[gmx-developers] support at lists.hpc.sjtu.edu.cn

[Yorquant Wang]

Dear All,

I recently met a error:"Software inconsistency error: pme_loadbal_do called
at an interval != nstlist" when I try to restart one of jobs.
I used GMX 5.1.2  on K80 GPU nodes with haswell CPU.

Is there anyone know how to solve this error?
Thank you very much!

cheer​s
Yukun Wang

below is the output log files:

                   :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

                            GROMACS is written by:
     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian Fritsch
  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) 2001-2015, 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 5.1.2
Executable:   /lustre/usr/gromacs/5.1-icc15-impi5-gpu/bin/gmx_mpi
Data prefix:  /lustre/usr/gromacs/5.1-icc15-impi5-gpu
Command line:
  gmx_mpi mdrun -deffnm 200DPPC-16-WT_COO-_150mV_2 -append -cpi -v
-resethway -noconfout

No previous checkpoint file present, assuming this is a new run.

Number of logical cores detected (16) does not match the number reported by
OpenMP (8).
Consider setting the launch configuration manually!

Running on 1 node with total 16 cores, 16 logical cores, 2 compatible GPUs
Hardware detected on host gpu35 (the node of MPI rank 0):
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
    SIMD instructions most likely to fit this hardware: AVX_256
    SIMD instructions selected at GROMACS compile time: AVX_256
  GPU info:
    Number of GPUs detected: 2
    #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
    #1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible

Reading file 200DPPC-16-WT_COO-_150mV_2.tpr, VERSION 5.0.4 (single
precision)
Note: file tpx version 100, software tpx version 103
Changing nstlist from 25 to 40, rlist from 1.038 to 1.08

The number of OpenMP threads was set by environment variable
OMP_NUM_THREADS to 8
Using 2 MPI processes
Using 8 OpenMP threads per MPI process

On host gpu35 2 compatible GPUs are present, with IDs 0,1
On host gpu35 2 GPUs auto-selected for this run.
Mapping of GPU IDs to the 2 PP ranks in this node: 0,1


NOTE: GROMACS was configured without NVML support hence it can not exploit
      application clocks of the detected Tesla K20m GPU to improve
performance.
      Recompile with the NVML library (compatible with the driver used) or
set application clocks manually.


Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity

WARNING: This run will generate roughly 38667 Mb of data


NOTE: DLB will not turn on during the first phase of PME tuning

starting mdrun '200dppc_membrane_16Maculatin-WT-COO-'
10000000000 steps, 20000000.0 ps (continuing from step 268830925, 537661.8
ps).

-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/rpm/rpmbuild/BUILD/gromacs-5.1.2/src/gromacs/ewald/pme-load-balancing.cpp,
line: 947

Software inconsistency error:
pme_loadbal_do called at an interval != nstlist
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


-------------------------------------------------------
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/rpm/rpmbuild/BUILD/gromacs-5.1.2/src/gromacs/ewald/pme-load-balancing.cpp,
line: 947

Software inconsistency error:
pme_loadbal_do called at an interval != nstlist
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Halting parallel program gmx mdrun on rank 1 out of 2
Halting parallel program gmx mdrun on rank 0 out of 2
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
srun: error: gpu35: tasks 0-1: Exited with exit code 1​


-- 
Yukun Wang
Postdoc
Institute for NanoBioTechnology at The Johns Hopkins University
Cell phone: +1 (443) 509 2191
Baltimore, MD USA
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