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@muscorum:~> migrate-mpi
migrate-mpi: error while loading shared libraries: libmpi.so.0: cannot
open shared object file: No such file or directory
avierstr@muscorum:~> migrate-n
migrate-n: error while loading shared libraries: libmpi.so.0: cannot
open shared object file: No such file or directory
avierstr@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@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@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@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@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@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
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
--
Brian Barrett
Open MPI developer
http://www.open-mpi.org/
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list
us...@open-mpi.org
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/
