Path: csiph.com!goblin2!goblin.stu.neva.ru!gothmog.csi.it!bofh.it!news.nic.it!robomod From: Andreas Tille Newsgroups: linux.debian.maint.java Subject: Re: Java-help for BBMap needed Date: Sun, 20 Mar 2016 18:20:02 +0100 Message-ID: References: X-Original-To: Debian Med Packaging Team X-Mailbox-Line: From debian-java-request@lists.debian.org Sun Mar 20 17:12:15 2016 Old-Return-Path: X-Amavis-Spam-Status: No, score=-4.981 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, LDO_WHITELIST=-5, MEDS2=2, MURPHY_DRUGS_REL8=0.02, RP_MATCHES_RCVD=-0.001] autolearn=no autolearn_force=no X-Policyd-Weight: using cached result; rate:hard: -6.1 X-Greylist: delayed 439 seconds by postgrey-1.35 at bendel; Sun, 20 Mar 2016 17:12:01 UTC MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.23 (2014-03-12) X-Mailing-List: archive/latest/19274 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/20160320171159.GH5834@an3as.eu Approved: robomod@news.nic.it Lines: 57 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: Debian Java List X-Original-Date: Sun, 20 Mar 2016 18:11:59 +0100 X-Original-Message-ID: <20160320171159.GH5834@an3as.eu> X-Original-References: <20160319084135.GI27272@an3as.eu> <87fuvlxj7o.fsf@bitburger.home.felix> <20160320170439.GG5834@an3as.eu> Xref: csiph.com linux.debian.maint.java:8948 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. > > -- > http://fam-tille.de > > _______________________________________________ > Debian-med-packaging mailing list > Debian-med-packaging@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > -- http://fam-tille.de