[gmx-users] About Plumed+Gromacs+MPI

Sun Dec 2 04:13:37 CET 2018

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

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?
Thanks a lot.

Best regards

Zhou Yong