ADL: Autodock MSVC

Jack Shultz js at drugdiscoveryathome.com
Tue Jun 30 09:31:52 PDT 2009


It looks like GetProcessTimes Function
http://msdn.microsoft.com/en-us/library/ms683223(VS.85).aspx

Is analogous but I don't know exactly how to implement it yet.

On Tue, Jun 30, 2009 at 12:25 PM, Jack Shultz<js at drugdiscoveryathome.com> wrote:
> as i see it looks like autodock depends on this struct found in the
> times.h header
>
>
> /*  Get Process Times, P1003.1b-1993, p. 92 */
> struct tms {
>        clock_t tms_utime;              /* user time */
>        clock_t tms_stime;              /* system time */
>        clock_t tms_cutime;             /* user time, children */
>        clock_t tms_cstime;             /* system time, children */
> };
>
> I ran a sed command to comment out all preprocessing references to times.h
>
> $ make
> make  all-am
> make[1]: Entering directory `/home/jshultz/autodocksuite-4.2.1/src/autodock-v1'
> g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\"
> -DPACKAGE_VERSION=\"4.2.1\" -DPACKAGE_STRING=\"autodock\ 4.2.1\"
> -DPACKAGE_BUGREPORT=\"autodock at scripps.edu\" -DPACKAGE=\"autodock\"
> -DVERSION=\"4.2.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1
> -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_POW=1 -DHAVE_SQRT=1
> -DHAVE_STRNCASECMP=1 -I.  -DNOSQRT -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE
> -I./../acro/include   -Wall -O3   -MT clmode.o -MD -MP -MF
> .deps/clmode.Tpo -c -o clmode.o clmode.cc
> clmode.cc: In function `void clmode(int, Real, char*, clock_t, tms,
> Boole, char*, Real (*)[3], Real*, Boole, char*)':
> clmode.cc:56: error: `tms_jobStart' has incomplete type
> timesyshms.h:38: error: forward declaration of `struct tms'
> clmode.cc: In function `void clmode(int, Real, char*, clock_t, tms,
> Boole, char*, Real (*)[3], Real*, Boole, char*)':
> clmode.cc:103: error: invalid use of undefined type `struct tms'
> timesyshms.h:38: error: forward declaration of `struct tms'
> clmode.cc:103: error:   initializing argument 5 of `int
> openFile(char*, char*, FILE**, clock_t, tms, Boole)'
> clmode.cc:318: error: invalid use of undefined type `struct tms'
> timesyshms.h:38: error: forward declaration of `struct tms'
> clmode.cc:318: error:   initializing argument 3 of `void
> success(char*, clock_t, tms)'
> make[1]: *** [clmode.o] Error 1
> make[1]: Leaving directory `/home/jshultz/autodocksuite-4.2.1/src/autodock-v1'
> make: *** [all] Error 2
>
> Is there a pre-defined struct in msvc or msys analogous to struct tms?
> If so can we just replace any reference in the code with such a
> struct. Otherwise how about defining a new struct tms?
>
>
> On Tue, Jun 23, 2009 at 1:11 PM, Sargis Dallakyan<sargis at scripps.edu> wrote:
>> Jack Shultz wrote:
>>>
>>> Hello,
>>>
>>> I'm trying to build autodock so it is compatible with the BOINC
>>> libraries. Some boinc developers think it would be better to avoid
>>> building this in cygwin. I tried this two years ago and gave up. I'm
>>> making another attempt. This time I'm trying to build it in visual
>>> studio c++. I am encountering many libraries and headers that are
>>> incompatible so I am looking for the right code modifications that
>>> will make this work. Has anyone else attempted this?
>>
>> I've tried this a couple of years ago too and managed to build autodock with
>> MS compiler. I tried this again after your post on gpuautodock, since I
>> couldn't use the Cygwin gcc with CUDA:
>> http://forums.nvidia.com/index.php?showtopic=42906
>>
>> I haven't push gpuautodock too hard since OpenCL might become a better
>> alternative to CUDA, and hopefully, more users will have CUDA or OpenCL
>> enabled graphics card.
>>
>> Regarding building autodock with visual studio c++: I came across this page
>> that discusses building OpenBabel with MinGW:
>> http://www.bioinformatics.org/molekel/wiki/pmwiki.php/Main/OpenBabel
>>
>> The changes that needs to be done in autodock are similar to what is written
>> in that page. However, I don't know Microsoft Visual Studio well enough to
>> make a project that would handle both autodock and autogrid.
>>
>> Cheers,
>> Sargis
>>
>>
>> --
>>
>> Sargis Dallakyan, Ph.D. - Research Programmer III
>> The Scripps Research Institute,
>> Dept. Molecular Biology,  MB-5,
>> 10550  North Torrey Pines Road,
>> La Jolla,  CA 92037-1000
>> Tel: (858) 784-9559
>> http://mgltools.scripps.edu/Members/sargis
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>



-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org



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