Gromacs-OpenMM on Windows

[Mohd Ismail]

Hi, on the download page, there are Linux-Gromacs-OpenMM and MacOS-Gromacs-OpenMM. Is there a way to install Gromacs-OpenMM on Windows?

Can I compile Gromcas-4.0.5 using Cygwin and install OpenMM-Windows, and link it somehow?

[Mark Friedrichs]

Hi Mohd,

One solution would be to download OpenMM Zephyr (https://simtk.org/project/xml/downloads ... oup_id=352) and use the mdrun_openmm executable. The Zephyr manual gives details on how to setup and run Gromacs/OpenMM simulations from the command line.

Mark

[Mohd Ismail]

Thank you. I found that solution when browsing the forum earlier.

On the other hand, the forum is really weird. If I enter the forum at different times, or from different links, I get different lists of topics. Anyone else is getting the same behavior? I tried reloading the forum thinking that it is a cookie problem. I have the same problem on IE8 and Firefox 3.6.

[Jack Shultz]

I am trying to compile on 64-bit windows 7. When I run cmake. I get the following

CMake Error: Parse error in cache file C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/CMakeCache.txt. Offending entry: MS-DOS style path detected_ C_/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/.svn/entries
CMake Error: Parse error in cache file C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/CMakeCache.txt. Offending entry: Preferred POSIX equivalent is_ /cygdrive/c/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/.svn/entries
CMake Error: Parse error in cache file C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/CMakeCache.txt. Offending entry: CYGWIN environment variable option "nodosfilewarning" turns off this warning.
CMake Error: Parse error in cache file C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/CMakeCache.txt. Offending entry: Consult the user's guide for more details about POSIX paths_
CMake Error: Parse error in cache file C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/CMakeCache.txt. Offending entry: http_//cygwin.com/cygwin-ug-net/using.html#using-pathnames
CMake Error: Parse error in cache file C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/CMakeCache.txt. Offending entry: exported
Configuring done

I get errors building the solution in Visual Studio Express 2008

1>LINK : warning LNK4044: unrecognized option '/D'; ignored
1>LINK : warning LNK4044: unrecognized option '/D'; ignored
1>LINK : warning LNK4044: unrecognized option '/D'; ignored
1>LINK : warning LNK4044: unrecognized option '/D'; ignored
1>LINK : warning LNK4044: unrecognized option '/D'; ignored
1>LINK : warning LNK4044: unrecognized option '/D'; ignored
1>LINK : warning LNK4044: unrecognized option '/FD'; ignored
1>LINK : warning LNK4044: unrecognized option '/EHsc'; ignored
1>LINK : warning LNK4044: unrecognized option '/MD'; ignored
1>LINK : warning LNK4044: unrecognized option '/FoOpenMM.dir\Release\'; ignored
1>LINK : warning LNK4044: unrecognized option '/FdC:/Users/jshultz/Documents/Visual'; ignored
1>LINK : fatal error LNK1181: cannot open input file 'MS-DOS.obj'
1>Build log was saved at "file://c:\Users\jshultz\Documents\Visual Studio 2008\Projects\OpenMM1.1-Source\src\OpenMM.dir\Release\BuildLog.htm"
1>OpenMM - 1 error(s), 141 warning(s)
2>------ Build started: Project: OpenMMCuda, Configuration: Release Win32 ------
2>Building (Device) NVCC Dependency File: C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/src/cuda/./src/kernels//kVerletUpdate.cu_OpenMMCuda_generated.cpp.NVCC-depend
2>
2>nvcc fatal : Visual Studio configuration file '(null)' could not be found for installation at 'C:\Program Files (x86)\Microsoft Visual Studio 9.0\VC\bin/../..'
2>Converting NVCC dependency to CMake (C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/src/cuda/./src/kernels//kVerletUpdate.cu_OpenMMCuda_generated.cpp.depend)
2>CMake Error at C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/platforms/cuda/cuda-cmake/make2cmake.cmake:33 (FILE):
2> file Internal CMake error when trying to open file:
2> C:/Users/jshultz/Documents/Visual Studio
2> 2008/Projects/OpenMM1.1-Source/src/src/cuda/./src/kernels//kVerletUpdate.cu_OpenMMCuda_generated.cpp.NVCC-depend
2> for reading.
2>Project : error PRJ0019: A tool returned an error code from "Converting NVCC dependency to CMake (C:/Users/jshultz/Documents/Visual Studio 2008/Projects/OpenMM1.1-Source/src/src/cuda/./src/kernels//kVerletUpdate.cu_OpenMMCuda_generated.cpp.depend)"
2>Build log was saved at "file://c:\Users\jshultz\Documents\Visual Studio 2008\Projects\OpenMM1.1-Source\src\platforms\cuda\sharedTarget\OpenMMCuda.dir\Release\BuildLog.htm"
2>OpenMMCuda - 1 error(s), 0 warning(s)
========== Build: 0 succeeded, 2 failed, 1 up-to-date, 0 skipped ==========

[Christopher Bruns]

It's not obvious to me what the trouble might be. We don't have much experience building on 64-bit Windows, nor on Windows 7.

Are you by any chance running the cygwin cmake executable rather than native windows cmake?

Does Zephyr run correctly on your system?

[Jack Shultz]

Using CMake 2.8.0 windows gui. I will try building again on xp 32-bit. Zephyr runs. I selected NVIDIA GPU. I tried running it from the command line and it fails to read the params.agb

Center of mass motion removal mode is Angular
We have the following groups for center of mass motion removal:
0: rest
There are: 32 Atoms
Could not find/read params.agb file needed for OBC/GBSA -- aborting: lib directo
ry=<C:/Program Files/GromacsOpenMM/share/gromacs/top>.

C:\Users\jshultz\Documents\ZephyrSims\alanylalanine_capped>

C:\Users\jshultz\Documents\ZephyrSims\alanylalanine_capped>dir *.agb
Volume in drive C has no label.
Volume Serial Number is E0EF-9C2B

Directory of C:\Users\jshultz\Documents\ZephyrSims\alanylalanine_capped

11/19/2008 02:15 AM 9,437 params.agb
1 File(s) 9,437 bytes
0 Dir(s) 3,693,780,992 bytes free

C:\Users\jshultz\Documents\ZephyrSims\alanylalanine_capped>

[Christopher Bruns]

When you run Zephyr binaries from the command line, you need to set certain environment variables correctly. This should be described in chapter 5 of the Zephyr manual. Failure to find params.agb suggests that the GMXLIB variable needs to be set to a particular directory within the Zephyr install. Alternatively, you could copy the file params.agb from the Zephyr install folder to your Gromacs install folder.

[Shashi Prakash]

Hi,
I am trying to use mdrun_openmm.exe (found in Zephyr install) from command line on 64-bit Windows 7. I have added the environment variables as mentioned in Chapter 5 of the Zephyr manual as follows:

set GMXLIB=C:\Zephybin\gmxlib
PATH=C:\Zephyr\bin\win32;%PATH%
set OPENMM_PLUGIN_DIR=C:\Zephyr\bin\win32\lin\openmm\nvidia

In spite of this, when I run the exe, I get
OpenMM Platform: Reference

I have no idea why it wouldn't run on Cuda even though all the drivers and CUDA Toolkit/SDK are in place.

Any help would be appreciated.

Thanks,
Shashi

[Shashi Prakash]

Update:
When I change the environment variable to point to OpenCL, it works. But, it doesn't work for CUDA.

What could be the reason behind it?

Thanks,
Shashi

[Peter Eastman]

That's quite strange that OpenCL would work but not CUDA. Just to check a few points:

- What GPU do you have?
- What happens when you run a simulation through the Zephyr application? Does CUDA work then?
- What version of CUDA do you have installed?
- Are the CUDA and OpenCL plugins both present in the plugins directory?

Peter