[gmx-users] grompp -debug gives MPI_INIT errors (but seems to run without -debug flag)

[Sabuj Pattanayek]

Hi,

I was having mdrun crashes so I decided to get more output from the 
grompp setup phase using the "-debug" flag. Whenever I run grompp with 
this flag I get the following errors (I tried the following with and 
without initiating lamboot):

grompp -debug -f em.mdp -c system_gro_b4em.gro -p system_gro.top -o 
system_gro_em.tpr

:-)  G  R  O  M  A  C  S  (-:
Gnomes, ROck Monsters And Chili Sauce
:-)  VERSION 3.2.1  (-:

-----------------------------------------------------------------------------
It seems that at least one rank invoked some MPI function before
invoking MPI_INIT.  The only information that I can give is that it
was PID 20844 on host localhost.
-----------------------------------------------------------------------------

..ok so I tried:

mpiexec grompp -debug -f em.mdp -c system_gro_b4em.gro -p system_gro.top 
-o system_gro_em.tpr

-----------------------------------------------------------------------------
It seems that at least one rank invoked some MPI function before
invoking MPI_INIT.  The only information that I can give is that it
was PID 20848 on host localhost.
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n0).

mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------

...ok so now I tried:

lamexec grompp -debug -f em.mdp -c system_gro_b4em.gro -p system_gro.top 
-o system_gro_em.tpr
lamexec (locate_aschema): grompp: No such file or directory

which grompp
/usr/bin/grompp
lamexec /usr/bin/grompp -debug -f em.mdp -c system_gro_b4em.gro -p 
system_gro.top -o system_gro_em.tpr
lamexec: cannot parse: Exec format error

lamexec "/usr/bin/grompp -debug -f em.mdp -c system_gro_b4em.gro -p 
system_gro.top -o system_gro_em.tpr"
lamexec (locate_aschema): /usr/bin/grompp -debug -f em.mdp -c 
system_gro_b4em.gro -p system_gro.top -o system_gro_em.tpr: No such file 
or directory

This problem seems to have been posted before but no resolution was given:
http://www.gromacs.org/pipermail/gmx-users/2004-April/010060.html
http://www.gromacs.org/pipermail/gmx-developers/2002-September/000321.html

The strange thing is that grompp works without the -debug flag. Both 
lam-mpi and gromacs were compiled with MPI use flags on a gentoo linux 
system:

[ebuild   R   ] sys-cluster/lam-mpi-7.0.6  +crypt 0 kB
[ebuild   R   ] sci-chemistry/gromacs-3.2.1  +mpi +xml2 0 kB

Any help would be greatly appreciated.
Thanks,
Sabuj Pattanayek