[Dock-fans] Fwd: increasing maxpts

Francesco Pietra chiendarret at gmail.com
Tue May 12 10:17:43 PDT 2009


Running 'solvgrid' with increased maxpts 100,000,000, still "maximum
number of grid points exceeded"

Increasing maxpts to 1000,000,000, compilation error:

cd chemgrids && make install
make[3]: Entering directory `/usr/local/dock6/src/docktools/chemgrids'
gfortran -c -O2 -fno-automatic -fno-second-underscore -o chemgrid.o  chemgrid.f
gfortran -c -O2 -fno-automatic -fno-second-underscore -o dist.o  dist.f
gfortran -c -O2 -fno-automatic -fno-second-underscore -o ddist.o  ddist.f
gfortran -c -O2 -fno-automatic -fno-second-underscore -o dconst.o  dconst.f
gfortran -c -O2 -fno-automatic -fno-second-underscore -o grdout.o  grdout.f
gfortran -c -O2 -fno-automatic -fno-second-underscore -o parmrec.o  parmrec.f
gfortran -O2 -fno-automatic -fno-second-underscore chemgrid.o dist.o
ddist.o dconst.o grdout.o parmrec.o  -o chemgrid
chemgrid.o: In function `MAIN__':
chemgrid.f:(.text+0x106a): relocation truncated to fit: R_X86_64_32S
against symbol `cmap_' defined in COMMON section in chemgrid.o
ddist.o: In function `ddist_':
ddist.f:(.text+0x353): relocation truncated to fit: R_X86_64_32S
against symbol `cmap_' defined in COMMON section in chemgrid.o
ddist.f:(.text+0x4aa): relocation truncated to fit: R_X86_64_32S
against symbol `cmap_' defined in COMMON section in chemgrid.o
ddist.f:(.text+0x4b7): relocation truncated to fit: R_X86_64_32S
against symbol `cmap_' defined in COMMON section in chemgrid.o
dconst.o: In function `dconst_':
dconst.f:(.text+0x353): relocation truncated to fit: R_X86_64_32S
against symbol `cmap_' defined in COMMON section in chemgrid.o
dconst.f:(.text+0x4ae): relocation truncated to fit: R_X86_64_32S
against symbol `cmap_' defined in COMMON section in chemgrid.o
dconst.f:(.text+0x4bb): relocation truncated to fit: R_X86_64_32S
against symbol `cmap_' defined in COMMON section in chemgrid.o
grdout.o: In function `grdout_':
grdout.f:(.text+0x2ae): relocation truncated to fit: R_X86_64_32S
against symbol `cmap_' defined in COMMON section in chemgrid.o
parmrec.o: In function `find_':
parmrec.f:(.text+0x51): relocation truncated to fit: R_X86_64_32S
against symbol `link_' defined in COMMON section in parmrec.o
parmrec.f:(.text+0x6a): relocation truncated to fit: R_X86_64_32S
against symbol `link_' defined in COMMON section in parmrec.o
parmrec.f:(.text+0x7d): additional relocation overflows omitted from the output
collect2: ld returned 1 exit status
make[3]: *** [chemgrid] Error 1
make[3]: Leaving directory `/usr/local/dock6/src/docktools/chemgrids'
make[2]: *** [install] Error 2
make[2]: Leaving directory `/usr/local/dock6/src/docktools'
make[1]: *** [utils] Error 2
make[1]: Leaving directory `/usr/local/dock6/src'
make: *** [install] Error 2
francesco at tya64:/usr/local/dock6/install$

thanks
francesco


---------- Forwarded message ----------
From: Francesco Pietra <chiendarret at gmail.com>
Date: Tue, May 12, 2009 at 5:57 PM
Subject: Re: [Dock-fans] increasing maxpts
To: "John J. Irwin" <jji at cgl.ucsf.edu>


Hi John:

maxpts increased in the header chemgrid.h from 10,000,000 to 100,000,000

Recompiled and, from 'make test', chemgrid2.dockout.dif ends with

">Could not open0../solvgrid_generation/chem52.cmg for reading
chemgrids.  Program will terminate."

Is that because file solvgrid_generation/chem52.cmg does not exist
because it was not generated in advance, or is that a real failure
that needs to be fixed in order to deal with dock3.5 score?

thanks
francesco



On Tue, May 12, 2009 at 2:28 PM, John J. Irwin <jji at cgl.ucsf.edu> wrote:
> Hi Francesco
>
> grep -i maxpts *.h
> that is where you want to change maxpts.
> here you have just changed a do/continue label with no effect on maxpts
> and introduced a column alignment problem
>
> John
>
> Francesco Pietra wrote:
>> Hi:
>>
>> Because the "maximum number of grid points exceeded" in running
>> 'solvgrid' with dock6.2 debian linux amd64,  tried to increase
>> 'maxpts' from 80 to 160 (nothing else was changed) in
>> /src/docktolls/chemgrids/chemgrid.f, as follows:
>>
>> c
>> c  --initialize grid
>> c
>>       do 160 n=1, maxpts
>>         aval(n)=0.0
>>         bval(n)=0.0
>>         esval(n)=0.0
>>         bump(n)='F'
>>    160 continue
>> c
>>       if (estype .eq. 0) then
>>         call dconst(3, grdcut, grddiv, grdpts, esfact, offset)
>>       else
>>         call ddist(3, grdcut, grddiv, grdpts, esfact, offset)
>>       endif
>> c
>>       call grdout(grdfil, 3, npts, grddiv, grdpts, offset)
>> c
>>       close (2)
>>       end
>>
>>
>> =============
>>
>> >From make install 2>&1 | tee out:
>>
>> make[3]: Entering directory `/usr/local/dock6/src/docktools/chemgrids'
>> gfortran -c -O2 -fno-automatic -fno-second-underscore -o chemgrid.o  chemgrid.f
>> chemgrid.f:168.6:
>>
>>       end
>>      1
>> Error: END DO statement expected at (1)
>> Error: Unexpected end of file in 'chemgrid.f'
>> make[3]: *** [chemgrid.o] Error 1
>> make[3]: Leaving directory `/usr/local/dock6/src/docktools/chemgrids'
>> make[2]: *** [install] Error 2
>> make[2]: Leaving directory `/usr/local/dock6/src/docktools'
>> make[1]: *** [utils] Error 2
>> make[1]: Leaving directory `/usr/local/dock6/src'
>> make: *** [install] Error 2
>> ====
>>
>> >From the screen while compiling:
>>
>> gfortran -c -O2 -fno-automatic -fno-second-underscore -o chemgrid.o  chemgrid.f
>> chemgrid.f:168.6:
>>
>>       end
>>      1
>> Error: END DO statement expected at (1)
>> Error: Unexpected end of file in 'chemgrid.f'
>> make[3]: *** [chemgrid.o] Error 1
>> make[3]: Leaving directory `/usr/local/dock6/src/docktools/chemgrids'
>> make[2]: *** [install] Error 2
>> make[2]: Leaving directory `/usr/local/dock6/src/docktools'
>> make[1]: *** [utils] Error 2
>> make[1]: Leaving directory `/usr/local/dock6/src'
>> make: *** [install] Error 2
>> francesco at tya64:/usr/local/dock6/install$
>>
>> ===============
>>
>> Compilers:
>>
>> francesco at tya64:~$ gcc --version
>> gcc (Debian 4.3.2-1.1) 4.3.2
>> Copyright (C) 2008 Free Software Foundation, Inc.
>>
>> francesco at tya64:~$ gfortran --version
>> GNU Fortran (Debian 4.3.2-1.1) 4.3.2
>> Copyright (C) 2008 Free Software Foundation, Inc.
>>
>>
>> Mathlib acml 4.2.0
>> ================
>>
>>
>>
>> While i'll try to proceed with maxpts 80 by making the grid coarser, i
>> am interested in the correct editing of chemgrid.f, or if 160 exceeds
>>
>> francesco pietra
>> _______________________________________________
>> Dock-fans mailing list
>> Dock-fans at docking.org
>> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>>
>


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