Re: [OMPI users] segfault on java binding from MPI.init()

2015-08-03 Thread Nate Chambers
Gilles, Yes I saw that github thread, but wasn't certain this was the same issue. Very possible that it is. Oddly enough, that github code doesn't crash for us. Adding a sleep call doesn't help. It's actually now crashing on the MPI.init(args) call itself, and the JVM is reporting the error.

Re: [OMPI users] segfault on java binding from MPI.init()

2015-08-03 Thread Gilles Gouaillardet
Nate, a similar issue has already been reported at https://github.com/open-mpi/ompi/issues/369, but we have not yet been able to figure out what is going wrong. right after MPI_Init(), can you add Thread.sleep(5000); and see if it helps ? Cheers, Gilles On 8/4/2015 8:36 AM, Nate Chambers

[OMPI users] segfault on java binding from MPI.init()

2015-08-03 Thread Nate Chambers
We've been struggling with this error for a while, so hoping someone more knowledgeable can help! Our java MPI code exits with a segfault during its normal operation, *but the segfault occurs before our code ever uses MPI functionality like sending/receiving. *We've removed all message calls and

Re: [OMPI users] pbs vs openmpi node allocation

2015-08-03 Thread Gus Correa
Hi Abhisek On 08/03/2015 12:59 PM, abhisek Mondal wrote: Hi, I'm using openmpi-1.6.4 to distribute a jobs in 2 different nodes using this command: /"mpirun --hostfile myhostfile -np 10 nwchem my_code.nw"/ Here, "myhostfile" contains: /cx0937 slots=5 / /cx0934 slots=5/ I am assuming by pbs

Re: [OMPI users] pbs vs openmpi node allocation

2015-08-03 Thread Andrus, Brian Contractor
Abhisek, Generally, if you built openmpi with PBS support, it will automatically using the appropriate nodes with ‘mpirun ’ If not, you can use the environment variables provided to your session: mpirun --hostfile $PBS_NODEFILE -np $(cat $PBS_NODEFILE|wc -l) Brian Andrus ITACS/Research

[OMPI users] pbs vs openmpi node allocation

2015-08-03 Thread abhisek Mondal
Hi, I'm using openmpi-1.6.4 to distribute a jobs in 2 different nodes using this command: *"mpirun --hostfile myhostfile -np 10 nwchem my_code.nw"* Here, "myhostfile" contains: *cx0937 slots=5* *cx0934 slots=5* But as I have to submit the jobs using .pbs script, I'm wondering in this case,