[gmx-users] SEGMENTATION FAULT (Core dumped)
Luca Banetta
luca.banetta at gmail.com
Tue Jun 28 08:57:51 CEST 2016
I try to launch the simulation with the line you wrote me Justin, but
unfortunately this fatal error appears:
Setting the total number of threads is only supported with thread-MPI
and Gromacs was compiled without thread-MPI
I worked on a HPC that is managed by another department in my
university, What do we have to say to them in order to compile gromacs
in the right way?
2016-06-27 16:35 GMT+02:00 Luca Banetta <luca.banetta at gmail.com>:
> Dear gromacs users,
> I currently work on a project about a polarizable model of acetone molecule.
> Unfortunately the simulations work using only 1 MPI thread. When we
> attempt to parallelize it this error appears:
> [compute-0-4:21947] *** Process received signal ***
> [compute-0-4:21947] Signal: Segmentation fault (11)
> [compute-0-4:21947] Signal code: Address not mapped (1)
> [compute-0-4:21947] Failing at address: (nil)
> [compute-0-4:21947] [ 0] /lib64/libpthread.so.0() [0x342720f500]
> [compute-0-4:21947] [ 1]
> /share/apps/gromacs-4.6.5/bin/../lib/libgmx_mpi.so.8(put_charge_groups_in_box+0x107)
> [0x2ab92aaefe87]
> [compute-0-4:21947] [ 2]
> /share/apps/gromacs-4.6.5/bin/../lib/libmd_mpi.so.8(relax_shell_flexcon+0x358f)
> [0x2ab92a593c9f]
> [compute-0-4:21947] [ 3] mdrun_mpi(do_md+0x3003) [0x42cfc3]
> [compute-0-4:21947] [ 4] mdrun_mpi(mdrunner+0x1442) [0x410ac2]
> [compute-0-4:21947] [ 5] mdrun_mpi(cmain+0x183e) [0x435dae]
> [compute-0-4:21947] [ 6] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3426a1ecdd]
> [compute-0-4:21947] [ 7] mdrun_mpi() [0x407139]
> [compute-0-4:21947] *** End of error message ***
>
>
> Someone have ever met something like this before? How this problem can be fixed?
>
> The mdp file used is :
> ;
> ; File 'mdout.mdp' was generated
> ; By user: spoel (291)
> ; On host: chagall
> ; At date: Mon Dec 15 13:52:23 2003
> ;
>
> ; VARIOUS PREPROCESSING OPTIONS
> title = Yo
> cpp = /usr/bin/cpp
> include =
> define =
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.0001
> nsteps = 1000000
> ; For exact run continuation or redoing part of a run
> init_step = 0
> ; mode for center of mass motion removal
> comm-mode = Linear
> ; number of steps for center of mass motion removal
> nstcomm = 1
> ; group(s) for center of mass motion removal
> comm-grps =
>
> ; LANGEVIN DYNAMICS OPTIONS
> ; Temperature, friction coefficient (amu/ps) and random seed
> ;ref-t = 100
> bd-fric = 0
> ld-seed = 1993
>
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol = 100
> emstep = 0.01
> ; Max number of iterations in relax_shells
> niter = 5
> ; Step size (1/ps^2) for minimization of flexible constraints
> fcstep = 5
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep = 1000
> nbfgscorr = 10
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout =
> nstvout =
> nstfout =
> ; Checkpointing helps you continue after crashes
> nstcheckpoint = 1000
> ; Output frequency for energies to log file and energy file
> nstlog = 50
> nstenergy = 50
> ; Output frequency and precision for xtc file
> nstxtcout = 1
> xtc-precision = 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps =
> ; Selection of energy groups
> energygrps =
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 20
> cutoff-scheme = Verlet
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc = xyz
> ; nblist cut-off
> rlist = 0.9
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 0.9
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw-switch = 0
> rvdw = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension = 1
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = Still
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 2
> ; Salt concentration in M for Generalized Born models
> gb_saltconc = 0
>
> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> implicit_solvent = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl = v-rescale
> ; Groups to couple separately
> tc-grps = System
> ; Time constant (ps) and reference temperature (K)
> tau_t = 0.1
> ref_t = 300
> ; Pressure coupling
> Pcoupl = berendsen
> Pcoupltype = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Random seed for Andersen thermostat
> andersen_seed = 815131
>
> ; SIMULATED ANNEALING
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing = no
> ; Number of time points to use for specifying annealing in each group
> annealing_npoints =
> ; List of times at the annealing points for each group
> annealing_time =
> ; Temp. at each annealing point, for each group.
> annealing_temp =
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = yes
> gen_temp = 300
> gen_seed = 1993
>
> ; OPTIONS FOR BONDS
> constraints = h-bonds
> ; Type of constraint algorithm
> constraint-algorithm = Lincs
> ; Do not constrain the start configuration
> unconstrained-start = no
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR = no
> ; Relative tolerance of shake
> shake-tol = 1e-04
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 4
> ; Number of iterations in the final step of LINCS. 1 is fine for
> ; normal simulations, but use 2 to conserve energy in NVE runs.
> ; For energy minimization with constraints it should be 4 to 8.
> lincs-iter = 1
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle = 30
> ; Convert harmonic bonds to morse potentials
> morse = no
>
> ; ENERGY GROUP EXCLUSIONS
> ; Pairs of energy groups for which all non-bonded interactions are excluded
> energygrp_excl =
>
> ; NMR refinement stuff
> ; Distance restraints type: No, Simple or Ensemble
> disre = No
> ; Force weighting of pairs in one distance restraint: Conservative or Equal
> disre-weighting = Conservative
> ; Use sqrt of the time averaged times the instantaneous violation
> disre-mixed = no
> disre-fc = 1000
> disre-tau = 0
> ; Output frequency for pair distances to energy file
> nstdisreout = 100
> ; Orientation restraints: No or Yes
> orire = no
> ; Orientation restraints force constant and tau for time averaging
> orire-fc = 0
> orire-tau = 0
> orire-fitgrp =
> ; Output frequency for trace(SD) to energy file
> nstorireout = 100
> ; Dihedral angle restraints: No, Simple or Ensemble
> dihre = No
> dihre-fc = 1000
> dihre-tau = 0
> ; Output frequency for dihedral values to energy file
> nstdihreout = 100
>
> ; Free energy control stuff
> free-energy = no
> init-lambda = 0
> delta-lambda = 0
> sc-alpha = 0
> sc-sigma = 0.3
>
> ; Non-equilibrium MD stuff
> acc-grps =
> accelerate =
> freezegrps =
> freezedim =
> cos-acceleration = 0
>
> ; Electric fields
> ; Format is number of terms (int) and for all terms an amplitude (real)
> ; and a phase angle (real)
> E-x =
> E-xt =
> E-y =
> E-yt =
> E-z =
> E-zt =
>
> ; User defined thingies
> user1-grps =
> user2-grps =
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
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