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