[gmx-users] grompp not possible with annealing - Gromacs 2019.1

Tue Sep 10 17:14:52 CEST 2019

Dear all,

I try to use simulation annealing, but unfortunately the grompp - command leads to an error.
It is not a known Gromacs error, but it doesn't finish the job and it says: Speicherzugriffsfehler (Speicherabzug geschrieben) (which means something like "Memory Access Error")

The only output file produced is the mdout.mdp, which content seems correct.

The screen text is given below as well as the grompp.mdp content and the details to the system used.

There have been some issues as well to get Gromacs installed on the workstation. Not sure if this could be connected.
Many thanks already for your help.

Greetings,
Steffi

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Screen text:

GROMACS:      gmx grompp, version 2019.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/pcm-mess/Schreibtisch/StTa/Vergleich_FF/OPLS/fixed_layer/freeze_grp/temp_grps/annealing
Command line:
  gmx grompp -f grompp_OPLS_anneal.mdp -v

checking input for internal consistency...
Setting the LD random seed to -28800458
processing topology...
Generated 330891 of the 330891 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 330891 of the 330891 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Other'
turning all bonds into constraints...

NOTE 1 [file unknown]:
  You are using constraints on all bonds, whereas the forcefield has been
  parametrized only with constraints involving hydrogen atoms. We suggest
  using constraints = h-bonds instead, this will also improve performance.

processing coordinates...
double-checking input for internal consistency...
Setting gen_seed to -1070611718
Velocities were taken from a Maxwell distribution at 280 K
Removing all charge groups because cutoff-scheme=Verlet
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
There are:  3600      Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Speicherzugriffsfehler (Speicherabzug geschrieben)
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Content grompp.mdp (as an example):

include                  = -I../top
define                   =
cutoff-scheme            = Verlet
integrator               = md
dt                       = 0.001
nsteps                   = 800000
nstxout                  = 2000
nstvout                  = 2000
nstlog                   = 2000
nstenergy                = 2000
nstlist                  = 10
ns-type                  = grid
pbc                      = xyz
rlist                    = 1
coulombtype              = PME
rcoulomb                 = 1
rvdw                     = 1
tcoupl                   = v-rescale
tc-grps                 = other
tau-t                    = 0.1
ref-t                    = 280
Pcoupl                   = Berendsen
pcoupltype               = anisotropic
tau-p                    = 10
compressibility          = 8.7e-5 8.7e-5 8.7e-5 0 0 0
ref-p                    = 1.0 1.0 1.0 0 0 0
constraints              = all-bonds
gen-vel                  = yes
gen-temp                 = 280
gen-seed                 = -1
annealing               = single
annealing-npoints       = 2
annealing-time           = 0 60
annealing-temp          = 280 280
------------------------------------------------------------------------------------------------

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System details:

GROMACS version:    2019.1
Precision:          single
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support:        CUDA
SIMD instructions:  AVX_512
FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 8.2.0
C compiler flags:    -mavx512f -mfma     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler:       /usr/bin/c++ GNU 8.2.0
C++ compiler flags:  -mavx512f -mfma    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
CUDA compiler:      /usr/local/cuda-10.1/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on Fri_Feb__8_19:08:17_PST_2019;Cuda compilation tools, release 10.1, V10.1.105
CUDA compiler flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;; ;-mavx512f;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
CUDA driver:        10.10
CUDA runtime:       10.10

Running on 1 node with total 44 cores, 88 logical cores, 1 compatible GPU
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Xeon(R) Gold 6152 CPU @ 2.10GHz
    Family: 6   Model: 85   Stepping: 4
    Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
    Number of AVX-512 FMA units: 2
  Hardware topology: Basic
    Sockets, cores, and logical processors:
      Socket  0: [   0  44] [   1  45] [   2  46] [   3  47] [   4  48] [   5  49] [   6  50] [   7  51] [   8  52] [   9  53] [  10  54] [  11  55] [  12  56] [  13  57] [  14  58] [  15  59] [  16  60] [  17  61] [  18  62] [  19  63] [  20  64] [  21  65]
      Socket  1: [  22  66] [  23  67] [  24  68] [  25  69] [  26  70] [  27  71] [  28  72] [  29  73] [  30  74] [  31  75] [  32  76] [  33  77] [  34  78] [  35  79] [  36  80] [  37  81] [  38  82] [  39  83] [  40  84] [  41  85] [  42  86] [  43  87]
  GPU info:
    Number of GPUs detected: 1
    #0: NVIDIA Quadro P6000, compute cap.: 6.1, ECC:  no, stat: compatible
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