[Dock-fans] Fwd: Re: Segmentation fault on running docking

Francesco Pietra chiendarret at yahoo.com
Thu Nov 8 01:09:08 PST 2007


On the below re-installation of dock, I added to my .bashrc

MPICH_HOME=/usr/local
export MPICH_HOME

and make a copy of 'mpirun' from /usr/local/bin to /usr/local/dock6/bin

The test did no more complain about mpirun (attached test8NovC.out)

Rigid docking with the protein deprived of HOH run correctly (attached
errors_rig_noHOH8Nov.out). However, top -i showed only two nodes involved. A
test.parallel with Amber9 showed all four nodes involved with sander.

Under these conditions, rigid docking with the protein containing HOH failed
(attached errors_rig_HOH8Nov.out) because of segmentation fault.

Thanks
francesco


--- Francesco Pietra <chiendarret at yahoo.com> wrote:

> Date: Wed, 7 Nov 2007 14:50:26 -0800 (PST)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Re: [Dock-fans] Segmentation fault on running docking
> To: Scott Brozell <sbrozell at scripps.edu>
> CC: dock-fans <dock-fans at docking.org>
> 
> 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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