[gmx-users] Gromacs 4.6 segmentation fault with mdrun

[Szilárd Páll]

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.waltz at 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
> >
> >
> >
> >
> >
> >
>
> --
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