[gmx-users] About Plumed+Gromacs+MPI

[yong zhou]

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. BerendsenPar Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof
 Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios Karkoulis
Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
   Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
  Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
  Teemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

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check out http://www.gromacs.org for more information.

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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)

[gmx-users] (no subject)

[Soham Sarkar]

Dear all,
This is the error I get while executing the grompp command
 " Program grompp, VERSION 4.5.6
Source code file: topio.c, line: 582
Fatal error:
Syntax error - File tris.itp, line 19
Last line read:
' #error CORRECT VERSION OF FORCE FIELD [TPPREV_jun16] WAS NOT "
I gave the command like:
" grompp -f ions.mdp -c solv.gro -o ions.tpr -p system.top
 "
I am attaching the input files. I have generated the tris.itp from tppmktop
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