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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> Link to this post:
> http://www.open-mpi.org/community/lists/users/2015/01/26215.php
