[Dock-fans] grid-convert segmentation fault

[Collignon, Barbara C.]

Hi Scott,

thanks a lot for your reply. 

I see...The error that you get should be related to the fact that DELPHI is compiled in 32 bit while DOCK6.2 is in 64 bit.

What I did:

On my laptop (32 bit platform), I compiled DOCK6.2 with gnu and I use the binary code of DELPHI for 32 bit.
Linux-5qvm : /home/barbara  > uname -a
Linux linux-5qvm 2.6.25.18-0.2-default #1 SMP 2008-10-21 16:30:26 +0200 i686 i686 i386 GNU/Linux

On the linux cluster (64 bit platform), it is working ONLY IF DOCK6.2 is compiled in 32 bit. DELPHI remains
in 32 bit.
bioinfo : /data1/bci/DOCK_desolv/DOCK_ace/RIGID/TEST_3.5  > uname -a
Linux bioinfo.lsd.ornl.gov 2.6.9-42.0.2.ELsmp #1 SMP Wed Aug 23 13:38:27 BST 2006 x86_64 x86_64 x86_64 GNU/Linux

Barbara 



-----Original Message-----
From: Scott Brozell [mailto:sbrozell at rci.rutgers.edu]
Sent: Tue 4/28/2009 9:29 PM
To: Collignon, Barbara C.
Cc: dock-fans at docking.org
Subject: Re: [Dock-fans] grid-convert segmentation fault
 
Hi,

Thanks for your input files.
Unfortunately, I cannot even get as far as you using DelPhi II on x86_64;
What delphi and platform are you using ?

Scott

% grid-convert -i gconv.in
...
Reading in grid box information.
Box center of mass                      :   41.483   33.072   48.120
Box dimensions                          :   34.187   37.462   37.293
Number of grid points per side [x y z]  :      115      126      126
Total number of grid points             :  1825740

Reading scoring grids.
 1339728  0.333333313 104 114 113  24.3895016  14.3409977  29.4734993
 maxgrid  2500000
do_us: off end of record
apparent state: unit 2 named rec+sph.phi
last format: list io
lately reading sequential unformatted external IO
Abort

% uname -a
Linux edu 2.6.18-92.1.22.el5 #1 SMP Tue Dec 16 11:57:43 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
$ ~/dock/help  delphi

  ___________________DelPhi II____________________
 /
 | A program to solve the PB equation             |
 | in 3D, using non-linear form, incorporating    |
 | 2 dielectric regions, ionic strength, periodic |
 | and focussing boundary conditions, utilizing   |
 | stripped optimum successive over-relaxation    |
 | and an improved algorithm for mapping the      |
 | Mol. Surface to the finite-Difference grid     |
 __________________          ____________________/
                     DelPhi II

  program started on Tue Apr 28 2009
              at 19:33:55
 parameter file fort.10 does not seem to     exist
 nonexistence or unexpected end of radius file
FORTRAN STOP

On Tue, Apr 21, 2009 at 07:53:19PM -0400, Collignon, Barbara C. wrote:
> 
> I did not find any solutions:
> 
> I still get:
> 
> Reading scoring grids.
>  1339728  0.333333313 104 114 113  24.3895016  14.3409977  29.4734993
>  maxgrid  2500000
> Writing general grid info to chem52.bmp
> Writing bump grid to chem52.bmp
> Writing Delphi grid info to chem52.phi
> Writing Delphi grid to chem52.phi
> Writing contact grid to chem52.cnt
> Segmentation fault
> 
> I sent you my input files, if you want to reproduce the bug...
> But maybe it is just a compilation problem.
> 
> I used to execute ./script_grid to build the pre-conputed grids
> 
> Barbara
> 
> 
> -----Original Message-----
> From: Scott Brozell [mailto:sbrozell at rci.rutgers.edu]
> Sent: Mon 4/20/2009 9:19 PM
> To: Collignon, Barbara C.
> Cc: dock-fans at docking.org
> Subject: Re: [Dock-fans] grid-convert segmentation fault
>  
> Hi,
> 
> On Fri, 17 Apr 2009, Collignon, Barbara C. wrote:
> 
> > I am using DOCK6.2, the compiled version for 32bit,
> > on both my laptop and our local Linux cluster.
> >
> > after generating the delphi grid, solvmap, chemgrids, contact
> > and energy grids, I do >grid-convert -i gconv.in
> >
> > At this point, I do not get errors anymore when reading the delphi grid.
> > Instead, I get a "segmentation fault", when writing the contact grid
> > to chem.cnt (from grid.cnt). (the same error on both my laptop and
> > our local Linux cluster)
> 
> Did you fix this issue ?
> What was the problem ?
> 
> thanks,
> Scott