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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