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 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/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
_______________________________________________
users mailing list
users@open-mpi.orghttp://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/
