Hi everyone, I have the following problem
Program: gmx mdrun, version 2016.4
Source file: src/gromacs/domdec/domdec.cpp (line 6542)
MPI rank: 0 (out of 64)
Fatal error:
There is no domain decomposition for 48 ranks that is compatible with the
given box and a minimum cell size of 1.75 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
…Log file
gmx mdrun -s /home/tmp1/lourival/infinita/cht/md-nanocht.tpr -deffnm md-nanocht -rdd 1.4
GROMACS version: 2016.4
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support: disabled
SIMD instructions: AVX_128_FMA
FFT library: fftw-3.2.1
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
Built on: Sat Sep 1 20:37:21 BRT 2018
Built by: [CMAKE]
Build OS/arch: Linux 2.6.32-279.14.1.el6.x86_64 x86_64
Build CPU vendor: AMD
Build CPU brand: AMD Opteron™ Processor 6212
Build CPU family: 21 Model: 1 Stepping: 2
Build CPU features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop
C compiler: /share/opt/gcc/4.7.3/bin/cc GNU 4.7.3
C compiler flags: -mavx -mfma4 -mxop -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler: /share/opt/gcc/4.7.3/bin/c++ GNU 4.7.3
C++ compiler flags: -mavx -mfma4 -mxop -std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
Running on 1 node with total 64 cores, 64 logical cores
Hardware detected:
CPU info:
Vendor: AMD
Brand: AMD Opteron™ Processor 6274
Family: 21 Model: 1 Stepping: 2
Features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop
SIMD instructions most likely to fit this hardware: AVX_128_FMA
SIMD instructions selected at GROMACS compile time: AVX_128_FMA
Hardware topology: Basic
Sockets, cores, and logical processors:
Socket 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] [ 14] [ 15]
Socket 1: [ 16] [ 17] [ 18] [ 19] [ 20] [ 21] [ 22] [ 23] [ 24] [ 25] [ 26] [ 27] [ 28] [ 29] [ 30] [ 31]
Socket 2: [ 32] [ 33] [ 34] [ 35] [ 36] [ 37] [ 38] [ 39] [ 40] [ 41] [ 42] [ 43] [ 44] [ 45] [ 46] [ 47]
Socket 3: [ 48] [ 49] [ 50] [ 51] [ 52] [ 53] [ 54] [ 55] [ 56] [ 57] [ 58] [ 59] [ 60] [ 61] [ 62] [ 63]
Can not increase nstlist because verlet-buffer-tolerance is not set or used
Input Parameters:
integrator = md
tinit = 0
dt = 0.001
nsteps = 50000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = -1732820134
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstcalcenergy = 100
nstenergy = 5000
nstxout-compressed = 5000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 10
ns-type = Grid
pbc = xyz
periodic-molecules = true
verlet-buffer-tolerance = -1
rlist = 0.7
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 0.7
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 0.7
DispCorr = No
table-extension = 1
fourierspacing = 0.16
fourier-nx = 20
fourier-ny = 24
fourier-nz = 36
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 0
epsilon-surface = 0
implicit-solvent = No
gb-algorithm = Still
nstgbradii = 1
rgbradii = 1
gb-epsilon-solvent = 80
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
tcoupl = V-rescale
nsttcouple = 10
nh-chain-length = 0
print-nose-hoover-chain-variables = false
pcoupl = Berendsen
pcoupltype = Semiisotropic
nstpcouple = 10
tau-p = 1
Program: gmx mdrun, version 2016.4
Source file: src/gromacs/domdec/domdec.cpp (line 6542)
MPI rank: 0 (out of 64)
Fatal error:
There is no domain decomposition for 48 ranks that is compatible with the
given box and a minimum cell size of 1.75 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
Has anyone had any similar experience and could help me?