Hi George,

Thanks for the info, I had to change the command  :

setenv LD_LIBRARY_PATH "/home/one/lib:${LD_LIBRARY_PATH}"
to :
export LD_LIBRARY_PATH="/usr/local/openmpi-1.1a1/lib:${LD_LIBRARY_PATH}"

but it still does not work.  Migrate starts, but after I pressed yes, than nothing happens, it seems to hang (with 1 or 2 processor usage)...

With lammpi, it seems to work... (see a bit below)
-----------------------------------------------


avierstr@muscorum:~> mpiexec --hostfile hostfile -np 1  migrate-n
migrate-n
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  compiled for a PARALLEL COMPUTER ARCHITECTURE
  Version 2.1.3
  Program started at   Mon Feb 13 11:21:25 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




mpiexec: killing job...
1 process killed (possibly by Open MPI)
avierstr@muscorum:~> 

--------------------------------------------------------

avierstr@muscorum:~/thomas> lamboot hostfile

LAM 7.1.1/MPI 2 C++/ROMIO - Indiana University

avierstr@muscorum:~/thomas> lamnodes
n0      muscorum.ugent.be:2:origin,this_node
avierstr@muscorum:~/thomas> mpiexec -np 2  migrate-n
migrate-n
migrate-n
  =============================================
  MIGRATION RATE AND POPULATION SIZE ESTIMATION
  using Markov Chain Monte Carlo simulation
  =============================================
  compiled for a PARALLEL COMPUTER ARCHITECTURE
  Version 2.1.3
  Program started at   Mon Feb 13 11:33:14 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
filedb 1: 0x40186600 0
filedb 2: 0x81bc6d0 6


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
Pseudo-random number generator: Least Congruental Generator
Random number seed (with internal timer)           1139826799
Start parameters:
   Theta values were generated  from the FST-calculation
   M values were generated from the FST-calculation
Migration model:
   Migration matrix model with variable Theta
Mutation rate is constant
Analysis strategy is                          Maximum likelihood
Markov chain settings:
   Short chains (short-chains):                           10
      Trees sampled (short-inc*samples):              100000
      Trees recorded (short-sample):                    5000
   Long chains (long-chains):                              3
      Trees sampled (long-inc*samples):              1000000
      Trees recorded (long-sample):                    50000
   Static heating scheme
      4 chains with  temperatures
       1.00, 1.50, 3.00, 6.00
      Swapping interval is 1
   Number of discard trees per chain:                  10000
Print options:
   Data file:                                         infile
   Output file:                                      outfile
   Print data:                                            No
   Print genealogies:                                     No
   Plot data: No
   Profile likelihood: Yes, tables and summary
             Percentile method
             with df=1 and for Theta and M=m/mu



Summary of data:
---------------
Datatype:                                       Sequence data
Number of loci:                                             1

Population                                    Locus  Gene copies
----------------------------------------------------------------
  1 BALTIC                                       1     82
  2 WE                                           1     39
  3 WS                                           1     63
  4 YTH                                          1     39
  5 SEI                                          1     48
  6 EL                                           1     36
  7 KILK                                         1     43
  8 GI                                           1     44
  9 RdA                                          1     30
 10 GU                                           1     37
Total of all populations                         1    461



Locus 1  :

Empirical Base Frequencies
------------------------------------------------------------
Locus     Nucleotide                        Transition/
          ------------------------------  Transversion ratio
          A       C       G       T(U)
------------------------------------------------------------
   1      0.3180  0.1400  0.1608  0.3812       2.00000

11:33:19   Equilibrate tree (first 10000 trees are not used)
                                                                               

George Bosilca wrote:
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@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 users@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 users@open-mpi.org http://www.open-mpi.org/mailman/ 
listinfo.cgi/users
        
_______________________________________________ users mailing list  
users@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/users@open-mpi.orghttp://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list


    

"Half of what I say is meaningless; but I say it so that the other  
half may reach you"
                                   Kahlil Gibran


_______________________________________________
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-- 
*********************************************************************
* 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/