[gmx-developers] gromacs 4.5 git + openmm-2.0 + OpenCL

[Rossen Apostolov]

  Hi,

We haven't tested the OpenCL platform.

CUDA is hardcoded in a few places, for example the openmm_cleanup 
routine (have a look at openmm_wrapper.cpp) which segfaults in your case.

Let me know if you get it to work though.

Rossen


On 08/16/2010 09:28 PM, Alexey Shvetsov wrote:
> Hi all!
>
> Recently i tryed to build gromacs 4.5 + openmm with opencl support.
> Seems it builds fine. Also i can do test run ( for example speptide in
> water box) but mdrun always segfaults when it finishing. right after
> writing last frame of trajectory.
>
> I get this in backtrace
>
> starting mdrun 'Protein in water'
> 5000 steps,     10.0 ps.
> step 4900, remaining runtime:     3 s
> Writing final coordinates.
>
> Back Off! I just backed up confout.gro to ./#confout.gro.1#
> step 5000, remaining runtime:     0 s          *** glibc detected ***
> /home/alexxy/Soft/openmm/bin/mdrun-gpu: free(): invalid pointer:
> 0x000000000137ed78 ***
> ======= Backtrace: =========
> /lib/libc.so.6(+0x71c45)[0x2aaaac99ec45]
> /lib/libc.so.6(cfree+0x6c)[0x2aaaac9a3b3c]
> /home/alexxy/Soft/openmm/lib/plugins/libOpenMMOpenCL.so(_ZN6OpenMM34OpenCLCalcHarmonicAngleForceKernelD1Ev+0x5c)[0x2aaaadc13d9c]
> /home/alexxy/Soft/openmm/lib/plugins/libOpenMMOpenCL.so(_ZN6OpenMM34OpenCLCalcHarmonicAngleForceKernelD0Ev+0x9)[0x2aaaadc13ea9]
> /home/alexxy/Soft/openmm/lib/libOpenMM.so(_ZN6OpenMM22HarmonicAngleForceImplD1Ev+0x1b)[0x2aaaaaf51d1b]
> /home/alexxy/Soft/openmm/lib/libOpenMM.so(_ZN6OpenMM22HarmonicAngleForceImplD0Ev+0x9)[0x2aaaaaf51d59]
> /home/alexxy/Soft/openmm/lib/libOpenMM.so(_ZN6OpenMM11ContextImplD1Ev+0x37)[0x2aaaaaf2c607]
> /home/alexxy/Soft/openmm/lib/libOpenMM.so(_ZN6OpenMM7ContextD2Ev+0x21)[0x2aaaaaf41631]
> /home/alexxy/Soft/openmm/bin/mdrun-gpu(openmm_cleanup+0xed)[0x531ebd]
> /home/alexxy/Soft/openmm/bin/mdrun-gpu(do_md_openmm+0x1480)[0x443270]
> /home/alexxy/Soft/openmm/bin/mdrun-gpu(mdrunner+0xbe3)[0x422713]
> /home/alexxy/Soft/openmm/bin/mdrun-gpu(main+0x1148)[0x43f278]
> /lib/libc.so.6(__libc_start_main+0xfd)[0x2aaaac94bb3d]
> /home/alexxy/Soft/openmm/bin/mdrun-gpu[0x41acc9]
> ======= Memory map: ========
> 00400000-00719000 r-xp 00000000 fe:09 1284469
>    /home/alexxy/Soft/openmm/bin/mdrun-gpu
> 00919000-0091a000 r--p 00319000 fe:09 1284469
>    /home/alexxy/Soft/openmm/bin/mdrun-gpu
> 0091a000-0091c000 rw-p 0031a000 fe:09 1284469
>    /home/alexxy/Soft/openmm/bin/mdrun-gpu
> 0091c000-019a1000 rw-p 00000000 00:00 0                                  [heap]