[Dock-fans] Segmentation fault on running docking

Francesco Pietra chiendarret at yahoo.com
Wed Nov 7 14:50:26 PST 2007


I have rebuilt the dock program as follows:

MPICH_HOME=/usr/local
export MPICH_HOME
cd install
(save copy config.h)
make distclean
./configure gnu parallel
make dock #


Then
cd test
make test 2>&1 | tee test7Nov.out


the out file (attached)


The last section of the out file (attached) shows that "mpirun" was looked for
in the wrong place if I correctly understand that it was looked for in
/usr/local/dock6/bin (actually it is in /usr/local/bin). Is it OK to copy
"mpirun" from /usr/local/bin to /usr/local/dock6/bin ?

Or rather adding

MPICH_HOME=/usr/local
export MPICH_HOME

to my .bashrc

(which only contains
MPI_HOME=/usr/local
export MPI_HOME)

Without doing anything than the above compilation and tests, 

mpirun -np 4 -i file.in -o file.out 2>&1 | errors.out

only runs to end for the protein without HOH residue. With the protein
embodying HOH, the problems set forth below (now attached error ..) arise.

Probably the docking for the HOH-containing protein should be rerun when mpi is
fixed, befor assuming that there are problems with the protein.

I am really sorry for presenting a much confused situation.

Thanks

francesco

Incidentally, I have carried out successfully test.parallel for Amber 9 (whose
parallel depends on OpenMPI, like DOCK).




--- Scott Brozell <sbrozell at scripps.edu> wrote:

> Hi,
> 
> On Wed, 7 Nov 2007, Francesco Pietra wrote:
> 
> > Having solved empirically, whitout external help, the problem (posted on
> last
> > week-end) of running grid when residue HOH is present within the pore, I am
> now
> 
> 
> Please post a reply to that thread with the problem resolution.
> 
> > faced by segfault in running rigid docking. That occurs both on parallel
> and
> > serial run. It also occurs with previous files for the protein without HOH,
> > where both rigid and flex run OK on mpirun -np 4. Thus, it seems that there
> is
> > now something wrong with dock6 and I don't understand what. 
> > 
> > Before these unsuccessful attempts, I had
> > (1) Unsuccessfully tried to recompile Antechamber with new respgen.c (on
> > Amber9), which did not affect previous compilation.
> > (2) Carried out "apt-get update" to Debian Linux amd64 etch (i.e., stable)
> > without taking notice of the little that was affected.
> > ---------------
> > 
> > While running:
> > 
> > mpirun -np 4 -i rigid.in -o rigid.out
> > 
> > the process halted (rigid_scored.mol2 0 bytes) because
> > 
> > Initialing MPI routines ....
> > [deb64:03540] *** Process received signal ***
> > [deb64:03540] Signal: Segmentation fault (11)
> > [deb64:03540] Signal code: Address not mapped (1)
> > [deb64:03540] Failing at address: 0x2b9ef5691000
> > dock6.mpi[3540]: segfault at 00002b9ef56910000 rip 0000000000447b1b rsp
> > 00007fff43c137b0 error 6
> > [deb64:03540] [0] /lib/libthread.so.0 [0x2b9e681bc410]
> > [deb64:03540] [1] dock6.mpi (_ZN60rient12match_ligandER7DOCKMol+0x40b)
> > [0x447b1b]
> > [deb64:03540] [2] dock6.mpi (main+0xaf5) [0x42cc75]
> > [deb64:03540] [3] dock6.mpi /lib/libc.so.6(__libc_start_main+0xda)
> > [0x2b9e682e14ca]
> > [deb64:03540] [4] dock6.mpi (__gxx_personality_v0+0xc2) [0x41b4ea]
> > [deb64:03540] *** End of error message ***
> > mpirun noticed that jpb rank 0 with PID 3537 on node deb64 exited on signal
> 15
> > (Terminated).
> > 3 additional processes aborted (not shown)
> > ---------------------------
> > 
> > I tried also flex with the protein endowed of HOH
> > 
> > mpirun -np 4 -i anchor_and_grow.in -o anchor_and_grow.out 2>&1 | tee
> errors.out
> > 
> > with an even more complex of libraries and mpi problems (see please
> attachment.
> > ------------------
> > 
> > Parallel dock had so far run correctly. DOCK6.1 had been compiled with:
> > 
> > ./configure gnu parallel
> > MPICH_HOME=/usr/local
> > export MPICH_HOME
> > make dock
> > 
> > I have now unsuccessfully deselected $AMBERHOME in my .bashrc, as expected
> > because it should be only relevant to running amber_score. I did not change
> > otherwise my .bashrc, where
> > 
> > DOCK_HOME=/usr/local/dock6
> > PATH=$PATH:$DOCK_HOME/bib; export DOCK_HOME PATH
> > MPI_HOME=/usr/local
> > export MPI_home
> > 
> > I have now tried the test
> > cd test/mpi
> > make 2>&1 | tee test_parallel.out
> > which passed OK.
> > 
> > Also:
> > which mpicxx
> > /usr/local/bin/mpicxx
> > 
> > Also:
> > updatedb
> > locate mpi.h
> > /usr/include/sc/util/group/memmtmpi.h
> > /usr/include/sc/util/group/messmpi.h
> > /usr/dock6/src/dock/base_mpi.h
> > /usr/local/include/mpi.h
> > /usr/local/openmpi-1.2.3/ompi/include/mpi.h
> > /usr/local/openmpi-1.2.3/ompi/include/mpi.h.in
> > /usr/local/openmpi-1.2.3/ompi/mpi/f77/prototypes_mpi.h
> > 
> > -----------------------
> > Also on serial trial, segfault:
> > 
> > dock6 -i rigid.in -o rigid out
> > 
> > dock6[3602]: segfault at 00002b4da6e0c000 rip 000000000043ffd1 rsp
> > 00007fff86593bc0 error 6
> > Segmentation fault
> > ---------------------------
> 
> It is curious that the dock mpi test is passing, but other dock runs
> are failing.  However, the failures suggest a machine problem.
> If you have updated the operating system then it is likely that
> executables will at least have to be re-linked and maybe re-compiled.
> If you are a miser then try re-linking.
> Otherwise rebuild dock:
> cd install
> # save any special config.h's
> make distclean
> ./configure ...
> make install
> # build parallel
> 
> Scott
> 
> 
> 


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