[Dock-fans] DOCK3.5 score "aborted core"

Scott Brozell sbrozell at scripps.edu
Tue Sep 18 08:33:50 PDT 2007


Hi,

Your test is still failing before it gets to dock:
make[3]: Entering directory `/home/andre/dock6/install/test/solvgrid_generation'
# generate DelPhi grid to be used by dock6
../../../bin/make_phimap  1> delphi.out
make[3]: *** [delphi_grid_generation] Error 1

You should examine
/home/andre/dock6/install/test/solvgrid_generation/delphi.out
If you run the tests this way
cd install;make test
then the differences will be automatically emitted.
Otherwise enter this
make check


However, I believe that this patch will fix your initial issue:

********>Bugfix 5:
Author:  Scott Brozell
Date:  September 17, 2007

Program:  dock6

Description:  DOCK3.5 score frees some memory twice during program exit.
This has been innocuous, but recent, probably 2.5 and later, GNU C
libraries detect the error and abort.  Here is the start of the error:
*** glibc detected *** ./dock6: double free or corruption (!prev):

Fix:  make the following changes to the file src/dock/score_chemgrid.cpp
-------------------------------------------------------------------------
*** src/dock/score_chemgrid.cpp	15 Dec 2006 01:34:41 -0000	1.22.2.2
--- src/dock/score_chemgrid.cpp	17 Sep 2007 20:22:51 -0000
***************
*** 268,276 ****

      phi = NULL;

-     vdwA = NULL;
-     vdwB = NULL;
-
  }
  /************************************************/
  Chemgrid_Score::~Chemgrid_Score()
--- 268,273 ----
***************
*** 285,293 ****

      delete[]phi;

-     delete[]vdwA;
-     delete[]vdwB;
-
  }
  /************************************************/
  void
--- 282,287 ----
--------------------------------------------------------------------------
Workaround:  ignore the error termination.


On Fri, 14 Sep 2007, Andre wrote:

> I defined the path. Hope the attached files are sufficient, apologies
> for the mistake.
>
> On 9/14/07, Scott Brozell <sbrozell at scripps.edu> wrote:
> >
> > The chemgrid tests were not run:
> >
> > cd chemgrid_generation && make test
> > make[2]: Entering directory `/home/andre/dock6/install/test/chemgrid_generation'
> >
> > The DelPhi executable does not exist.
> >     Skipping this test.
> >
> >
> > Please define the environment variable
> > DELPHI_PATH to the full path of DelPhi.
> > And rerun the tests:
> > cd install;make test
> >
> > Scott
> >
> > On Fri, 14 Sep 2007, Andre wrote:
> >
> > > Hi Scott
> > >
> > > Attached is the make.out file after running the test.
> > > Failures in grid generation include:
> > >             Type:                                     Output file attached
> > > 1) nchemgrid_GB_grid_generation: OUTCHEM.dif (known failure i think)
> > > 2) Processing test bump1:             bump1.dockout.dif
> > > 3) Processing test grid2:                grid2.dockout.dif
> > > 4) Calculating GB grid for Zou GB/SA: OUTCHEM.dif
> > >
> > > Please let me know if you need anything else.
> > > Thank you very much for helping
> > >
> > > On 9/14/07, Scott Brozell <sbrozell at scripps.edu> wrote:
> > > >
> > > > What version of DOCK did you use ?
> > > > What were the results from the install/test/chemgrid_generation
> > > > and install/test/chemgrid_score tests ?
> > > >
> > > > thanks,
> > > > Scott
> > > >
> > > > On Wed, 12 Sep 2007, BA S wrote:
> > > >
> > > > > I am having trouble docking a ligand utilizing DOCK3.5 scoring. I get
> > > > > the following error.
> > > > >
> > > > > Initializing Library File Routines...
> > > > > Initializing Orienting Routines...
> > > > > Initializing Bump Filter Routines...
> > > > >  Reading the bump grid from chem52.bmp
> > > > > Initializing Dock3.5 Score Routines...
> > > > >  Reading chemgrids from chem52.cmg
> > > > >  Reading DelPhi grid from chem52.phi
> > > > >
> > > > > -----------------------------------
> > > > > Elapsed time for docking:      217 seconds
> > > > >
> > > > >  Anchors:               1
> > > > >  Orientations:          1000
> > > > >  Conformations:         1000
> > > > >
> > > > >  Energy Score:        -6696.385742
> > > > >           vdw:        -6696.385742
> > > > >            es:            0.000000
> > > > >
> > > > > 1 Molecules Processed
> > > > > Total elapsed time:     217 seconds
> > > > > *** glibc detected *** ./dock6: double free or corruption (!prev):
> > > > > 0x08182080 ***
> > > > > ======= Backtrace: =========
> > > > > /lib/tls/i686/cmov/libc.so.6[0xb7d947cd]
> > > > > /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7d97e30]
> > > > > /usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb7f56d11]
> > > > > /usr/lib/libstdc++.so.6(_ZdaPv+0x1d)[0xb7f56d6d]
> > > > > ./dock6[0x805776f]
> > > > > ./dock6[0x80b7b61]
> > > > > ./dock6[0x80661ae]
> > > > > /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xdc)[0xb7d42ebc]
> > > > > ./dock6(__gxx_personality_v0+0x14d)[0x804b651]
> > > > > ======= Memory map: ========
> > > > > 08048000-080f9000 r-xp 00000000 08:11 3671101    /home/andre/dock6/bin/dock6
> > > > > 080f9000-080fa000 rw-p 000b0000 08:11 3671101    /home/andre/dock6/bin/dock6
> > > > > 080fa000-082e2000 rw-p 080fa000 00:00 0          [heap]
> > > > > b45ad000-b46ae000 rw-p b45ad000 00:00 0
> > > > > b6100000-b6121000 rw-p b6100000 00:00 0
> > > > > b6121000-b6200000 ---p b6121000 00:00 0
> > > > > b62f9000-b7d2d000 rw-p b62f9000 00:00 0
> > > > > b7d2d000-b7e68000 r-xp 00000000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> > > > > b7e68000-b7e69000 r--p 0013b000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> > > > > b7e69000-b7e6b000 rw-p 0013c000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> > > > > b7e6b000-b7e6e000 rw-p b7e6b000 00:00 0
> > > > > b7e6e000-b7e79000 r-xp 00000000 08:11 1933376    /lib/libgcc_s.so.1
> > > > > b7e79000-b7e7a000 rw-p 0000a000 08:11 1933376    /lib/libgcc_s.so.1
> > > > > b7e7a000-b7e9f000 r-xp 00000000 08:11 1936620    /lib/tls/i686/cmov/libm-2.5.so
> > > > > b7e9f000-b7ea1000 rw-p 00024000 08:11 1936620    /lib/tls/i686/cmov/libm-2.5.so
> > > > > b7ea1000-b7ea2000 rw-p b7ea1000 00:00 0
> > > > > b7ea2000-b7f81000 r-xp 00000000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> > > > > b7f81000-b7f84000 r--p 000de000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> > > > > b7f84000-b7f86000 rw-p 000e1000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> > > > > b7f86000-b7f8c000 rw-p b7f86000 00:00 0
> > > > > b7f8c000-b7f9f000 r-xp 00000000 08:11 1936638
> > > > > /lib/tls/i686/cmov/libpthread-2.5.so
> > > > > b7f9f000-b7fa1000 rw-p 00013000 08:11 1936638
> > > > > /lib/tls/i686/cmov/libpthread-2.5.so
> > > > > b7fa1000-b7fa3000 rw-p b7fa1000 00:00 0
> > > > > b7fae000-b7fb1000 rw-p b7fae000 00:00 0
> > > > > b7fb1000-b7fca000 r-xp 00000000 08:11 1933333    /lib/ld-2.5.so
> > > > > b7fca000-b7fcc000 rw-p 00019000 08:11 1933333    /lib/ld-2.5.so
> > > > > bf8f2000-bf907000 rw-p bf8f2000 00:00 0          [stack]
> > > > > ffffe000-fffff000 r-xp 00000000 00:00 0          [vdso]
> > > > > Aborted (core dumped)
> > > > > andre at andre-desktop:~/dock6/bin$ ./dock6 -i dock3_5_score.in >& dock.out
> > > > > *** glibc detected *** ./dock6: double free or corruption (!prev):
> > > > > 0x08182080 ***
> > > > > ======= Backtrace: =========
> > > > > /lib/tls/i686/cmov/libc.so.6[0xb7d4c7cd]
> > > > > /lib/tls/i686/cmov/libc.so.6(cfree+0x90)[0xb7d4fe30]
> > > > > /usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0xb7f0ed11]
> > > > > /usr/lib/libstdc++.so.6(_ZdaPv+0x1d)[0xb7f0ed6d]
> > > > > ./dock6[0x805776f]
> > > > > ./dock6[0x80b7b61]
> > > > > ./dock6[0x80661ae]
> > > > > /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xdc)[0xb7cfaebc]
> > > > > ./dock6(__gxx_personality_v0+0x14d)[0x804b651]
> > > > > ======= Memory map: ========
> > > > > 08048000-080f9000 r-xp 00000000 08:11 3671101    /home/andre/dock6/bin/dock6
> > > > > 080f9000-080fa000 rw-p 000b0000 08:11 3671101    /home/andre/dock6/bin/dock6
> > > > > 080fa000-082e2000 rw-p 080fa000 00:00 0          [heap]
> > > > > b4565000-b4666000 rw-p b4565000 00:00 0
> > > > > b6100000-b6121000 rw-p b6100000 00:00 0
> > > > > b6121000-b6200000 ---p b6121000 00:00 0
> > > > > b62b1000-b7ce5000 rw-p b62b1000 00:00 0
> > > > > b7ce5000-b7e20000 r-xp 00000000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> > > > > b7e20000-b7e21000 r--p 0013b000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> > > > > b7e21000-b7e23000 rw-p 0013c000 08:11 1936612    /lib/tls/i686/cmov/libc-2.5.so
> > > > > b7e23000-b7e26000 rw-p b7e23000 00:00 0
> > > > > b7e26000-b7e31000 r-xp 00000000 08:11 1933376    /lib/libgcc_s.so.1
> > > > > b7e31000-b7e32000 rw-p 0000a000 08:11 1933376    /lib/libgcc_s.so.1
> > > > > b7e32000-b7e57000 r-xp 00000000 08:11 1936620    /lib/tls/i686/cmov/libm-2.5.so
> > > > > b7e57000-b7e59000 rw-p 00024000 08:11 1936620    /lib/tls/i686/cmov/libm-2.5.so
> > > > > b7e59000-b7e5a000 rw-p b7e59000 00:00 0
> > > > > b7e5a000-b7f39000 r-xp 00000000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> > > > > b7f39000-b7f3c000 r--p 000de000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> > > > > b7f3c000-b7f3e000 rw-p 000e1000 08:11 9433       /usr/lib/libstdc++.so.6.0.8
> > > > > b7f3e000-b7f44000 rw-p b7f3e000 00:00 0
> > > > > b7f44000-b7f57000 r-xp 00000000 08:11 1936638
> > > > > /lib/tls/i686/cmov/libpthread-2.5.so
> > > > > b7f57000-b7f59000 rw-p 00013000 08:11 1936638
> > > > > /lib/tls/i686/cmov/libpthread-2.5.so
> > > > > b7f59000-b7f5b000 rw-p b7f59000 00:00 0
> > > > > b7f66000-b7f69000 rw-p b7f66000 00:00 0
> > > > > b7f69000-b7f82000 r-xp 00000000 08:11 1933333    /lib/ld-2.5.so
> > > > > b7f82000-b7f84000 rw-p 00019000 08:11 1933333    /lib/ld-2.5.so
> > > > > bfcce000-bfce3000 rw-p bfcce000 00:00 0          [stack]
> > > > > ffffe000-fffff000 r-xp 00000000 00:00 0          [vdso]
> > > > > Aborted (core dumped)
> > > > >
> > > > >
> > > > >
> > > > > I am using an Intel 6600 quad core with Ubuntu linux 7.04 (32bit
> > > > > version fully updated). Is it perhaps a CPU specific or Linux
> > > > > distribution specific problem?
> > > > >
> > > > > Attached is my INCHEM file for CHEMGRID generation, gconvert.in file
> > > > > to to convert the chemgrids and the dock.in file (dock3_5_score.in).
> > > > > The "sa0_solv.pdb" receptor used was created in Chimera using the "del
> > > > > HC" command. The rec+sph.crg file used to generate the electrostatics
> > > > > grid with Delphi was made by combining the selected_spheres.pdb and
> > > > > sa0_solv.pdb and saving it as rec+sph.pdb and then renaming it (is
> > > > > this correct).
> > > > >


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