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

Francesco Pietra chiendarret at yahoo.com
Thu Nov 8 08:42:40 PST 2007


I forgot to mention that for both the naked protein and the protein embodying a
single HOH residue, I went on with all the spheres generated by sphgen_cpp. The
array of spheres generated for the HOH-containing protein (seen from
"showsphere < sphgen_cpp_cluster.in as pdb file, 74 KB) is huge and dense,
encompassing the whole protein. This results in  a grid.nrg of 149 MB.

For unclear reasons (because I operated the same way), the array of spheres is
not so dense for the naked protein, resulting in sphgen_cpp_cluster1.pdb 15KB
and grid.nrg 80MB.

I wonder whether a grid.nrg of 149MB may pose problems to the docking
procedure, resulting in the errors described below.

Thanks
francesco


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

> Date: Thu, 8 Nov 2007 01:09:08 -0800 (PST)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Fwd: Re: [Dock-fans] Segmentation fault on running docking
> To: Scott Brozell <sbrozell at scripps.edu>
> CC: dock-fans <dock-fans at docking.org>
> 
> 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
> > > 
> > > 
> > > 
> > 
> > 
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam protection around 
> > http://mail.yahoo.com 
> 
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com 
> 
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com 


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test7Nov.out.tar.bz2
Type: application/x-bzip
Size: 3385 bytes
Desc: pat250645930
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071108/d742b708/attachment-0005.bin 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: errors_rig_HOH.out.tar.bz2
Type: application/x-bzip
Size: 600 bytes
Desc: pat740259797
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071108/d742b708/attachment-0006.bin 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: test8NovC.out.tar.bz2
Type: application/x-bzip
Size: 3422 bytes
Desc: pat2094446940
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071108/d742b708/attachment-0007.bin 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: errors_rig_noHOH8Nov.out.tar.bz2
Type: application/x-bzip
Size: 191 bytes
Desc: pat1456698440
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071108/d742b708/attachment-0008.bin 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: errors_rig_HOH.out.tar.bz2
Type: application/x-bzip
Size: 600 bytes
Desc: pat1426967275
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20071108/d742b708/attachment-0009.bin 


More information about the Dock-fans mailing list