[gmx-users] how to accelerate mdrun process

[Mark Abraham]

Hi,

As in the other thread, please do a Release buildnof GROMACS, not debug.

Mark

On Fri., 28 Jun. 2019, 15:46 kalpana, <kalpanadynasty at gmail.com> wrote:

> Hi everyone,
> Kindly help to accelerate this mdrun process as you could see that its
> showing following timing for the command along with provided gmx -version.
>
>   gmx mdrun -deffnm md_0_1 -ntmpi 5 -ntomp 6 -pin on -v
>
> starting mdrun 'protein in water'
> 5000000 steps,  10000.0 ps.
> step 17000, will finish Wed Jul  3 22:01:39 2019imb F  2% imb F  5%
>
>  gmx --version
>
> GROMACS version:    2019.3
> Precision:          single
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
> GPU support:        CUDA
> SIMD instructions:  AVX_512
> FFT library:        fftw-3.3.8-sse2-avx
> RDTSCP usage:       enabled
> TNG support:        enabled
> Hwloc support:      hwloc-1.11.6
> Tracing support:    disabled
> C compiler:         /usr/bin/gcc GNU 8.3.0
> C compiler flags:    -mavx512f -mfma     -g -fno-inline
> C++ compiler:       /usr/bin/c++ GNU 8.3.0
> C++ compiler flags:  -mavx512f -mfma    -std=c++11   -g -fno-inline
> CUDA compiler:      /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
> driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on
> Wed_Apr_24_19:10:27_PDT_2019;Cuda compilation tools, release 10.1,
> V10.1.168
> CUDA compiler
>
> flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;;
> ;-mavx512f;-mfma;-std=c++11;-g;-fno-inline;
> CUDA driver:        10.10
> CUDA runtime:       N/A
>
>
> Thanks and regards
> Kalpana
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>