[gmx-users] Gromacs 4.6 segmentation fault with mdrun
sebastian.waltz at physik.uni-freiburg.de
Mon Nov 12 16:12:05 CET 2012
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
Back Off! I just backed up pdz_cis_ex_200ns_test.xtc to
Back Off! I just backed up pdz_cis_ex_200ns_test.edr to
starting mdrun 'Protein in water'
3500000 steps, 7000.0 ps.
Since I have no idea whats going wrong any help is welcomed.
Attached you find the log file.
Thanks a lot
More information about the gromacs.org_gmx-users