Hi James, Don't use the OpenMM accelerated mdrun for explicit solvent simulations. For such runs any modern CPU with 4-8 cores will probably be as fast or faster than most GPUs.
However, do consider the 4.6 *native* heterogeneous GPU-accelerated code. This new efficient code can provide 2-4x speedup and uses both CPU and GPU. To get the latest 4.6 version use the 4.6-beta3 release (http://goo.gl/XFPoe) or even better, get the code from git (git clone git:// git.gromacs.org/gromacs -b release-4-6). Let us know how things worked out! Cheers, -- Szilárd On Mon, Jan 7, 2013 at 8:05 AM, James Starlight <[email protected]>wrote: > Today I've tried to test gpu performance on the benchmark system ( > explicit solvent with pme ) > > grompp-gpu -f md_sd.mdp -c conf -p topol.top -o md_test > mdrun-gpu -device > "OpenMM:platform=Cuda,DeviceID=1,Memtest=15,force-device=no" -v > -deffnm md_test > > that produce the error > > Program mdrun-gpu, VERSION 4.5.5 > Source code file: /home/own/gromacs_gpu/src/kernel/openmm_wrapper.cpp, > line: 1365 > > Fatal error: > OpenMM exception caught while initializating: cudaMemcpyToSymbol: > SetSim copy to cSim failed invalid device symbol > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > In the mailing list archive I've found the same error with the same > card posted some time ago > > http://article.gmane.org/gmane.science.biology.gromacs.user/55577/match=openmm+exception+caught+while+initializating+cudaMemcpyToSymbol+setsim+copy+cSim+failed+invalid+device+symbol > > >From that topic I've understood that 670 graphic card is not supported > yet in Gromacs (4.55). I've checked the manual for the 4.6 beta > version and does not found anything about supporting of that card in > the lattest gromacs realeses as well. IS there any ways to solve that > problem ? Could that error be linked with some others ? E.g I've > installed nvidia drivers + cuda first and openMM 4.01 than. During > gromacs compilation I've not forced with any errors. > > Thanks for help > James > > 2013/1/6 Justin Lemkul <[email protected]>: > > > > > > On 1/6/13 1:53 PM, James Starlight wrote: > >> > >> OK! > >> > >> I've compilated gromacs-gpu from the source using that tutorial for > >> the Debian OS > >> > >> > http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html > >> > >> The only thing that it lack is the installation mdrun_d-gpu but i'm > >> not sure that double precission can be used with gpu. > >> > >> Could someone provide me with some tutorial which would show me basic > >> mdrun options with the calculation on my gpu as well as some testing > >> system? > >> > > > > Everything you need to know (including benchmark systems) is posted at > > http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs. > > > > The invocation of mdrun-gpu is like any other mdrun, with GPU-specific > > information available by reading mdrun-gpu -h. > > > > > > -Justin > > > > -- > > ======================================== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
