[gmx-users] About Plumed+Gromacs+MPI

[Justin Lemkul]

On 12/1/18 10:13 PM, yong zhou wrote:
> Dear all,
>
> I have compiled the plumed+gromacs with the following options
>
> CC=/usr/lib64/openmpi3/bin/mpicc FC=/usr/lib64/openmpi3/bin/mpif90 F77=/usr/lib64/openmpi3/bin/mpif90 CXX=/usr/lib64/openmpi3/bin/mpicxx CMAKE_PREFIX_PATH=//usr/lib64/openmpi3/ cmake3 .. -DGMX_BUILD_OWN_FFTW=on -DGMX_MPI=on -DCMAKE_C_COMPILER=/usr/lib64/openmpi3/bin/mpicc -DCMAKE_CXX_COMPILER=/usr/lib64/openmpi3/bin/mpicxx -DGMX_GPU=on -DNVML_INCLUDE_DIR=/usr/local/cuda-9.0/include -DNVML_LIBRARY=/usr/lib64/libnvidia-ml.so -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/home/yzhou/xtal/gromacs
>
> But with running the tutorial of Plumed, I got the following errors.
>
>                      :-) GROMACS - gmx mdrun, 2016.5 (-:
>
>                              GROMACS is written by:
>       Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar
>   Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof
>   Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
>      Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson
>    Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff    Erik Marklund
>     Teemu Murtola       Szilard Pall       Sander Pronk      Roland Schulz
>    Alexey Shvetsov     Michael Shirts     Alfons Sijbers     Peter Tieleman
>    Teemu Virolainen  Christian Wennberg    Maarten Wolf
>                             and the project leaders:
>          Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2017, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> 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 2016.5
> Executable:   /home/yzhou/xtal/gromacs/bin/gmx_mpi
> Data prefix:  /home/yzhou/xtal/gromacs
> Working dir:  /home/yzhou/data/simulation/plumed/belfast-8/second
> Command line:
>    gmx_mpi mdrun -s topol -plumed plumed -multi 2 -replex 20
>
>
> Back Off! I just backed up md1.log to ./#md1.log.18#
>
> Back Off! I just backed up md0.log to ./#md0.log.18#
>
> Running on 1 node with total 10 cores, 10 logical cores, 1 compatible GPU
> Hardware detected on host localhost.localdomain (the node of MPI rank 0):
>    CPU info:
>      Vendor: Intel
>      Brand:  Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
>      SIMD instructions most likely to fit this hardware: AVX2_256
>      SIMD instructions selected at GROMACS compile time: AVX2_256
>
>    Hardware topology: Basic
>    GPU info:
>      Number of GPUs detected: 1
>      #0: NVIDIA GeForce GTX 1080 Ti, compute cap.: 6.1, ECC:  no, stat: compatible
>
> Reading file topol1.tpr, VERSION 4.6.5 (single precision)
> Reading file topol0.tpr, VERSION 4.6.5 (single precision)
> Note: file tpx version 83, software tpx version 110
> Note: file tpx version 83, software tpx version 110
> This is simulation 1 out of 2 running as a composite GROMACS
> multi-simulation job. Setup for this simulation:
>
> Using 1 MPI process
> Using 5 OpenMP threads
>
> This is simulation 0 out of 2 running as a composite GROMACS
> multi-simulation job. Setup for this simulation:
>
> Using 1 MPI process
> Using 5 OpenMP threads
>
> 1 compatible GPU is present, with ID 0
> 1 GPU auto-selected for this run.
> Mapping of GPU ID to the 2 PP ranks in this node: 0,0
>
> 1 compatible GPU is present, with ID 0
> 1 GPU auto-selected for this run.
> Mapping of GPU ID to the 2 PP ranks in this node: 0,0
>
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2016.5
> Source file: src/programs/mdrun/runner.cpp (line 677)
> Function:    double (* gmx::my_integrator(unsigned int))(FILE*, t_commrec*, int, const t_filenm*, const gmx_output_env_t*, gmx_bool, int, gmx_vsite_t*, gmx_constr_t, int, t_inputrec*, gmx_mtop_t*, t_fcdata*, t_state*, t_mdatoms*, t_nrnb*, gmx_wallcycle_t, gmx_edsam_t, t_forcerec*, int, int, int, gmx_membed_t*, real, real, int, long unsigned int, gmx_walltime_accounting_t)
> MPI rank:    1 (out of 2)
>
> Feature not implemented:
>
> -------------------------------------------------------
> Program:     gmx mdrun, version 2016.5
> Source file: src/programs/mdrun/runner.cpp (line 677)
> Function:    double (* gmx::my_integrator(unsigned int))(FILE*, t_commrec*, int, const t_filenm*, const gmx_output_env_t*, gmx_bool, int, gmx_vsite_t*, gmx_constr_t, int, t_inputrec*, gmx_mtop_t*, t_fcdata*, t_state*, t_mdatoms*, t_nrnb*, gmx_wallcycle_t, gmx_edsam_t, t_forcerec*, int, int, int, gmx_membed_t*, real, real, int, long unsigned int, gmx_walltime_accounting_t)
> MPI rank:    0 (out of 2)
>
> Feature not implemented:
> SD2 integrator has been removed
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> SD2 integrator has been removed
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
> Would you please tell me what is wrong with the process and how to solve the problem?

The error message is quite clear:

Feature not implemented:
SD2 integrator has been removed

Tutorials do not always keep up with development, so you cannot necessarily use any tutorial you find with any version of GROMACS. Use whatever version they suggest, or simply use an integrator that is supported by your chosen version of GROMACS (see the online manual for what those options are).

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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