[gmx-users] CUDA fails to allocate memory to mdrun

Thu Apr 2 14:14:10 CEST 2015

That seems to have addressed the problem.
Thanks and regards
Akshay

     On Monday, 30 March 2015 11:15 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:

 Hi,

You can run with CPU-GPU load balancing disabled (-notunepme), that
should avoid the error. You will likely not loose much performance as
the performance difference between the first two grid settings in the
tuning output seems to be marginal.

Cheers,
--
Szilárd

On Mon, Mar 30, 2015 at 12:31 PM, Akshay Kumar Ganguly
<akshayganguly at yahoo.co.in> wrote:
>
>
>
> Hi!
> I'm running gromacs v5.0.4 on a 32-bit CentOS 6.5 OS with CUDA toolkit v4.0 and the latest nvidia linux driver (v340.24) for a Quadro K4200.
>
> My explicit solvent runs crash during pme grid optimization citing the following error -
>
> -------- -------- ----------------------------------------------------------------------------- -------- --------
>
> There are: 75766 Atoms
> Initial temperature: 301.154 K
>
> Started mdrun on rank 0 Mon Mar 30 14:30:54 2015
>            Step          Time        Lambda
>              0        0.00000        0.00000
>
>    Energies (kJ/mol)
>          Angle    Proper Dih.  Improper Dih.          LJ-14    Coulomb-14
>    6.92142e+03    9.29820e+03    3.90420e+02    3.61267e+03    4.01187e+04
>        LJ (SR)  Disper. corr.  Coulomb (SR)  Coul. recip. Position Rest.
>    2.14594e+05  -9.79483e+03  -1.47636e+06    6.97759e+03    2.17547e-01
>      Potential    Kinetic En.  Total Energy    Temperature Pres. DC (bar)
>    -1.20424e+06    1.89766e+05  -1.01448e+06    3.01035e+02  -2.11354e+02
>  Pressure (bar)  Constr. rmsd
>    -4.75277e+02    2.75540e-05
>
> step  80: timed with pme grid 60 60 60, coulomb cutoff 1.000: 3398.8 M-cycles
>            Step          Time        Lambda
>            100        0.20000        0.00000
>
>    Energies (kJ/mol)
>          Angle    Proper Dih.  Improper Dih.          LJ-14    Coulomb-14
>    7.24215e+03    9.27752e+03    4.13476e+02    3.61128e+03    4.00927e+04
>        LJ (SR)  Disper. corr.  Coulomb (SR)  Coul. recip. Position Rest.
>    2.17175e+05  -9.83595e+03  -1.47626e+06    4.92524e+03    8.51347e+02
>      Potential    Kinetic En.  Total Energy    Temperature Pres. DC (bar)
>    -1.20251e+06    1.87791e+05  -1.01472e+06    2.97902e+02  -2.13130e+02
>  Pressure (bar)  Constr. rmsd
>    -2.43339e+02    2.65826e-05
>
> step  160: timed with pme grid 52 52 52, coulomb cutoff 1.102: 3359.8 M-cycles
>
> -------------------------------------------------------
> Program mdrun, VERSION 5.0.4
> Source code file: /nmr/gromacs-5.0.4/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu, line: 61
>
> Fatal error:
> cudaMallocHost of size 2851616 bytes failed: out of memory
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ------------------------------------------------------------------------------------------------------------------------------------------------
>
> The size of the failed allocation varies from error to error but it generally ranges from 2.5 to 5 mB.
> While it is likely that the newer toolkits(v5-7) have resolved this issue, I am unable to use them since they lack support for 32-bit OSs.
>
> I would be obliged if you could suggest a way to free up some page-linked memory (at least that's what google says the problem is but I'm still all at sea as far as the solution goes) for mdrun and/or provide a patch for pmalloc_cuda.cu.
>  The problem looks to be limited to complex systems [(large proteins (>150 residues) in explicit water (~25000 molecules) cubes] as I am able to run smaller ones (~100 residues) with ease in explicit solvent using the GPU for non-bonded calculations (mdrun -v -deffnm $prot_md -nb gpu).
>
> I have attached herewith the corresponding log file and mdp.
>
> Regards,
>
>  Akshay Kumar Ganguly
>
> Graduate Student,Dr. Neel S. Bhavesh lab,
> Structural and Computational Biology Group,
> International Centre for Genetic Engineering and Biotechnology,
> New Delhi - 67
>
>
>
> --
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