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From: Andy Vierstraete (andy.vierstraete_at_[hidden])
Date: 2006-02-10 10:31:12


Hi Brian and Peter,

I tried the nightly build like Brian said, and I was able to compile
Migrate without errors-message (that was not the case before, like Peter
suggested, I had to set openmpi in my path). But is is still not
running : now it can't find "libmpi.so.0", and the directory where the
file is, is in my path.
If I install openmpi 1.0.1 again, I get the same errormessages as last time

I'll try it again with lam-mpi, and see if that works for compiling
Migrate correctly and if it runs on this pc...

avierstr_at_muscorum:~> migrate-mpi
migrate-mpi: error while loading shared libraries: libmpi.so.0: cannot
open shared object file: No such file or directory
avierstr_at_muscorum:~> migrate-n
migrate-n: error while loading shared libraries: libmpi.so.0: cannot
open shared object file: No such file or directory
avierstr_at_muscorum:~> echo $PATH
/home/avierstr/bin:/usr/local/bin:/usr/bin:/usr/X11R6/bin:/bin:/usr/games:/opt/gnome/bin:/opt/kde3/bin:/usr/lib/mit/bin:/usr/lib/mit/sbin:/usr/local/openmpi-1.1a1/bin:/usr/local/Modeltest3.7/source:/usr/local/mrbayes-3.1.2:/usr/local/bin:/usr/local/MrModeltest2.2:/usr/local/paup4b10:/usr/local/mrbayes-3.1.2-mpi:/usr/local/openmpi-1.1a1/lib:/usr/local/migrate-2.1.3-mpi/src:/usr/local/openmpi-1.1a1/bin:/usr/local/Modeltest3.7/source:/usr/local/mrbayes-3.1.2:/usr/local/bin:/usr/local/MrModeltest2.2:/usr/local/paup4b10:/usr/local/mrbayes-3.1.2-mpi:/usr/local/openmpi-1.1a1/lib:/usr/local/migrate-2.1.3-mpi/src:/usr/local/Modeltest3.7/source:/usr/local/mrbayes-3.1.2:/usr/local/bin:/usr/local/MrModeltest2.2:/usr/local/paup4b10:/usr/local/mrbayes-3.1.2-mpi:/usr/local/openmpi-1.1a1/lib:/usr/local/migrate-2.1.3-mpi/src
avierstr_at_muscorum:~> mpiexec -np 2 migrate-mpi
orted: error while loading shared libraries: liborte.so.0: cannot open
shared object file: No such file or directory
[muscorum:12220] ERROR: A daemon on node localhost failed to start as
expected.
[muscorum:12220] ERROR: There may be more information available from
[muscorum:12220] ERROR: the remote shell (see above).
[muscorum:12220] ERROR: The daemon exited unexpectedly with status 127.
avierstr_at_muscorum:~>

Peter Beerli wrote:

>Dear Brian,
>
>The original poster intended to run migrate-n in parallel mode, but the
>stdout fragment shows that the program was compiled for a non-MPI
>architecture
>(either single CPU or SMP pthreads) [I talked with him list-offline
>and it used pthreads].
>A version for parallel runs shows this fact in its first couple of
>lines, like this (<@@@@):
> =============================================
> MIGRATION RATE AND POPULATION SIZE ESTIMATION
> using Markov Chain Monte Carlo simulation
> =============================================
> compiled for a PARALLEL COMPUTER ARCHITECTURE
><@@@@@@@@@@@@@@@@@@@@@@@@@
> Version debug 2.1.3 [x]
> Program started at Wed Feb 8 12:29:35 2006
>
>As far as I am concerned migrate-n compiles and runs on openmpi
>1.0.1. There might be some use in running
>the program multiple times completely independently through openmpi
>or lam for simulation purposes, but
>that would not be a typical use of the program that can distribute
>multiple genetic loci on multiple nodes and only having
>the master handling input and output (when compiled using configure;
>make mpis or configure;make mpi)
>
>
>Peter
>----
>Peter Beerli,
>Computational Evolutionary Biology Group
>School of Computational Science (SCS)
>and Biological Sciences Department
>150-T Dirac Science Library
>Florida State University
>Tallahassee, Florida 32306-4120 USA
>Webpage: http://www.csit.fsu.edu/~beerli
>Phone: 850.645.1324
>Fax: 850.644.0094
>
>
>
>
>
>On Feb 8, 2006, at 11:24 AM, Brian Barrett wrote:
>
>
>
>>I think we fixed this over this last weekend. I believe the problem
>>was our mis-handling of standard input in some cases. I believe I was
>>able to get the application running (but I could be fooling myself
>>there...). Could you download the latest nightly build from the URL
>>below and see if it works for you? The fixes are scheduled to be
>>part of Open MPI 1.0.2, which should be out real soon now.
>>
>> http://www.open-mpi.org/nightly/trunk/
>>
>>Thanks,
>>
>>Brian
>>
>>On Feb 3, 2006, at 10:23 AM, Andy Vierstraete wrote:
>>
>>
>>
>>>Hi,
>>>
>>>I have installed Migrate 2.1.2, but it fails to run on open-MPI (it
>>>does run on LAM-MPI : see end of mail)
>>>
>>>my system is Suse 10 on Athlon X2
>>>
>>>hostfile : localhost slots=2 max_slots=2
>>>
>>>I tried different commands :
>>>
>>>1. does not start : error message :
>>>******************************************
>>>
>>>avierstr_at_muscorum:~/thomas> mpiexec -np 2 migrate-mpi
>>>mpiexec noticed that job rank 1 with PID 0 on node "localhost"
>>>exited on
>>>signal 11.
>>>[muscorum:07212] ERROR: A daemon on node localhost failed to start as
>>>expected.
>>>[muscorum:07212] ERROR: There may be more information available from
>>>[muscorum:07212] ERROR: the remote shell (see above).
>>>[muscorum:07212] The daemon received a signal 11.
>>>1 additional process aborted (not shown)
>>>
>>>************************************************
>>>
>>>2. starts a non-ending loop :
>>>************************************************
>>>
>>>avierstr_at_muscorum:~/thomas> mpirun -np 2 --hostfile ./hostfile
>>>migrate-mpi
>>>migrate-mpi
>>> =============================================
>>> MIGRATION RATE AND POPULATION SIZE ESTIMATION
>>> using Markov Chain Monte Carlo simulation
>>> =============================================
>>> Version 2.1.2
>>> Program started at Fri Feb 3 15:58:57 2006
>>>
>>>
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>>igration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>>
>>>****************************************************************
>>>
>>>
>>>
>>>
>>>
>>>3. with LAM-MPI on Suse 8.2 it works after lamboot hostfile :
>>>****************************************************************
>>>
>>>avierstr_at_molfyl1:~/migrate-2.1.0/src> mpiexec -np 2 ./migrate-n
>>> =============================================
>>> MIGRATION RATE AND POPULATION SIZE ESTIMATION
>>> using Markov Chain Monte Carlo simulation
>>> =============================================
>>> Version 2.1.0
>>> Program started at Fri Feb 3 14:05:05 2006
>>>
>>>
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>> =============================================
>>> MIGRATION RATE AND POPULATION SIZE ESTIMATION
>>> using Markov Chain Monte Carlo simulation
>>> =============================================
>>> Version 2.1.0
>>> Program started at Fri Feb 3 14:05:05 2006
>>>
>>>
>>> Settings for this run:
>>> D Data type currently set to: DNA sequence model
>>> I Input/Output formats
>>> P Parameters [start, migration model]
>>> S Search strategy
>>> W Write a parmfile
>>> Q Quit the program
>>>
>>>
>>> Are the settings correct?
>>> (Type Y or the letter for one to change)
>>>y
>>>
>>>
>>>Reading BALTIC ...
>>>Reading WE ...
>>>Reading WS ...
>>>Reading YTH ...
>>>Reading SEI ...
>>>Reading EL ...
>>>Reading KILK ...
>>>Reading GI ...
>>>Reading RdA ...
>>>Reading GU ...
>>>
>>>
>>>Options in use:
>>>---------------
>>>Datatype: DNA sequence data
>>>Random number seed (with internal timer) 1138971909
>>>Start parameters:
>>> Theta values were generated from the FST-calculation
>>> M values were generated from the FST-calculation
>>>Migration model:
>>> ...........
>>>
>>>--
>>>*********************************************************************
>>>* 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/
>>>
>>>_______________________________________________
>>>users mailing list
>>>users_at_[hidden]
>>>http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>>
>>--
>> Brian Barrett
>> Open MPI developer
>> http://www.open-mpi.org/
>>
>>
>>_______________________________________________
>>users mailing list
>>users_at_[hidden]
>>http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>
>_______________________________________________
>users mailing list
>users_at_[hidden]
>http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
>

-- 
*********************************************************************
* 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/