[gmx-users] Simulations on GPU

[Igor Leontyev]

Finally, I compiled and ran simulations with gpu version of gromacs-4.5.1. 
There were several issues:



1) Precompiled OpenMM2.0 libraries and headers must be downloaded (which 
requires registration on their web page) and installed, otherwise cmake 
doesn't find some source files.

2) cmake should be called outside the original source directory with the 
path of the directory as an argument.

3) To run the obtained mdrun-gpu binary the CUDA dev driver should be 
installed, otherwise the program does not find 'CUDA'. This step appeared to 
be the most problematic for me. According to OpenMM manual the driver must 
be installed with turned off x-windows service which can be done by the 
command "init 3". In Ubuntu this command has no effect, while switching the 
graphical interface off/on is done by



"sudo service gdm stop/start"



 It turned out that in Ubuntu-10.04 the CUDA driver installation script does 
not work properly even with turned off gdm. This issue and its solution is 
described at http://ubuntuforums.org/showthread.php?t=1467074



Thank you for comments,



Igor

> Szilárd Páll wrote:
> Dear Igor,
>
> Your output look _very_ weird, it seems as if CMake internal
> variable(s) were not initialized, which I have no clue how could have
> happened - the build generator works just fine for me. The only thing
> I can think of is that maybe your CMakeCache is corrupted.
>
> Could you please rerun cmake in a _clean_ build directory? Also, are
> you able to run cmake for CPU build (no -D options)?
>
> --
> Szilárd
>
>
>
> On Wed, Oct 6, 2010 at 2:48 AM, Igor Leontyev <ileontyev at ucdavis.edu> 
> wrote:
>> Szilárd wrote:
>>>
>>> The beta versions are all outdated, could you please use the latest
>>> source distribution (4.5.1) instead (or git from the
>>> release-4-5-patches branch)?
>>
>> The result is the same for both the distribution 4.5.1 and git from the
>> release-4-5-patches. See the output bellow.
>> =========================================
>>
>> PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
>> LD_LIBRARY_PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/lib:/home/leontyev/programs/bin/cuda/lib64:
>> CPPFLAGS=-I//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/include
>> -I//usr/local/opt/bin/mpi/openmpi-1.4.2/include
>> LDFLAGS=-L//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/lib
>> -L//usr/local/opt/bin/mpi/openmpi-1.4.2/lib
>> OPENMM_ROOT_DIR=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git/openmm
>>
>> cmake src -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>> -DCMAKE_INSTALL_PREFIX=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git
>> CMake Error at gmxlib/CMakeLists.txt:124 (set_target_properties):
>> set_target_properties called with incorrect number of arguments.
>>
>>
>> CMake Error at gmxlib/CMakeLists.txt:126 (install):
>> install TARGETS given no ARCHIVE DESTINATION for static library target
>> "gmx".
>>
>>
>> CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
>> set_target_properties called with incorrect number of arguments.
>>
>>
>> CMake Error at mdlib/CMakeLists.txt:13 (install):
>> install TARGETS given no ARCHIVE DESTINATION for static library target
>> "md".
>>
>>
>> CMake Error at kernel/CMakeLists.txt:43 (set_target_properties):
>> set_target_properties called with incorrect number of arguments.
>>
>>
>> CMake Error at kernel/CMakeLists.txt:44 (set_target_properties):
>> set_target_properties called with incorrect number of arguments.
>>
>>
>> CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18
>> (CUDA_INCLUDE_DIRECTORIES):
>> Unknown CMake command "CUDA_INCLUDE_DIRECTORIES".
>>
>>
>> CMake Warning (dev) in CMakeLists.txt:
>> No cmake_minimum_required command is present. A line of code such as
>>
>> cmake_minimum_required(VERSION 2.8)
>>
>> should be added at the top of the file. The version specified may be 
>> lower
>> if you wish to support older CMake versions for this project. For more
>> information run "cmake --help-policy CMP0000".
>> This warning is for project developers. Use -Wno-dev to suppress it.
>>
>> -- Configuring incomplete, errors occurred!