Hi Ross,
Yes we are using the version 12.3 of the GPU code.
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.3
|
| 04/24/2013
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
| Duncan Poole (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------
|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2012, (In review).
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
I am sending the input files to your email.
Thanks!
Richard
On Wed, Jul 17, 2013 at 5:53 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Wed Jul 17 2013 - 16:30:02 PDT
