[gmx-users] Gromacs 4.6 segmentation fault with mdrun

[sebastian]

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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