Dear Yoshihisa,
Granted this should not be failing in this way but I have to question why
you would want to run with mpirun -np 1? - All it does is add overhead and
slow the simulation down. It is also a configuration that is not tested,
hence why it has not been noticed that it was failing.
We'll take a look.
All the best
Ross
On 6/17/13 11:19 PM, "Nakashima, Yoshihisa" <nakashima_y.jp.fujitsu.com>
wrote:
>Dear Amber community
>
>Hello,
>
>I tried to run Cellulose NVE included in Amber12_GPU_BMT suite with
>GPGPU(K20X).
>The case of serial version (pmemd.cuda) and the parallel version
>(pmemd.cuda.MPI) with 2process + 2GPU were OK,
>but the caes of the parallel version (pmemd.cuda.MPI) with 1process +
>1GPU,
>the following message was desplayed and this test failed.
>
>***********
># mpiexec -np 1 pmemd.cuda.MPI -O -i mdin -p prmtop -c inpcrd -o
>mdout_intel_gpu1pro_0618
>
>gpu_download_partial_forces: download failed unspecified launch failure
>
>==========================================================================
>=========
>= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>= EXIT CODE: 255
>= CLEANING UP REMAINING PROCESSES
>= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>==========================================================================
>=========
>**************
>
>(e.g. the case of no problem)
>No problem: # mpiexec -np 2 pmemd.cuda.MPI -O -i mdin -p prmtop -c inpcrd
>-o mdout_intel_gpu2pro_0618
>No problem: # pmemd.cuda -O -i mdin -p prmtop -c inpcrd -o
>mdout_intel_gpu1pro_0618
>
>
>This problems is only this case (pmemd.cuda.MPI + 1 GPU) .
>With other 8 BMT (Cellulose NPT, TRPCage and so on), there is no problem.
>
>I don't know why the problem occur.
>Could you give me an advice to solve this problem ?
>
>
>
>Following is information
>
>- Configuration
>OS RHEL6.1
>CPU 2x Xeon E5-2680
>Amber version: 12 (Patched bugfix from 1 to 18)
>AmberTools version: 13 (Patched bugfix from 1 to 9)
>MPI: MPICH2-1.5
>GNU: 4.4.5
>GPU: 2x K20X
>GPU Device Driver: 304.64
>CUDA: 5.0
>
>
>- Input file is following, it is the same as the file that is described
>on Amber's web site.
>(http://ambermd.org/gpus/benchmarks.htm)
>
>5) Cellulose NVE = 408,609 atoms
>************
>Typical Production MD NVE with
>GOOD energy conservation.
> &cntrl
> ntx=5, irest=1,
> ntc=2, ntf=2, tol=0.000001,
> nstlim=10000,
> ntpr=1000, ntwx=1000,
> ntwr=10000,
> dt=0.002, cut=8.,
> ntt=0, ntb=1, ntp=0,
> ioutfm=1,
> /
> &ewald
> dsum_tol=0.000001,
> /
>**************
>
>
>- The last part of output file is
>
>**************
>--------------------------------------------------------------------------
>------
> 4. RESULTS
>--------------------------------------------------------------------------
>------
>
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
>| CHECK d/dx switch(x): max rel err = 0.8987E-11 at 2.875760
> ---------------------------------------------------
>|---------------------------------------------------
>| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>| with 50.0 points per unit in tabled values
>| Relative Error Limit not exceeded for r .gt. 2.52
>| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>| with 50.0 points per unit in tabled values
>| Relative Error Limit not exceeded for r .gt. 2.92
>|---------------------------------------------------
>************
>
>
>Thank you for your support.
>
>Best wishes,
>Y. Nakashima
>
>
>
>
>----
>-----------------------------------------
>Yoshihisa Nakashima
>Tel: +81-44-754-3174
>E-mail:(nakashima_y.jp.fujitsu.com)
>
>
>
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Received on Wed Jun 19 2013 - 05:30:03 PDT
