[gmx-developers] GROMACS 2018.8 PERFORMANCE
Erik Lindahl
erik.lindahl at gmail.com
Fri Dec 11 21:10:26 CET 2020
Hi Navneet,
This is not a development (i.e., sorce code) question, so:
1. Please post general questions to the forums at
https://gromacs.bioexcel.eu instead.
2. We tend to support/care about the current version (Gromacs 2020 right
now), and also look at critical science errors for the previous version
(Gromacs 2019), but won't spend time on even older stuff - so start by
repeating any issue with a current version.
Cheers,
Erik
On Fri, Dec 11, 2020 at 8:03 PM Navneet Kumar <navneetcdl at gmail.com> wrote:
> Hello Everyone!
>
>
> I have installed Gromacs 2018.8 on two different workstations. Workstation
> having NVIDIA Quadro RTX 5000 (3072 CUDA Cores) gives better performance
> (approx 350 ns per day for lysozyme) than the NVIDIA Quadro RTX 6000 (4608
> CUDA Cores) (approx 200 ns per day). Please see the log file for the both.
> It seems there are some problems while installation. Please help.
>
> ______________________________________________________________________________________________________________________________________
>
> NVIDIA Quadro RTX 6000,
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS: gmx mdrun, version 2018.8
> Executable: /usr/local/gromacs-2018.8/bin/gmx
> Data prefix: /usr/local/gromacs-2018.8
> Working dir: /home/pglab-6000/Desktop/new
> Command line:
> gmx mdrun -v -deffnm md_0_1
>
> GROMACS version: 2018.8
> 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: disabled
> Tracing support: disabled
> Built on: 2020-12-11 17:22:07
> Built by: root at pglab6000-ThinkStation-P520 [CMAKE]
> Build OS/arch: Linux 5.4.0-54-generic x86_64
> Build CPU vendor: Unknown
> Build CPU brand: Unknown
> Build CPU family: 0 Model: 0 Stepping: 0
> Build CPU features: Unknown
> C compiler: /usr/bin/gcc-7 GNU 7.5.0
> C compiler flags: -mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast
> C++ compiler: /usr/bin/g++-7 GNU 7.5.0
> C++ compiler flags: -mavx512f -mfma -std=c++11 -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
> CUDA compiler: /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
> driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on
> Sun_Jul_28_19:07:16_PDT_2019;Cuda compilation tools, release 10.1, V10.1.243
> 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;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
> CUDA driver: 10.20
> CUDA runtime: 10.10
>
>
> Running on 1 node with total 10 cores, 20 logical cores, 1 compatible GPU
> Hardware detected:
> CPU info:
> Vendor: Intel
> Brand: Intel(R) Xeon(R) W-2155 CPU @ 3.30GHz
> Family: 6 Model: 85 Stepping: 4
> Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh
> cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq
> pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt
> x2apic
> Number of AVX-512 FMA units: 2
> Hardware topology: Basic
> Sockets, cores, and logical processors:
> Socket 0: [ 0 10] [ 1 11] [ 2 12] [ 3 13] [ 4 14] [
> 5 15] [ 6 16] [ 7 17] [ 8 18] [ 9 19]
> GPU info:
> Number of GPUs detected: 1
> #0: NVIDIA Quadro RTX 6000, compute cap.: 7.5, ECC: no, stat:
> compatible
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
> Lindahl
> GROMACS: High performance molecular simulations through multi-level
> parallelism from laptops to supercomputers
> SoftwareX 1 (2015) pp. 19-25
> -------- -------- --- Thank You --- -------- --------
>
> --------------------------------------------------------------------------------------------------------------------
>
> NVIDIA Quadro RTX 5000
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS: gmx mdrun, version 2018.8
> Executable: /usr/local/gromacs-2018.8/bin/gmx
> Data prefix: /usr/local/gromacs-2018.8
> Working dir: /home/pglab-5000/Desktop/Test_Simualtion
> Command line:
> gmx mdrun -v -deffnm md_0_1
>
> GROMACS version: 2018.8
> 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: disabled
> Tracing support: disabled
> Built on: 2020-12-09 23:44:03
> Built by: root at pglab5000-ThinkStation-P520 [CMAKE]
> Build OS/arch: Linux 5.4.0-42-generic x86_64
> Build CPU vendor: Unknown
> Build CPU brand: Unknown
> Build CPU family: 0 Model: 0 Stepping: 0
> Build CPU features: Unknown
> C compiler: /usr/bin/gcc-8 GNU 8.4.0
> C compiler flags: -mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops
> -fexcess-precision=fast
> C++ compiler: /usr/bin/c++ GNU 9.3.0
> C++ compiler flags: -mavx512f -mfma -std=c++11 -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast
> CUDA compiler: /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
> driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on
> Sun_Jul_28_19:07:16_PDT_2019;Cuda compilation tools, release 10.1, V10.1.243
> 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;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
> CUDA driver: 11.10
> CUDA runtime: 10.10
>
>
> Running on 1 node with total 10 cores, 20 logical cores, 1 compatible GPU
> Hardware detected:
> CPU info:
> Vendor: Intel
> Brand: Intel(R) Xeon(R) W-2155 CPU @ 3.30GHz
> Family: 6 Model: 85 Stepping: 4
> Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh
> cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq
> pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt
> x2apic
> Number of AVX-512 FMA units: 2
> Hardware topology: Basic
> Sockets, cores, and logical processors:
> Socket 0: [ 0 10] [ 1 11] [ 2 12] [ 3 13] [ 4 14] [
> 5 15] [ 6 16] [ 7 17] [ 8 18] [ 9 19]
> GPU info:
> Number of GPUs detected: 1
> #0: NVIDIA Quadro RTX 5000, compute cap.: 7.5, ECC: no, stat:
> compatible
>
>
> _____________________________________________________________________________________________________________________________________________________
>
> --
>
>
>
>
>
>
> Thanks & Regards
> _______________________________________________________
>
> [image: photo]
> *NAVNEET KUMAR*
>
> Doctoral Student
> Dept. of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research, Sector 67,
> S.A.S. Nagar - 160062, Punjab (INDIA)
> P +918017967647 <+918017967647> |
> E navneetcdl at gmail.com <navneetcdl at gmail.com>
>
> <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
>
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>
>
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--
Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
University
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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