Let us know what you find -- we have no experience with the MrBayes
software.
Thanks!
On Dec 13, 2005, at 9:46 AM, Robert LeBlanc wrote:
> We run Mr. Bayes here. If you want to send me your Bayes file, I
> can give it
> a run here and see if I get the same results.
>
> Robert LeBlanc
> BioAg Computer Support
> Brigham Young University
>
> -----Original Message-----
> From: lam-bounces_at_[hidden] [mailto:lam-bounces_at_[hidden]] On
> Behalf Of
> Andy Vierstraete
> Sent: Tuesday, December 13, 2005 1:56 AM
> To: lam_at_[hidden]
> Subject: LAM: LAM and MrBayes hangs on larger file
>
> Hi,
>
> I installed LAM-MPI and MrBayes, and with a testfile with 34 taxa, it
> runs without problems. When I try to start a larger file (174 taxa),
> MrBayes starts reading the first 111 taxa, and then it stops and
> nothing
> happens anymore.
> When I remove node 1 (mermis.ugent.be), than MrBayes (parallel
> version)
> runs that file without problems.
>
> node 2 : Molfyl1 : Suse 8.2 on dual Athlon MP2000
> node 1 : Mermis : Suse 10 (32-bit version) on Athlon 64 3000+
>
> Any suggestions what the problem is and how to solve it ??
>
> Thanks a lot,
>
> Andy
>
>
> this is the output :
> ----------------------------------------------------------------------
> --
>
> avierstr_at_molfyl1:~/david> lamboot ../hostfile
>
> LAM 7.1.1/MPI 2 C++/ROMIO - Indiana University
>
> Enter passphrase for key '/home/avierstr/.ssh/id_dsa':
> Enter passphrase for key '/home/avierstr/.ssh/id_dsa':
> avierstr_at_molfyl1:~/david> lamnodes
> n0 molfyl1.UGent.be:2:origin,this_node
> n1 mermis.ugent.be:1:
> avierstr_at_molfyl1:~/david> mpiexec mb311mpi
> MrBayes v3.1.1
>
> (Bayesian Analysis of Phylogeny)
>
> (Parallel version)
> (3 processors available)
>
> by
>
> John P. Huelsenbeck and Fredrik Ronquist
>
> Section of Ecology, Behavior and Evolution
> Division of Biological Sciences
> University of California, San Diego
> johnh_at_[hidden]
>
> School of Computational Science
> Florida State University
> ronquist_at_[hidden]
>
> Distributed under the GNU General Public License
>
> Type "help" or "help <command>" for information
> on the commands that are available.
>
>
> MrBayes > execute CE.pau
>
> Executing file "CE.pau"
> UNIX line termination
> Longest line length = 123
> Parsing file
> Expecting NEXUS formatted file
> Reading data block
> Allocated matrix
> Matrix has 174 taxa and 244 characters
> Data matrix is interleaved
> Data is Protein
> Missing data coded as N
> Gaps coded as -
> Setting default partition (does not divide up characters).
> Taxon 1 -> ArabidopsisNsHb1
> Taxon 2 -> EuryaleNsHb
> Taxon 3 -> MarchantiaNsHb
> Taxon 4 -> TremaNsHb
> Taxon 5 -> OryzaNsHb1
> Taxon 6 -> PhyscomitrellaNsHb
> Taxon 7 -> CanavaliaSHb
> Taxon 8 -> LupinSHb
> Taxon 9 -> SesbaniaSHb
> Taxon 10 -> CasuarinaSHb
> Taxon 11 -> AgrtumGCS
> Taxon 12 -> BacsubGCS
> Taxon 13 -> Chrvio1GCS
> Taxon 14 -> EsccolGCS
> Taxon 15 -> GeosulGCS
> Taxon 16 -> HalmarGCS
> Taxon 17 -> SinmelGCS
> Taxon 18 -> VibvulGCS
> Taxon 19 -> AerperPgb
> Taxon 20 -> MetacePgb
> Taxon 21 -> Halmar
> Taxon 22 -> Mycavi1
> Taxon 23 -> Myxxan1
> Taxon 24 -> Nospun2
> Taxon 25 -> Solusi1
> Taxon 26 -> Syncys
> Taxon 27 -> Xanaxo
> Taxon 28 -> Agrtum1
> Taxon 29 -> Borper1
> Taxon 30 -> Burcep1
> Taxon 31 -> Chlaur
> Taxon 32 -> Deirad
> Taxon 33 -> Exiguo
> Taxon 34 -> Kinrad
> Taxon 35 -> Lepint
> Taxon 36 -> Mycavi2
> Taxon 37 -> Staaur
> Taxon 38 -> Acifer3
> Taxon 39 -> Bdebac2
> Taxon 40 -> Borper2
> Taxon 41 -> Camjej
> Taxon 42 -> Mycavi3
> Taxon 43 -> Novaro
> Taxon 44 -> CyanmerSDgb
> Taxon 45 -> Thapse1SDgb
> Taxon 46 -> Chocri1FHb
> Taxon 47 -> Chocri22x2Hb
> Taxon 48 -> Thapse22x2Hb
> Taxon 49 -> Chlrei12x2Hb
> Taxon 50 -> Paramecium
> Taxon 51 -> Arabidopsis
> Taxon 52 -> Oryza
> Taxon 53 -> BacantF
> Taxon 54 -> DeiradF
> Taxon 55 -> EsccolF
> Taxon 56 -> ExiguoF
> Taxon 57 -> MagmagF
> Taxon 58 -> MyctubF
> Taxon 59 -> OceiheF
> Taxon 60 -> RhodopirellF
> Taxon 61 -> PseaerF
> Taxon 62 -> RalmetF
> Taxon 63 -> StaaurF
> Taxon 64 -> Strave1F
> Taxon 65 -> VibchoF
> Taxon 66 -> Aquaeox
> Taxon 67 -> Brajap1x
> Taxon 68 -> Camjejx
> Taxon 69 -> Chrvio2x
> Taxon 70 -> Deshafx
> Taxon 71 -> Gloviox
> Taxon 72 -> Rhobalx
> Taxon 73 -> Vitstex
> Taxon 74 -> Pseaerx
> Taxon 75 -> Thefusx
> Taxon 76 -> Aspnid1
> Taxon 77 -> Debhan1
> Taxon 78 -> Dicdis1
> Taxon 79 -> Gialam
> Taxon 80 -> Neucra1
> Taxon 81 -> Saccer1
> Taxon 82 -> Schpom1
> Taxon 83 -> HomoNgb
> Taxon 84 -> GallusNgb
> Taxon 85 -> DanioNgb
> Taxon 86 -> HomoCygb
> Taxon 87 -> GallusCygb
> Taxon 88 -> DanioCygb1
> Taxon 89 -> HomoA
> Taxon 90 -> SqualusA
> Taxon 91 -> AnserA
> Taxon 92 -> HomoB
> Taxon 93 -> AnserB
> Taxon 94 -> SqualusB
> Taxon 95 -> HomoMb
> Taxon 96 -> ThunnusMb
> Taxon 97 -> GallusMb
> Taxon 98 -> GalgalEyegb
> Taxon 99 -> TetnigHbX
> Taxon 100 -> XentroHbX
> Taxon 101 -> PetmatHb2
> Taxon 102 -> MyxgluHb3
> Taxon 103 -> Cioint1
> Taxon 104 -> CauareHbC
> Taxon 105 -> Lumterb
> Taxon 106 -> Lumterc
> Taxon 107 -> MacdecB
> Taxon 108 -> MacdecC
> Taxon 109 -> Tylhet2B
> Taxon 110 -> Tylhet2A
> Taxon 111 -> AmpornDHP
>
> (Pressed CTRL-C)
>
>
> sending sig_INT to mpirun
> ----------------------------------------------------------------------
> ------
> -
> One of the processes started by mpirun has exited with a nonzero exit
> code. This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
>
> PID 9651 failed on node n0 (157.193.95.1) due to signal 15.
> ----------------------------------------------------------------------
> ------
> -
> mpirun failed with exit status 15
> avierstr_at_molfyl1:~/david>
>
> --
> *********************************************************************
> * Youth is a wonderful thing. What a crime to waste it on children. *
> * (George Bernard Shaw) *
> *********************************************************************
>
>
> Andy Vierstraete
> Department of Biology
> University of Ghent
> K. L. Ledeganckstraat 35
> B-9000 Gent
> Belgium
> phone : 09-264.52.66
> fax : 09-264.87.93
> http://allserv.UGent.be/~avierstr/
>
> _______________________________________________
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>
> _______________________________________________
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--
{+} Jeff Squyres
{+} The Open MPI Project
{+} http://www.open-mpi.org/
|
