[OMPI users] UnsatisfiedLinkError - libmpi_java.so.0.0.0

2013-07-21 Thread Saliya Ekanayake 
Hi,

I obtained the nightly build openmpi-1.9a1r28881 (on 7/19/13) and built it
with java enabled using,

./configure --enable-mpi-java --prefix=/N/u/sekanaya/build

Then I wrote a simple MPI program to print the rank of the process,
following user guide from http://www.open-mpi.org/papers/mpi-java-spec/

I built my code using mpijavac and then tried running it as,

mpirun -np 2 java Main

where Main is my class name (not in a package) and I was running inside the
folder containing Main.class.

I get the following error when doing so,

Exception in thread "main" java.lang.UnsatisfiedLinkError:
/N/u/sekanaya/build/lib/libmpi_java.so.0.0.0:
/N/u/sekanaya/build/lib/libmpi.so.0: undefined symbol: opal_maffinity_setup


Any suggestion on fixing this?

Thank you in advance,

Saliya



-- 
Saliya Ekanayake esal...@gmail.com
Cell 812-391-4914 Home 812-961-6383
http://saliya.org

Re: [OMPI users] After OS Update MPI_Init fails on one host

2013-07-21 Thread Kevin H. Hobbs 
On 07/20/2013 04:14 PM, Ralph Castain wrote:
> Ah! That would indicate an issue with the external hwloc
> package they provided, which is the big reason we don't
> recommend installing from packages.

I'll happily report the bug to the hwloc developers.

I'll also add what we've found here to the bug on the Fedora
bugzilla.

Is there anything more I can do on this list to figure out the
nature of the bug?

> We have internal copies of hwloc and libevent that ensure (a)
> they are at the proper level, and (b) they are configured
> properly for OMPI's use.

It does look like Fedora's hwloc is ahead of OMPI's.

Fedora 18 has openmpi-1.6.3 and hwloc-1.4.2.

The source of openmpi-1.6.5 has hwloc-1.3.2.

How can I tell what the configuration differences are?

The entire configure section of the .spec file in
hwloc-1.4.2-2.fc18.src.rpm is :

  %configure
  %{__make} %{?_smp_mflags} V=1

I don't see anything that looks like any hwloc configure options
are being set.

How do I tell how OMPI configures it's bundled hwloc?

> We've had that debate with the Fedora folks recently - they
> won't take our advice,

I admit to having a bias against bundled dependencies, but I
don't want to get in the middle of a debate.

> so I'm afraid you'll just need to build from source to have
> something usable.

Yes, that solves my problem, but if I can I'd like to leave at
least a trail of breadcrumbs that the next person to encounter
the bug can follow.

Better yet, I'd like to figure out the actual nature of the bug
and report it in the proper place.



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