Help Wanted - build gpu autodock

Message boards : Number crunching : Help Wanted - build gpu autodock

To post messages, you must log in.

AuthorMessage
Profile Jack Shultz
Avatar

Send message
Joined: 10 Apr 09
Posts: 503
Credit: 120,150
RAC: 0
Message 598 - Posted: 13 Jun 2009, 15:42:24 UTC

I tried to compile this on windows last night. I ran into some trouble.
http://sourceforge.net/projects/gpuautodock/

I have vista 64-bit. 64-bit cuda and I have visual studio c++. My c++ is in the x86 programs directory so I am wondering if it is compatible with 64-bit cuda.

I am trying to build in cygwin because it has a configure make installation instruction. Cygwin provides a posix environment in windows.

I get this error:

$ cd Downloads/gpuautodock/src/autodock-4.0.1/
$ make
nvcc -c *.cu -D_DEBUG -g -use_fast_math -I. -I/common/inc -DCUDA_READY -DNOSQRT -DUSE_8A_NBCUTOFF -DDO_NOT_CROSSOVER_IN_QUAT -DWRITEPDBQSTATE -I./../acro/include
/bin/sh: nvcc: command not found
make: *** [select_alloc_wrapper.o] Error 127
$

If you have win xp and a cuda capable device...you might have better luck.
ID: 598 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Heavy Metal Dungeon Keeper

Send message
Joined: 2 May 09
Posts: 22
Credit: 81,216
RAC: 0
Message 619 - Posted: 16 Jun 2009, 14:48:55 UTC - in response to Message 598.  
Last modified: 16 Jun 2009, 15:22:27 UTC

Hi Jack

Are you using Visual Studio 2008, if so have you got the Visual Studio Service Pack 1 installed along with .net Framework 3.5

http://www.microsoft.com/visualstudio/en-gb/technicalresources/default.mspx

Also have you got the gcc packages installed in Cygwin
ID: 619 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile Jack Shultz
Avatar

Send message
Joined: 10 Apr 09
Posts: 503
Credit: 120,150
RAC: 0
Message 620 - Posted: 16 Jun 2009, 15:25:56 UTC - in response to Message 619.  

I made some further attempts at this and I will share these error messages soon.
ID: 620 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Gerry Rough
Avatar

Send message
Joined: 1 May 09
Posts: 19
Credit: 91,491
RAC: 0
Message 625 - Posted: 17 Jun 2009, 15:07:09 UTC

Not sure if this helps with the GPU app or not, but I thought you might be interested in this GPU related post on the BOINCstats web site.

(Click for detailed stats)
ID: 625 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile Jack Shultz
Avatar

Send message
Joined: 10 Apr 09
Posts: 503
Credit: 120,150
RAC: 0
Message 628 - Posted: 17 Jun 2009, 22:54:38 UTC - in response to Message 627.  

It looks like we should change our focus from gpu autodock to the gpu code for gromacs. There are preview releases available at SimTK for openMM Gromacs.

I'll explain more in a separate thread
ID: 628 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile Jack Shultz
Avatar

Send message
Joined: 10 Apr 09
Posts: 503
Credit: 120,150
RAC: 0
Message 2262 - Posted: 23 Feb 2010, 18:24:38 UTC - in response to Message 2253.  

Hello,

The cygwin environment does have 32 bit gcc compiler only. There is mingw compiler that produces 64 bit code. It may be related to your problems. I have posted the tutorial about 64bit compilation of Autodock here:
http://autodock.scripps.edu/faqs-help/how-to/how-to-compile-autodock-as-native-64-bit-windows-application


Thanks Wojciech, I will look over this the next few days. I hit a wall in my integration of OpenMM GROMACS. Andrew deffinitely wants to see a GPU app running. I'll see what we can do.

Also there is a project called GPU ROCS on SIMTK.ORG that I looked at briefly.
ID: 2262 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile robertmiles

Send message
Joined: 13 Oct 09
Posts: 105
Credit: 21,462
RAC: 0
Message 2294 - Posted: 1 Mar 2010, 21:36:29 UTC - in response to Message 598.  
Last modified: 1 Mar 2010, 21:45:04 UTC

I tried to compile this on windows last night. I ran into some trouble.
http://sourceforge.net/projects/gpuautodock/

If you have win xp and a cuda capable device...you might have better luck.


Will a machine with 64-bit Vista and a CUDA capable device offer any help?

I also have a machine with 32-bit Vista but no CUDA-capable device.

Note - I'm still looking for a way to learn enough C++ to be able to offer any help modifying the source code, unless I get error messages very detailed about exactly what changes are needed.

I believe that the C++ compiler is supposed to be in the x86 directory if it runs in 32-bit mode, but under a 64-bit version of Vista. I don't know if that also restricts it to compiling programs with the CPU part to run in 32-bit mode, but I suspect that it does.

Vista comes with the ability to run programs in 32-bit mode already built in, due to both user desire and the delay in getting many application programs converted to 64-bit mode.
ID: 2294 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile Jack Shultz
Avatar

Send message
Joined: 10 Apr 09
Posts: 503
Credit: 120,150
RAC: 0
Message 2296 - Posted: 2 Mar 2010, 16:12:35 UTC - in response to Message 2294.  

Here is some helpful information. If you want a Visual studio solution that builds GROMACS, you can find some older versions of GROMACS here
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Gromacs_binaries/i686%2F%2FMS_Windows

Last weekend I had to update my home environment becaues my preview release of Win7 was expiring. I will try to learn more about GPU programing and see if I can modify this existing solution to use a GPU.

ID: 2296 · Rating: 0 · rate: Rate + / Rate - Report as offensive

Message boards : Number crunching : Help Wanted - build gpu autodock


©2017 All rights reserved | Design by Digital BioPharm Ltd