Re: [OMPI users] segmentation fault with java MPI

[Marko Blatzheim]

Hi Gilles,

 

I checked out openMPI Master 2 weeks ago.

JVM is: java version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

command line is: mpirun -np 2 java -jar MPI_open.jar

 

The segmentation fault is in the line with: test = is.readObject();

 

package mpi_open;

import java.io.ByteArrayInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Random;
import mpi.File;
import mpi.MPI;
import mpi.MPIException;
import mpi.Status;

public class MPI_open {

    public static void main(String[] args) throws MPIException, IOException, ClassNotFoundException {
       
        MPI.Init(args);
        int myRank = MPI.COMM_WORLD.getRank();
        if (myRank == 0) {
            // create file
            int num = 1000000;
            Random r = new Random(1234);
            ArrayList<Serializable> obj0 = new ArrayList<>(num);
            double[] obj1 = new double[num];
            for (int j = 0; j < num; j++) {
                double d = r.nextGaussian();
                obj0.add(d);
                obj1[j] = d;
            }
            obj0.trimToSize();

            System.out.println("objects created");

            java.io.File f = new java.io.File("testfile0");
            ObjectOutputStream out = null;
            try {
                out = new ObjectOutputStream(new FileOutputStream(f));
                System.out.println("out1");
                out.writeObject(obj1);
                System.out.println("out2");
            } catch (java.lang.ClassCastException x) {
                throw x;
            } finally {
                if (out != null) {
                    out.close();
                }
            }

            System.out.println("file 1 done");

            java.io.File f1 = new java.io.File("testfile1");
            ObjectOutputStream out1 = null;
            try {
                out1 = new ObjectOutputStream(new FileOutputStream(f1));
                out1.writeObject(obj0);
            } catch (java.lang.ClassCastException x) {
                throw x;
            } finally {
                if (out1 != null) {
                    out1.close();
                }
            }
            System.out.println("file 2 done");

            String filename = "testfile1";
            byte[] readbuf;

            File myfile = new File(MPI.COMM_SELF, filename, MPI.MODE_RDONLY);
            int filesize = (int) myfile.getSize();
            readbuf = new byte[filesize];
            Status status = myfile.read(readbuf, filesize, MPI.BYTE);
            Object test = null;

            ByteArrayInputStream in = new ByteArrayInputStream(readbuf);
            ObjectInputStream is = new ObjectInputStream(in);
            System.out.println("Program fine until this line!");
            test = is.readObject();
        }

        MPI.Finalize();
    }
}

 

Thanks

Marko

 

Gesendet: Montag, 25. Januar 2016 um 01:04 Uhr
Von: "Gilles Gouaillardet" <gil...@rist.or.jp>
An: "Open MPI Users" <us...@open-mpi.org>
Betreff: Re: [OMPI users] segmentation fault with java MPI

Marko,

i wrote a test program based on your code snippet and it works for me.

could you please :
- post a standalone test case that is ready to be compiled and ran
- which version of OpenMPI are you using ?
- which JVM are you using ? (vendor and version)
- post your full command line

Cheers,

Gilles

On 1/25/2016 8:23 AM, Marko Blatzheim wrote:
> String filename = "testfile";
> byte[] readbuf;
>
> File myfile = new File(MPI.COMM_SELF, filename, MPI.MODE_RDONLY);
> int filesize = (int) myfile.getSize();
> readbuf = new byte[filesize];
>
> byte[] copyarray = new byte[filesize];
> Status status = myfile.read(readbuf, filesize, MPI.BYTE);
> Object test = null;
> if (myrank == 0) {
> ByteArrayInputStream in = new ByteArrayInputStream(readbuf);
> ObjectInputStream is = new ObjectInputStream(in);
> test = is.readObject(); // This line causes a
> segmnentation fault
> }

_______________________________________________
users mailing list
us...@open-mpi.org
Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users
Link to this post: http://www.open-mpi.org/community/lists/users/2016/01/28360.php