This is a GTX 780 right?
On Wed, Jul 17, 2013 at 4:01 PM, Hailin Huang <hailin.huang.my.liu.edu>wrote:
> 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
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 17 2013 - 16:30:03 PDT
