Felix Natter <fnat...@gmx.net> writes: > hello Andreas,
hello again Andreas, > Felix Natter <fnat...@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? You wrote: >> 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. _Maybe_ you can also use mpjexpress (libmpj-java) [1]? current/stream/mpi/MPIWrapper.java:82: error: cannot find symbol MPI.COMM_WORLD.bcast(bLength,1,MPI.INT,0); // can't probe a broadcast, so send message size first ^ symbol: method bcast(int[],int,Datatype,int) location: variable COMM_WORLD of type Intracomm current/stream/mpi/MPIWrapper.java:83: error: cannot find symbol MPI.COMM_WORLD.bcast(b,b.length,MPI.BYTE,0); // broadcast the actual message ^ symbol: method bcast(byte[],int,Datatype,int) location: variable COMM_WORLD of type Intracomm by patching this: Intracomm.getSize() -> Intracomm.Size() Intracomm.getRank() -> Intracomm.Rank() Intracomm.bcase(byte[],int,Datatype,int) -> Intracomm.Bcast(Object, int, Datatype, int) (I don't know what's "below" this...) Otherwise, [3] might be worth checking, but adding java support to openmpi is probably a better solution. [1] http://mpjexpress.org/docs/javadocs/mpi/Intracomm.html [2] http://mpjexpress.org/docs/javadocs/mpi/Intracomm.html#Bcast%28java.lang.Object,%20int,%20int,%20mpi.Datatype,%20int%29 [3] www.hpjava.org/mpiJava.html Cheers and Best Regards, -- Felix Natter
