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From: George Bosilca (bosilca_at_[hidden])
Date: 2006-02-10 11:27:55


There are 2 things that have to be done in order to be able to run a
Open MPI application. First the runtime environment need access to
some of the files in the bin directory so you have to add the Open
MPI bin directory to your path. And second, as we use shared
libraries the OS need to know where they can be found. This is done
using the LD_LIBRARY_PATH environment variable. So suppose that one
has compiled Open MPI like this:
./configure --prefix=/home/one/opt
He has to add in his tcsh startup script (.tcshrc):
setenv PATH "/home/one/opt/bin:${PATH}"
setenv LD_LIBRARY_PATH "/home/one/lib:${LD_LIBRARY_PATH}"

That should fix your problem. Enjoy.

     george.

On Feb 10, 2006, at 10:31 AM, Andy Vierstraete wrote:

> 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/
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users

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