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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