtime heap.

Regards,
Oscar

El 22/01/15 a las 08:07, Gilles Gouaillardet escribió:

Alexander,

i was able to reproduce this behaviour.

basically, bad things happen when the garbage collector is invoked ...
i was even able to reproduce some crashes (but that happen at random
stages) very early in the code
by manually inserting calls to the garbage collector (e.g. System.gc();)

Cheers,

Gilles

On 2015/01/19 9:03, Alexander Daryin wrote:

Hi
I am using Java MPI bindings and periodically get fatal erros. This is illustrated by the following model Java program. 

import mpi.MPI;
import mpi.MPIException;
import mpi.Prequest;
import mpi.Request;
import mpi.Status;

import java.nio.ByteBuffer;
import java.util.Random;

public class TestJavaMPI {

    private static final int NREQ = 16;
    private static final int BUFFSIZE = 0x2000;
    private static final int NSTEP = 1000000000;

    public static void main(String... args) throws MPIException {
        MPI.Init(args);
        Random random = new Random();
        Prequest[] receiveRequests = new Prequest[NREQ];
        Request[] sendRequests = new Request[NREQ];
        ByteBuffer[] receiveBuffers = new ByteBuffer[NREQ];
        ByteBuffer[] sendBuffers = new ByteBuffer[NREQ];
        for(int i = 0; i < NREQ; i++) {
            receiveBuffers[i] = MPI.newByteBuffer(BUFFSIZE);
            sendBuffers[i] = MPI.newByteBuffer(BUFFSIZE);
receiveRequests[i] = MPI.COMM_WORLD.recvInit(receiveBuffers[i], BUFFSIZE, MPI.BYTE, MPI.ANY_SOURCE, MPI.ANY_TAG); 
            receiveRequests[i].start();
sendRequests[i] = MPI.COMM_WORLD.iSend(sendBuffers[i], 0, MPI.BYTE, MPI.PROC_NULL, 0); 
        }
        for(int step = 0; step < NSTEP; step++) {
            if( step % 128 == 0 ) System.out.println(step);
            int index;
            do {
                Status status = Request.testAnyStatus(receiveRequests);
                if( status != null )
receiveRequests[status.getIndex()].start();
                index = Request.testAny(sendRequests);
            } while( index == MPI.UNDEFINED );
            sendRequests[index].free();
sendRequests[index] = MPI.COMM_WORLD.iSend(sendBuffers[index], BUFFSIZE, MPI.BYTE, 
                    random.nextInt(MPI.COMM_WORLD.getSize()), 0);
        }
        MPI.Finalize();
    }
}
On Linux, this produces a segfault after about a million steps. On OS X, instead of segfault it prints the following error message
java(64053,0x127e4d000) malloc: *** error for object 0x7f80eb828808: incorrect checksum for freed object - object was probably modified after being freed. 
*** set a breakpoint in malloc_error_break to debug
[mbp:64053] *** Process received signal ***
[mbp:64053] Signal: Abort trap: 6 (6)
[mbp:64053] Signal code:  (0)
[mbp:64053] [ 0] 0 libsystem_platform.dylib 0x00007fff86b5ff1a _sigtramp + 26 
[mbp:64053] [ 1] 0   ??? 0x0000000000000000 0x0 + 0
[mbp:64053] [ 2] 0   libsystem_c.dylib 0x00007fff80c7bb73 abort + 129
[mbp:64053] [ 3] 0 libsystem_malloc.dylib 0x00007fff8c26ce06 szone_error + 625 [mbp:64053] [ 4] 0 libsystem_malloc.dylib 0x00007fff8c2645c8 small_free_list_remove_ptr + 154 [mbp:64053] [ 5] 0 libsystem_malloc.dylib 0x00007fff8c2632bf szone_free_definite_size + 1856 [mbp:64053] [ 6] 0 libjvm.dylib 0x000000010e257d89 _ZN2os4freeEPvt + 63 [mbp:64053] [ 7] 0 libjvm.dylib 0x000000010dea2b0a _ZN9ChunkPool12free_all_butEm + 136 [mbp:64053] [ 8] 0 libjvm.dylib 0x000000010e30ab33 _ZN12PeriodicTask14real_time_tickEi + 77 [mbp:64053] [ 9] 0 libjvm.dylib 0x000000010e3372a3 _ZN13WatcherThread3runEv + 267 [mbp:64053] [10] 0 libjvm.dylib 0x000000010e25d87e _ZL10java_startP6Thread + 246 [mbp:64053] [11] 0 libsystem_pthread.dylib 0x00007fff8f1402fc _pthread_body + 131 [mbp:64053] [12] 0 libsystem_pthread.dylib 0x00007fff8f140279 _pthread_body + 0 [mbp:64053] [13] 0 libsystem_pthread.dylib 0x00007fff8f13e4b1 thread_start + 13 
[mbp:64053] *** End of error message ***

OpenMPI version is 1.8.4. Java version is 1.8.0_25-b17.

Best regards,
Alexander Daryin
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