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

[Felix Natter]

hello Andreas,

Felix Natter <fnatter at gmx.net> writes:
>>   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])
>
> [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]?

I think we need to use Size() [1], Rank() [2] etc
(probably all methods starting with a capital letter):

[1] http://mpjexpress.org/docs/javadocs/mpi/Comm.html#Size%28%29
[2] http://mpjexpress.org/docs/javadocs/mpi/Comm.html#Rank%28%29

Can you patch this?

Cheers and Best Regards,
-- 
Felix Natter