[gmx-users] Gromacs 4.6 segmentation fault with mdrun

sebastian 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


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.

Segmentation fault

Since I have no idea whats going wrong any help is welcomed.
Attached you find the log file.

Thanks a lot


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