On 22/09/13 02:28 AM, Ranjeev wrote: > Btw, my assembly of the panda genome terminated with PBS: job killed: node 2 > (compute-0-4) requested job terminate, 'EOF' (code 1099) - received SISTER_EOF >attempting to communicate with sister MOM's. >
This is a Torque error I think. I found this: http://www.open-mpi.org/community/lists/users/2011/03/16017.php > > On Sun, Sep 22, 2013 at 12:21 PM, Ranjeev <[email protected] > <mailto:[email protected]>> wrote: > > Hi > > Thanks I was using torque and specified the nodes only with Infiniband > and it seemed to have added those n parameters by itself. Btw, if I have a > node with 192Gb RAM and 24 processors, how many processes do you recommend > per node? I notice each process consuming considerable RAM and start to use > swap when I use 24 processes per node. > > > > On Fri, Sep 20, 2013 at 7:08 PM, Sébastien Boisvert > <[email protected] <mailto:[email protected]>> > wrote: > > On 19/09/13 11:26 PM, Ranjeev wrote: > > HI, > > I'm using openmpi and torque - I managed to test Ray once and > worked fine (for a single node). > The next time I run the network test takes forever. Doesn't go > beyond the last line > > Ray command: > mpiexec -n 2 Ray \ > -n \ > 40 \ > > > > Do you want 2 ranks or 40 ranks ? > > > > -p \ > /home/ranjeev/NTM/L007_R1.fq \ > /home/ranjeev/NTM/L007_R2.fq \ > -o \ > /home/ranjeev/temp/Ray/test3 > > Rank 0 wrote /home/ranjeev/temp/Ray/test3/__RayCommand.txt > > k-mer length: 21 > Rank 1: assembler memory usage: 24972 KiB > Rank 0: assembler memory usage: 24976 KiB > Rank 1: assembler memory usage: 90796 KiB > Rank 1: Rank= 1 Size= 2 ProcessIdentifier= 12290 > Rank 0: assembler memory usage: 90804 KiB > Rank 0: Rank= 0 Size= 2 ProcessIdentifier= 18150 > Rank 0: testing the network, please wait... > > Rank 0 is testing the network [0/1000] > > > Regards, > Ranjeev > > > > -- > " PENAFIAN: E-mel ini dan apa-apa fail yang dikepilkan bersamanya > ("Mesej") adalah ditujukan hanya untuk kegunaan penerima(-penerima) yang > termaklum di atas dan mungkin mengandungi maklumat sulit. Anda dengan ini > dimaklumkan bahawa mengambil apa jua tindakan bersandarkan kepada, membuat > penilaian, mengulang hantar, menghebah, mengedar, mencetak, atau menyalin > Mesej ini atau sebahagian daripadanya oleh sesiapa selain daripada > penerima(-penerima) yang termaklum di atas adalah dilarang. Jika anda telah > menerima Mesej ini kerana kesilapan, anda mesti menghapuskan Mesej ini dengan > segera dan memaklumkan kepada penghantar Mesej ini menerusi balasan e-mel. > Pendapat-pendapat, rumusan-rumusan, dan sebarang maklumat lain di dalam Mesej > ini yang tidak berkait dengan urusan rasmi Universiti Malaya adalah difahami > sebagai bukan dikeluar atau diperakui oleh mana-mana pihak yang disebut. > > > DISCLAIMER: This e-mail and any files transmitted with it ("Message") > is intended only for the use of the recipient(s) named above and may contain > confidential information. You are hereby notified that the taking of any > action in reliance upon, or any review, retransmission, dissemination, > distribution, printing or copying of this Message or any part thereof by > anyone other than the intended recipient(s) is strictly prohibited. If you > have received this Message in error, you should delete this Message > immediately and advise the sender by return e-mail. Opinions, conclusions and > other information in this Message that do not relate to the official business > of University of Malaya shall be understood as neither given nor endorsed by > any of the forementioned. " > > > ------------------------------------------------------------------------------ LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
