Hi Sebastian, That is very likely a bug so I'd appreciate if you could provide a bit more information, like:
- OS, compiler - results of runs with the following configurations: - "mdrun -nb cpu" (to run CPU-only with Verlet scheme) - "GMX_EMULATE_GPU=1 mdrun -nb gpu" (to run GPU emulation using plain C kernels); - "mdrun" without any arguments (which will use 2x(n/2 cores + 1 GPU)) - "mdrun -ntmpi 1" without any other arguments (which will use n cores + the first GPU) - please attach the log files of all failed and a successful run as well as the mdrun.debug file from a failed runs that you can obtain with "mdrun -debug 1" Note that a backtrace would be very useful and if you can get one I'd be grateful, but for now the above should be minimum effort and I'll provide simple introductions to get a backtrace later (if needed). Thanks, -- Szilárd On Mon, Nov 12, 2012 at 6:22 PM, sebastian < sebastian.wa...@physik.uni-freiburg.de> wrote: > On 11/12/2012 04:12 PM, sebastian wrote: > > Dear GROMACS user, > > > > I am running in major problems trying to use gromacs 4.6 on my desktop > > with two GTX 670 GPU's and one i7 cpu. On the system I installed the > > CUDA 4.2, running fine for many different test programs. > > Compiling the git version of gromacs 4.6 with hybrid acceleration I get > > one error message of a missing libxml2 but it compiles with no further > > complaints. The tools I tested (like g_rdf or grompp usw.) work fine as > > long as I generate the tpr files with the right gromacs version. > > Now, if I try to use mdrun (GMX_GPU_ID=1 mdrun -nt 1 -v -deffnm ....) > > the preparation seems to work fine until it starts the actual run. It > > stops with a segmentation fault: > > > > Reading file pdz_cis_ex_200ns_test.tpr, VERSION > > 4.6-dev-20121002-20da718-dirty (single precision) > > > > Using 1 MPI thread > > > > Using 1 OpenMP thread > > > > > > 2 GPUs detected: > > > > #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: > compatible > > > > #1: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC: no, stat: > compatible > > > > > > 1 GPU user-selected to be used for this run: #1 > > > > > > Using CUDA 8x8x8 non-bonded kernels > > > > > > * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING * > > > > We have just committed the new CPU detection code in this branch, > > > > and will commit new SSE/AVX kernels in a few days. However, this > > > > means that currently only the NxN kernels are accelerated! > > > > Since it does run on a pure CPU run (without the verlet cut-off scheme) > does it maybe help to change the NxN kernels manually in the .mdp file > (how can I do so)? Or is there something wrong using the CUDA 4.2 > version or what so ever. The libxml2 should not be a problem since the > pure CPU run works. > > > In the mean time, you might want to avoid production runs in 4.6. > > > > > > Back Off! I just backed up pdz_cis_ex_200ns_test.trr to > > ./#pdz_cis_ex_200ns_test.trr.4# > > > > > > Back Off! I just backed up pdz_cis_ex_200ns_test.xtc to > > ./#pdz_cis_ex_200ns_test.xtc.4# > > > > > > Back Off! I just backed up pdz_cis_ex_200ns_test.edr to > > ./#pdz_cis_ex_200ns_test.edr.4# > > > > starting mdrun 'Protein in water' > > > > 3500000 steps, 7000.0 ps. > > > > Segmentation fault > > > > > > Since I have no idea whats going wrong any help is welcomed. > > Attached you find the log file. > > > > Help is really appreciated since I want to use my new desktop including > the GPU's > > > Thanks a lot > > > > Sebastian > > > > > > > > > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists