Path: csiph.com!news.mixmin.net!aioe.org!gothmog.csi.it!bofh.it!news.nic.it!robomod From: Felix Natter Newsgroups: linux.debian.maint.java Subject: Re: Java-help for BBMap needed Date: Sun, 20 Mar 2016 18:10:03 +0100 Message-ID: References: X-Mailbox-Line: From debian-java-request@lists.debian.org Sun Mar 20 17:04:59 2016 Old-Return-Path: X-Amavis-Spam-Status: No, score=-7.681 tagged_above=-10000 required=5.3 tests=[BAYES_00=-2, FREEMAIL_FROM=0.001, LDO_WHITELIST=-5, MURPHY_DRUGS_REL8=0.02, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H2=-0.001, RP_MATCHES_RCVD=-0.001] autolearn=ham autolearn_force=no X-Policyd-Weight: using cached result; rate: -7 User-Agent: Gnus/5.130006 (Ma Gnus v0.6) Emacs/24.4 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Provags-ID: V03:K0:cX0loo7s/UI40+GkIFI+kSDqUeQuanT+T4D7DUs4o8G6E0xoP6U oRv1/qT3VYSOy3mn91dc50aWGOZCjGUqKsswptrij1/Y/5Ud5a0U3UzucEwFPQdKYU1BPT+ Rews1R2T3vFQkgLLxqZlRuE3J8e7D+jxePkB+rYcTKVZ+tPQEG5t8Lq4av/0NIfJ+0/wGIb EQErIRTRFIDWkJOImdRpg== X-Ui-Out-Filterresults: notjunk:1;V01:K0:x6nQMBmVwr0=:Je8XS/+mrrD+JjJx/IDuKt dTlo5hOqQ/ELN7LOyLnKHSciiX2b+lYcNIkaxgdvp4z6itvF6PO6vx4ZoDpOsXM0/0pI0l48q dRyGUCJNe7WyRFdcp86pDFnnWgCS1jsOO92pSyVnkZcZSiQe9nk7sNmkpAFX9y9PETqUEHscS MwlZKZGiC8uyfSfyeMsS3dWjZ4P3epQGgRyhht7X5Rx32ojFuVipkhp9zZLrVyLG3bUAF3cxp 7XCiloFTZ08AvrnCmVwzPhOg/8b1C28cw5PdJg6PKXRqgHacAW7PcYCvv1Ap4gDcKvZodyNVI 4sXw52FWTZlZnE8uxcN3dxVNHCtmOVf6BElK2f76zd6qeR710+zYj4RoQcAoHpXY0zlMlK7Il zEAqj8oN1I/ivPWKYnMloGWSS2xKuqYgMY4TNeGXeU4O7JKpJLO8msSpxtkMcUrqXfVLQyp8f AX4s0usFNoI27N51gL2QEqPvf267m41Rb3Mc7nI0Ao20AqKzaeal1c3A+HnmlkbizHdzLb1/3 qCkcE1P0a8rBkKWeQyvDr2ZxRQIB+uJVwR9vqSU1GWyr0NzOhIalVzBvb3hB8via70Pd7Q3/p +16Z64sZX2pHzRnuJ5xzo5wOPVVVb8v5LgIsHtz00VinnNg/9ywwX3iB6uIXUjYF/+UAjSU+7 FIVdrysNL8573sboft5eGx/p4wqdvAfkgW0BNCoQNPJGT5IleRnCwtTlwanceadoHsY6JR4W0 vN7ZN6CN3B6cU/VBauBCk/dZXH7dBikFnEeHLrattracVelYBmtCeU4tlKyExIU9oS9bJXxjx us3vwRp X-Mailing-List: archive/latest/19273 List-ID: List-URL: List-Archive: https://lists.debian.org/msgid-search/871t75qdwp.fsf@bitburger.home.felix Approved: robomod@news.nic.it Lines: 32 Organization: linux.* mail to news gateway Sender: robomod@news.nic.it X-Original-Cc: Debian Med Packaging Team , Debian Java List X-Original-Date: Sun, 20 Mar 2016 18:04:22 +0100 X-Original-Message-ID: <871t75qdwp.fsf@bitburger.home.felix> X-Original-References: <20160319084135.GI27272@an3as.eu> <87fuvlxj7o.fsf@bitburger.home.felix> Xref: csiph.com linux.debian.maint.java:8947 hello Andreas, Felix Natter 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