# Issue with segmentation fault **URL:** \ **Category:** User discussions\ **Tags:** mdrun-crash\ **Created:** [February 15, 2022, 6:10am UTC](https://gromacs.bioexcel.eu/t/issue-with-segmentation-fault/3669 "2022-02-15T06:10:10Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![Vidya](https://avatars.discourse-cdn.com/v4/letter/v/58f4c7/32.png) [@Vidya](https://gromacs.bioexcel.eu/u/Vidya)\ **Post date:** [February 15, 2022, 6:10am UTC](https://gromacs.bioexcel.eu/t/issue-with-segmentation-fault/3669/1 "2022-02-15T06:10:11Z")
GROMACS version: 2021.2, 2019.6 GROMACS modification: Yes Here post your question I am facing a segmentation fault issue with GROMACS patched with plumed and I was wondering if you could help me. I am trying to run a replica averaged MD simulation by calculating the backbone chemical shifts for a protein (using [PLUMED: CS2BACKBONE](https://www.plumed.org/doc-v2.6/user-doc/html/_c_s2_b_a_c_k_b_o_n_e.html)). I have tried this with gromacs-2021.2 patched with plumed-2.7.3 to end with the segmentation fault. I did follow through a couple of discussions that have dealt with similar issues and according to [HREX bug patched with Gromacs-2020.2 · Issue #605 · plumed/plumed2 · GitHub](https://github.com/plumed/plumed2/issues/605), I have tried to run the multi simulations with gromacs-2019.6 patched with plumed-2.6.3 as well. However, the segmentation fault occurs with both the versions of gromacs and plumed (with and without the use of GPU). Please note that the multi simulations run fine when the plumed instructions are not supplied, which if I am not wrong could mean that my system is not blowing up. The command used and error message are as follows mpiexec -np 4 gmx\_mpi mdrun -v -deffnm md -plumed plumed -multidir a b c d (I have also tried mpiexec -np 16 gmx\_mpi mdrun -v -deffnm md -multidir a b c d -plumed plumed) Reading file md.tpr, VERSION 2019.6 (single precision) Reading file md.tpr, VERSION 2019.6 (single precision) Reading file md.tpr, VERSION 2019.6 (single precision) Reading file md.tpr, VERSION 2019.6 (single precision) Changing nstlist from 5 to 80, rlist from 1 to 1.151 This is simulation 3 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Using 8 OpenMP threads Changing nstlist from 5 to 80, rlist from 1 to 1.151 This is simulation 0 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Using 8 OpenMP threads Changing nstlist from 5 to 80, rlist from 1 to 1.151 This is simulation 2 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Using 8 OpenMP threads Changing nstlist from 5 to 80, rlist from 1 to 1.151 This is simulation 1 out of 4 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Using 8 OpenMP threads 1 GPU selected for this run. Mapping of GPU IDs to the 8 GPU tasks in the 4 ranks on this node: PP:0,PME:0,PP:0,PME:0,PP:0,PME:0,PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PME tasks will do all aspects on the GPU 1 GPU selected for this run. Mapping of GPU IDs to the 8 GPU tasks in the 4 ranks on this node: PP:0,PME:0,PP:0,PME:0,PP:0,PME:0,PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PME tasks will do all aspects on the GPU 1 GPU selected for this run. Mapping of GPU IDs to the 8 GPU tasks in the 4 ranks on this node: PP:0,PME:0,PP:0,PME:0,PP:0,PME:0,PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PME tasks will do all aspects on the GPU 1 GPU selected for this run. Mapping of GPU IDs to the 8 GPU tasks in the 4 ranks on this node: PP:0,PME:0,PP:0,PME:0,PP:0,PME:0,PP:0,PME:0 PP tasks will do (non-perturbed) short-ranged interactions on the GPU PME tasks will do all aspects on the GPU ## starting mdrun ‘Protein in water’ 500000 steps, 1000.0 ps. starting mdrun ‘Protein in water’ 500000 steps, 1000.0 ps. starting mdrun ‘Protein in water’ 500000 steps, 1000.0 ps. starting mdrun ‘Protein in water’ 500000 steps, 1000.0 ps. ## Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. * * * ## mpiexec noticed that process rank 3 with PID 0 on node exited on signal 11 (Segmentation fault). The mdp options used are ; Run parameters integrator = md ; leap-frog integrator nsteps = 500000 ; 0.002 \* 500000 = 1000 ps (1 ns) dt = 0.002 ; 2 fs comm\_mode = Linear ; remove center of mass translation nstcomm = 1 ; [steps] frequency of mass motion removal comm\_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps ; energygrps = Protein Non-Protein ; Bond parameters continuation = no ; first dynamics run constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs\_iter = 2 ; accuracy of LINCS lincs\_order = 6 ; also related to accuracy ; Neighborsearching ns\_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics coulomb-modifier = Potential-shift-Verlet vdw-type = Cut-off vdw-modifier = Potential-shift-Verlet pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = nose-hoover ; modified Berendsen thermostat nsttcouple = -1 nh-chain-length = 1 tc-grps = Protein Non-protein ; two coupling groups - more accurate tau\_t = 0.5 0.5 ; time constant, in ps ref\_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau\_p = 2.0 ; time constant, in ps ref\_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen\_vel = yes ; assign velocities from Maxwell distribution gen\_temp=300 gen\_seed= -1 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing = periodic periodic ; Number of time points to use for specifying annealing in each group annealing\_npoints = 5 5 ; List of times at the annealing points for each group annealing\_time = 0 100 200 300 600 0 100 200 300 600 ; Temp. at each annealing point, for each group. annealing\_temp = 300 300 454 454 300 300 300 454 454 300 Kindly help in resolving the issue. Thanks and best regards, Vidya