[Debian-med-packaging] Java-help for BBMap needed

[Andreas Tille]

Hi again,

the issue below has a simple explanation: I do not need mpj but rather
mpi which should be available by enabling the java interface in the
openmpi source package.

Sorry for the confusion

    Andreas.

On Sun, Mar 20, 2016 at 06:04:39PM +0100, Andreas Tille wrote:
>  
> > >   symbol:   method getRank()
> > >   location: variable COMM_WORLD of type Intracomm
> > > current/stream/mpi/MPIWrapper.java:49: error: cannot find symbol
> > > 				Shared.MPI_NUM_RANKS=MPI.COMM_WORLD.getSize();
> > > 				                                   ^
> > >   symbol:   method getSize()
> > 
> > It looks like bbmap requires the methods getRank() and getSize()
> > on mpi.Intracomm, and this method does not seem to be available in
> > mpj-0.42+dfsg.
> > (I couldn't find it in mpj-0.44 either [3] [4])
> 
> Apropos mpj:  Its maintained by the Debian team for historical reasons.
> I'd be happy to move it to pkg-java Git in case Debian Java team wants
> to take over.
>  
> > [3] https://sourceforge.net/projects/mpjexpress/files/
> > [4] http://mpjexpress.org/docs/javadocs/mpi/Intracomm.html
> > 
> > Maybe we should ask the mpjexpress folks which
> > mpjexpress to use or how to fix/patch bbmap [5]?
> > 
> > Does anyone on this list know more about MPI for java?
> 
> I'd be really happy for any further hint.
>  
> > [5] https://anonscm.debian.org/git/debian-med/bbmap.git/tree/current/stream/mpi/MPIWrapper.java
> > 
> > Cheers and Best Regards,
> 
> Thanks for your help
> 
>      Andreas.
> 
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