MPI problem/Configuring PETSc
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Sachin Pandey
Jan 19, 2012, 4:22:39 PM1/19/12
to pflotran-users
Hello,
I am having problems running PFLOTRAN examples. Following the wiki
instructions (MPI, HDF5, BLAS/LAPACK not previously installed):
./configure --download-mpich=yes --download-hdf5=yes --download-f-
blas-lapack=yes
After making pflotran, running an example (from 1D_Tracer directory):
mpirun -np 2 pflotran
does not work (command mpirun/mpiexec is not found). So I installed
MPICH2 first (example MPI problem runs smoothly) and used PETSc
configuration:
./configure --with-mpi-dir=/home/pandeys/Local/mpich2/mpich2-install/
lib --download-hdf5=yes --download-f-blas-lapack=yes
This works (PETSc make test successful), but running the pflotran
example returns:
HYDU_create_process (/home/pandeys/Local/mpich2/mpich2-1.3.1/src/pm/
hydra/utils/launch/launch.c:69): execvp error on file pflotran (No
such file or directory)
Here is some basic system info...I am using bash:
Linux efml 2.6.38-13-generic-pae #53-Ubuntu SMP Mon Nov 28 19:41:58
UTC 2011 i686 i686 i386 GNU/Linux
PETSC_DIR = /home/pandeys/Local/petsc/petsc-dev
PETSC_ARCH = darwin-gnu-cxx-debug
g++ --version
g++ (Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
Thanks,
-Sachin
I am having problems running PFLOTRAN examples. Following the wiki
instructions (MPI, HDF5, BLAS/LAPACK not previously installed):
./configure --download-mpich=yes --download-hdf5=yes --download-f-
blas-lapack=yes
After making pflotran, running an example (from 1D_Tracer directory):
mpirun -np 2 pflotran
does not work (command mpirun/mpiexec is not found). So I installed
MPICH2 first (example MPI problem runs smoothly) and used PETSc
configuration:
./configure --with-mpi-dir=/home/pandeys/Local/mpich2/mpich2-install/
lib --download-hdf5=yes --download-f-blas-lapack=yes
This works (PETSc make test successful), but running the pflotran
example returns:
HYDU_create_process (/home/pandeys/Local/mpich2/mpich2-1.3.1/src/pm/
hydra/utils/launch/launch.c:69): execvp error on file pflotran (No
such file or directory)
Here is some basic system info...I am using bash:
Linux efml 2.6.38-13-generic-pae #53-Ubuntu SMP Mon Nov 28 19:41:58
UTC 2011 i686 i686 i386 GNU/Linux
PETSC_DIR = /home/pandeys/Local/petsc/petsc-dev
PETSC_ARCH = darwin-gnu-cxx-debug
g++ --version
g++ (Ubuntu/Linaro 4.5.2-8ubuntu4) 4.5.2
Thanks,
-Sachin
Hammond, Glenn
Jan 19, 2012, 4:44:41 PM1/19/12
to pflotra...@googlegroups.com
Go to the pflotran/src/pflotran directory and type:
./pflotran
And tell me what you get.
Glenn
Sachin Pandey
Jan 19, 2012, 5:56:12 PM1/19/12
to pflotran-users
Sachin Pandey
Jan 20, 2012, 12:54:11 PM1/20/12
to pflotran-users
I physically put the input file into /pflotran/src/pflotran and it
worked. I guess that was my mistake!
worked. I guess that was my mistake!
Lichtner, Peter C
Jan 20, 2012, 1:03:35 PM1/20/12
to <pflotran-users@googlegroups.com>
Alternative give the path to pflotran in mpirun:
mpirun -np xxxx .../pflotran/src/pflotran/pflotran
Replace ... with your configuration.
...Peter
<><><><><><><><><><><><><><><><><><><><><>
Peter C. Lichtner (lich...@lanl.gov)
LANL EES-16: MS D469
(505) 667-3420 (o), 665-3285 (fax), 795-2881 (cell)
Los Alamos National Laboratory
SM-30 Bikini Atoll Road
Los Alamos, NM 87545
<><><><><><><><><><><><><><><><><><><><><>
Hammond, Glenn
Jan 20, 2012, 5:42:14 PM1/20/12
to pflotra...@googlegroups.com
OK. This indicates that pflotran is compiled fine. The problem is with the mpich libs. I would suggest re-configuring petsc with --download-mpich=yes and then place link to mpirun in your path. My the way, how are running pflotran?
mpirun -n # pflotran
? I would also recommend compiling with --c-language=c and not c++. I see g++ below and that leads me to believe that you are compiling with c++. It should still run, but since most pflotran uses use gcc, it is difficult to help with errors.
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