[Dock-fans] Segmentation fault on docking and Prepare issues solved

Francesco Pietra chiendarret at yahoo.com
Sat Nov 10 13:29:44 PST 2007


The house is now fully in order.

The errors below at "errors_rig_HOH8Nov.out" were not from mpi, rather from
faulty input files, though for elusive reasons. With my pore protein and
150-atoms ligand, starting from previous "Prepare" and without any further
modification to the system, I carried out from scratch all other steps as from
Dock tutorials. As final step, the best pose from flex_docking was subjected to
amber re-scoring with "everything" option.

As to the alleged issue "4 vs 2 nodes involved", I have now noticed from "top
-i" that with heavy calculations, such as amber score everything, all four
nodes are involved (100% cpus, 0.3% memory out of the 4GB per node) as
requested by "mpirun -np 4 dock6.mpi". At later stages of the calculation, only
two nodes are active according to "top -i".

For less heavy calculations, such as amber score ligand, the change from 4 to 2
nodes involved is quite rapid. For light calculations, I was not rapid enough
to see 4 nodes involved. 2 nodes at the for "top -i" check.

Don't know if this is intrinsic to the dock programs or something resulting
from MPICK pointing to OpenMPI as in my system. At any event, all procedures
finished OK.

I remind the problems encountered in the "Prepare" step when a single residue
HOH is present in the pore (as determined by X-ray diffraction of O). Chimera's
DockPrep was unable to deal correctly with the protein pdb file. 

It was only using LEaP that the problem could be solved. First, on the
knowledge that Chimera's DockPrep deals better with prmtop and inpcrd rather
than pdb file from Amber, I prepared such prmtop and inpcrd with Amber9's LEaP
(leaprc.ff99SB and leaprc.gaff). Chimera accepted these files, while DockPrep
complained about incorrect valency for one H. In fact, the HOH residue showed a
bond between the two hydrogens. Curiously, the shape was correct for the water
molecule (H-O-H angle 104.5, H-H distance 1.51). Against all previous
experience, I prepared a pdb file from these prmtop/inpcrd with ambpdb. This
pdb showed the HOH correctly (with same geometry as above) and DockPrep
finished without any complain.

Having presented the facts (sorry for being unable to theorize about) I finish
with a question. Is any best promising route to follow now for carrying out
Amber9 MD with the complex protein-ligand and from that back to DOCK?

Thanks
francesco

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

> Hi,
> 
> On Thu, 8 Nov 2007, Francesco Pietra wrote:
> 
> > 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)
> 
> 
> Yes.   Your attached error was
> Processing test mpi
> /bin/mpirun -np 2 ../../../bin/dock6.mpi -i mpi.dockin -o mpi.dockmpiout
> make[3]: /bin/mpirun: Command not found
> 
> MPICH_HOME needs to be defined; this is the command used in the tests:
> $(MPICH_HOME)/bin/mpirun
> 
> 
> > 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.
> 
> 
> errors_rig_noHOH8Nov.out
> Initializing MPI Routines...
> Initializing MPI Routines...
> Initializing MPI Routines...
> Initializing MPI Routines...
> 
> is just four lines !  Where are the docking results ?
> 
> 
> errors_rig_HOH8Nov.out
> Initializing MPI Routines...
> Initializing MPI Routines...
> Initializing MPI Routines...
> Initializing MPI Routines...
> [deb64:20728] *** Process received signal ***
> [deb64:20728] Signal: Segmentation fault (11)
> [deb64:20728] Signal code: Address not mapped (1)
> [deb64:20728] Failing at address: 0x2acf65505000
> [deb64:20728] [ 0] /lib/libpthread.so.0 [0x2aced8030410]
> [deb64:20728] [ 1] dock6.mpi(_ZN6Orient12match_ligandER7DOCKMol+0x40b)
> [0x447b1b]
> [deb64:20728] [ 2] dock6.mpi(main+0xaf5) [0x42cc75]
> [deb64:20728] [ 3] /lib/libc.so.6(__libc_start_main+0xda) [0x2aced81554ca]
> [deb64:20728] [ 4] dock6.mpi(__gxx_personality_v0+0xc2) [0x41b4ea]
> 
> 
> This still looks like an mpi issue.
> Is it true that you have run sander.MPI successfully ?
> 
> 
> > 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.
> 
> 
> So there is only one water molecule difference, but the sphere file size
> increases by a factor of 5 and the grid by a factor of 2 ?
> Something is fishy here.  What does visualization of the sphere files show ?
> 
> test8NovC.out  shows possible failures:
> # Select spheres within 10 Ang of ligand
> ../../../bin/sphere_selector struct.sph lig.mol2 3.0
> ../dockdif -t 3 selected_spheres.sph.save selected_spheres.sph
> diffing selected_spheres.sph.save with selected_spheres.sph
> possible FAILURE:  check selected_spheres.sph.dif
> ==============================================================
> # Convert selected spheres into pdb format for viewing
> ../../../bin/showsphere < select.in > /dev/null
> ../dockdif selected_cluster.pdb.save selected_cluster.pdb
> diffing selected_cluster.pdb.save with selected_cluster.pdb
> possible FAILURE:  check selected_cluster.pdb.dif
> ==============================================================
> ...
> Processing test mpi
> /usr/local/bin/mpirun -np 2 ../../../bin/dock6.mpi -i mpi.dockin -o
> mpi.dockmpiout
> Initializing MPI Routines...
> Initializing MPI Routines...
> ../dockdif -t 8 mpi.dockmpiout.save mpi.dockmpiout
> diffing mpi.dockmpiout.save with mpi.dockmpiout
> possible FAILURE:  check mpi.dockmpiout.dif
> 
> 
> What are these dif's ?
> (Please if the files are small then just cut and paste the contents into
> the email rather than attaching them.)
> 
> 
> > I wonder whether a grid.nrg of 149MB may pose problems to the docking
> > procedure, resulting in the errors described below.
> 
> 
> Perhaps, but the behavior as far as I can tell indicates a failure
> before reading of the grid.
> 
> 
> Scott
> 
> On Wed, 7 Nov 2007, Francesco Pietra wrote:
> 
> > 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 #
> > 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.
> > 
> > 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
> > > 
> 
> 
> 
> 
> 


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