Hi Richard,
Can you confirm that you are running version 12.3 of the GPU code please.
Check the mdout file where it writes info about the GPUs in use and
citation information. This corresponds to AMBER 12 up to bugfix.18. If you
have an earlier version please upgrade and this should fix the problem. If
you still see the problem with the latest version of the code please post
your input files for the run that takes the shortest time to crash and
we'll try and debug it.
All the best
Ross
On 7/17/13 2:23 PM, "Hailin Huang" <hailin.huang.my.liu.edu> wrote:
>Dear Amber Users,
>
>I am simulating 4 variations of the protein kinase A (PKA) tetramer using
>explicit solvent. One of them has 1 Mg ion between each R-C subunits.
>First
>I did the minimization with 10 kcal/mol restraint weight on the backbone.
>Then, when I tried to run the heating simulation, the calculation stopped
>at step 0, without leaving any error messages in the output file.
>
>The end of the output file looks like this:
>
>NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
>-3062.5
> Etot = -409445.2805 EKtot = 0.0000 EPtot =
>-409445.2805
> BOND = 49371.8329 ANGLE = 1469.1848 DIHED =
>10100.8048
> 1-4 NB = 2093.2049 1-4 EEL = 24175.6479 VDWAALS =
>97254.9978
> EELEC = -593910.9535 EHBOND = 0.0000 RESTRAINT =
>0.0000
> EKCMT = 0.0000 VIRIAL = 70377.8192 VOLUME =
>1064336.6826
> Density =
>0.8515
>
>--------------------------------------------------------------------------
>----
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>==========================================================================
>=====
>
>
>In the log file, I got the message "cudaMemcpy GpuBuffer::Download failed
>unspecified launch failure". This problem did not occur when I run the
>other 3 variations of PKA structures (one with 2 Mg ions, one with no Mg
>ions and one with no ADPs).
>
>I have tried to run the simulation using GTX 680, 690, 780, and on the
>Stampede supercomputers that use Tesla K20m, I got the same result.
>
>Then I changed the size of the solvent box (from 12A to 10A), the problem
>went away and the calculation completed successfully. However, same
>problem
>happened again in the later NVT equilibration simulation. This time the
>calculation stopped in the middle:
>
>NSTEP = 1599000 TIME(PS) = 3598.000 TEMP(K) = 299.24 PRESS =
>22.1
> Etot = -432512.9372 EKtot = 90851.5391 EPtot =
>-523364.4763
> BOND = 3740.6596 ANGLE = 10689.2110 DIHED =
>21485.9623
> 1-4 NB = 4601.7696 1-4 EEL = 47865.1134 VDWAALS =
>74622.8763
> EELEC = -687021.9668 EHBOND = 0.0000 RESTRAINT =
>651.8984
> EAMBER (non-restraint) = -524016.3746
> EKCMT = 38312.0157 VIRIAL = 37612.0350 VOLUME =
>1465745.9675
> Density =
>1.0384
>
>--------------------------------------------------------------------------
>----
>
>Same message in the log file "cudaMemcpy GpuBuffer::Download failed
>unspecified launch failure".
>
>
>When I was simulating 4 variations of the heterodimer of PKA (half size of
>the tetramer), same error occurred in the heating stage for the structure
>with no Mg ions and the structure with no ADPs, while the ones with 1 Mg
>and 2 Mg ions are running just fine. So I changed the size of solvent box
>from 10A to 8A and this got rid of the problem again. Now I am running the
>NVT equilibration and "expecting" the calculations to stop in the middle
>just like what happened to the tetramer with 1 Mg (hopefully not).
>
>
>I would be really grateful if anyone could give me an idea what is going
>on
>and possibly with a solution to this annoying "cudaMemcpy
>GpuBuffer::Download failed unspecified launch failure" problem.
>
>
>Thank you!
>
>Best,
>Richard
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Received on Wed Jul 17 2013 - 15:00:02 PDT
