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! 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. Thanks a lot Sebastian
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