ADL: Using AutoDock with more than the default number of points for dimension?

D.BIO- Gerard Pujadas gerard.pujadas at urv.net
Tue Feb 22 07:05:24 PST 2005


Dear Michael,

first of all, thanks for your kind message. I use a PC with Mandrake Linux 9.0

>I have recompiled Autodock (3.05) with MAX_GRID_PTS 256 on several
>Linux distributions and haven't met this problem yet. You say it's
>ligand-dependent: have you tracked this dependence? What type of
>system do you have?

I have contacted a Unix guru in my University in 
order to use gdb and search where AutoDock hangs.

Here is all the information about the things I have done:

1) I have used the /src/autodock folder that is 
obtained after untaring the 
dist305.20011213.tar.gz

2) I have adapted the Makefile to be used in a Linux machine

3) I have modified the line starting with 
"#define MAX_GRID_PTS 128" in the 
/src/autodock/autocomm.h file to "#define 
MAX_GRID_PTS 306"

4) $ make clean

5) $ make

6) $ gdb ../autodock3

===========================================================================

RUNNING GDB:

GNU gdb 5.3-22mdk (Mandrake Linux)
Copyright 2002 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "i586-mandrake-linux-gnu"...
(gdb) run -p 1e8w.dpf -l 1e8w.dlg
Starting program: 
/home/programes/executables/AutoDock/dist305/src/autodock/autodock3 
-p 1e8w.dpf -l 1e8w.dlg

Program received signal SIGSEGV, Segmentation fault.
0x4015a04b in _IO_vfscanf () from /lib/i686/libc.so.6
Current language:  auto; currently c

===========================================================================

AFTER :

(gdb) where
#0  0x4015a04b in _IO_vfscanf () from /lib/i686/libc.so.6
#1  0xbf22ddb0 in ?? ()
#2  0x40164b15 in vsscanf () from /lib/i686/libc.so.6
#3  0x4016100d in sscanf () from /lib/i686/libc.so.6
#4  0x08054a33 in readmap(char*, int*, int*, 
float*, char*, char*, int*, int*, long, char*, 
char*, float[8][306] (*) [306], float*, float*, 
float*, tms, char) (P_B_HaveMap=0x3fd76000 
<Address 0x3fd76000 out of bounds>,
     P_Imap=0xbf22eb50, P_NumAtmMaps=0x3fd76000, P_ExtSpacing=0x3fd76000,
     AtmTypStr=0x3fd76000 <Address 0x3fd76000 out 
of bounds>, ExtFldFileName=0xbffbf460 
"1e8w.maps.fld",
     ExtGridPts1=0xbfba5810, ExtGridPts=0xbfba5800, jobStart=6039561,
     line=0xbffbf060 "map 1e8w.A.map", ' ' 
<repeats 23 times>, 
ExtMacromolFileName=0xbffbf1e0 "1e8w.pdbqs",
     map=0x927afe0, MapCenter=0xbffb0640, 
MapMax=0xbffa98a0, MapMin=0xbffa9880, tmsJobStart=
       {tms_utime = 1, tms_stime = 0, tms_cutime = 
0, tms_cstime = 0}, B_charMap=0 '\0') at 
readmap.cc:226
#5  0x08049a23 in main (argc=5, argv=0xbffff6d4, 
envp=0xbffff6ec) at main.cc:573
#6  0x401157f7 in __libc_start_main () from /lib/i686/libc.so.6

===========================================================================

AFTER (list):

(gdb) l
573             readmap( &B_havemap, &imap, &num_atm_maps, &spacing,
574                 atm_typ_str, FN_gdfld, gridpts1, gridpts,
575                 jobStart, line, FN_receptor, map, map_center,
576                 mapmax, mapmin, tms_jobStart, B_charMap );
577             (void) fflush(logFile);
578             break;
579 
//______________________________________________________________________________
580
581         case DPF_MOVE:
582             /*

Our machine has the following memory 
characteristics (top command output) when one of 
the jobs that ends with a "Segmentation fault" 
message is running (a job that uses a grid with 
306 points in each dimension and a separation 
point of 0.1 Å):

top - 14:45:59 up 16:54,  5 users,  load average: 
0.26, 0.15, 0.06Tasks:  74 total,   2 running, 
72 sleeping,   0 stopped,   0 zombie
Cpu(s):  87.7% user,  10.3% system,   0.0% nice,   2.0% idle
Mem:   1031756k total,   586348k used,   445408k free,    70472k buffers
Swap:   811240k total,    28728k used,   782512k free,   124288k cached

   PID USER      PR  NI  VIRT  RES  SHR S %CPU 
%MEM    TIME+ 
Command                                                                 
16370 programe  17   0  360m 360m  952 R 97.3 
35.8   0:12.13 
autodock3                                                               
16371 gerard    10   0   972  972  772 R  0.3 
0.1   0:00.05 
top                                                                     
     1 root       9   0    88   56   52 S  0.0 
0.0   0:04.56 
init                                                                    
     2 root       8   0     0    0    0 S  0.0 
0.0   0:00.00 
keventd                                                                 
     3 root       9   0     0    0    0 S  0.0 
0.0   0:00.09 
kapmd                                                                   
     4 root      18  19     0    0    0 S  0.0  0.0   0:00.00 ksoftirqd_CPU0
     5 root       9   0     0    0    0 S  0.0 
0.0   0:02.22 
kswapd                                                                  


I have also the following line in our /etc/bashrc file:

ulimit -s unlimited

It seems that changing #define MAX_GRID_PTS 128" 
in the /src/autodock/autocomm.h file affects the 
program. Perphaps I need to change something more 
before compilation?

What is also very strange is that the same 
problem reproduces in a computer of the 
Supercomputation Center where I have an account. 
At first, they change "#define MAX_GRID_PTS 126" 
by "#define MAX_GRID_PTS 256" and it worked but 
now it doesn't work and they have a Segmentation 
fault problem.

Gerard

-- 
======================== NOTE: NEW ADDRESS AND E-MAIL ========================
Dr. Gerard Pujadas
Grup de recerca en "Vi i Salut"
Dept. Bioquímica i Biotecnologia           room 106
Campus de Sant Pere Sescelades		   e-mail: gerard.pujadas at urv.net
Univ. Rovira i Virgili                     phone: 34-977 559565
C/ Marcel·lí Domingo                       fax: 34-977 559597
43007 Tarragona (CATALONIA)
State: Spain (European Union)
===========================================================================





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