# Gromacs Drude **URL:** \ **Category:** User discussions\ **Created:** [December 2, 2020, 8:06am UTC](https://gromacs.bioexcel.eu/t/gromacs-drude/1180 "2020-12-02T08:06:04Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![bellafrizzo](https://avatars.discourse-cdn.com/v4/letter/b/b487fb/32.png) [@bellafrizzo](https://gromacs.bioexcel.eu/u/bellafrizzo)\ **Post date:** [December 2, 2020, 8:06am UTC](https://gromacs.bioexcel.eu/t/gromacs-drude/1180/1 "2020-12-02T08:06:04Z")
Hello there, I’m increasing the size of my system to exploit muticore performances as for my initial simulation I could only use one core. However, I have the usual segmentation fault during energy minimization. Here the .log file Log file opened on Wed Dec 2 09:00:03 2020 Host: b-an01.hpc2n.umu.se pid: 733089 rank ID: 0 number of ranks: 1 :-) GROMACS - gmx mdrun, 2016-dev (-: ``` GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar ``` Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright © 1991-2000, University of Groningen, The Netherlands. Copyright © 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2016-dev Executable: /hpc2n/eb/software/MPI/GCC/6.4.0-2.28/impi/2017.3.196/GROMACS/2016.x-drude-20180214-g3f7439a/bin/gmx Data prefix: /hpc2n/eb/software/MPI/GCC/6.4.0-2.28/impi/2017.3.196/GROMACS/2016.x-drude-20180214-g3f7439a Command line: gmx mdrun -deffnm em -v GROMACS version: 2016-dev Precision: single Memory model: 64 bit MPI library: thread\_mpi OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 32) GPU support: disabled SIMD instructions: AVX2\_256 FFT library: fftw-3.3.6-pl2-fma-sse2-avx-avx2-avx2\_128 RDTSCP usage: enabled TNG support: enabled Tracing support: disabled Built on: Thu Sep 19 18:47:11 UTC 2019 Built by: easybuild@b-cn0823.hpc2n.umu.se [CMAKE] Build OS/arch: Linux 4.15.0-62-generic x86\_64 Build CPU vendor: Intel Build CPU brand: Intel® Xeon® CPU E5-2690 v4 @ 2.60GHz Build CPU family: 6 Model: 79 Stepping: 1 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt lahf mmx msr nonstop\_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /hpc2n/eb/software/Compiler/GCC/6.4.0-2.28/impi/2017.3.196/bin64/mpicc GNU 6.4.0 C compiler flags: -march=core-avx2 -O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -mt\_mpi -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds C++ compiler: /hpc2n/eb/software/Compiler/GCC/6.4.0-2.28/impi/2017.3.196/bin64/mpicxx GNU 6.4.0 C++ compiler flags: -march=core-avx2 -O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -mt\_mpi -std=c++0x -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds Running on 1 node with total 28 cores, 28 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel® Xeon® CPU E5-2690 v4 @ 2.60GHz Family: 6 Model: 79 Stepping: 1 Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma hle htt lahf mmx msr nonstop\_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic SIMD instructions most likely to fit this hardware: AVX2\_256 SIMD instructions selected at GROMACS compile time: AVX2\_256 ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers SoftwareX 1 (2015) pp. 19-25 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 (2013) pp. 845-54 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 -------- -------- — Thank You — -------- -------- ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 -------- -------- — Thank You — -------- -------- Changing rlist from 1.26 to 1.2 for non-bonded 4x4 atom kernels Input Parameters: integrator = steep tinit = 0 dt = 0.001 nsteps = -1 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 3073646060 emtol = 1000 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 1 nstvout = 0 nstfout = 0 nstlog = 100 nstcalcenergy = 1 nstenergy = 1 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 10 ns-type = Grid pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.2 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Potential-switch rvdw-switch = 1 rvdw = 1.2 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.12 fourier-nx = 192 fourier-ny = 192 fourier-nz = 192 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 = No nsttcouple = -1 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p (3x3): ref-p[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = false QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = false Shake-SOR = false shake-tol = 0.0001 lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = false rotation = false interactiveMD = false disre = No disre-weighting = Conservative disre-mixed = false dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 0 deform (3x3): deform[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} simulated-tempering = false E-x: n = 0 E-xt: n = 0 E-y: n = 0 E-yt: n = 0 E-z: n = 0 E-zt: n = 0 swapcoords = no drude = true drudemode = scf drude-t = 1 drude-hardwall = false drude-r = 0.02 drude-hyper = false drude-khyp = 1.6736e+07 drude-hyp-power = 4 nbtholecut = 0 drude-tsteps = 20 userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 2.607e+06 ref-t: 0 tau-t: 0 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[0]: 0 Initializing Domain Decomposition on 28 ranks Dynamic load balancing: off Initial maximum inter charge-group distances: two-body bonded interactions: 0.412 nm, LJ-14, atoms 89570 89582 multi-body bonded interactions: 0.412 nm, Proper Dih., atoms 89570 89582 Minimum cell size due to bonded interactions: 0.453 nm Guess for relative PME load: 0.09 Will use 24 particle-particle and 4 PME only ranks This is a guess, check the performance at the end of the log file Using 4 separate PME ranks, as guessed by mdrun Optimizing the DD grid for 24 cells with a minimum initial size of 0.453 nm The maximum allowed number of cells is: X 44 Y 44 Z 44 Domain decomposition grid 4 x 3 x 2, separate PME ranks 4 PME domain decomposition: 4 x 1 x 1 Interleaving PP and PME ranks This rank does only particle-particle work. Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 1 Y 1 Z 1 The initial domain decomposition cell size is: X 5.06 nm Y 6.75 nm Z 10.13 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 1.200 nm multi-body bonded interactions (-rdd) 1.200 nm Using 28 MPI threads Using 1 OpenMP thread per tMPI thread Will do PME sum in reciprocal space for electrostatic interactions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- — Thank You — -------- -------- Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Cut-off’s: NS: 1.2 Coulomb: 1.2 LJ: 1.2 Long Range LJ corr.: 2.9276e-04 System total charge: -0.034 Generated table with 1100 data points for Ewald. Tabscale = 500 points/nm Generated table with 1100 data points for LJ6Switch. Tabscale = 500 points/nm Generated table with 1100 data points for LJ12Switch. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1100 data points for 1-4 LJ12. Tabscale = 500 points/nm Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00, Ewald -1.000e-05 Initialized non-bonded Ewald correction tables, spacing: 1.02e-03 size: 1176 Using SIMD 4x8 non-bonded kernels Removing pbc first time Pinning threads with an auto-selected logical core stride of 1 Linking all bonded interactions to atoms There are 276500 shells in the system, will do an extra communication step for selected coordinates and forces Initiating Steepest Descents Atom distribution over 24 domains: av 47729 stddev 188 min 47472 max 48018 Started Steepest Descents on rank 0 Wed Dec 2 09:00:07 2020 Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = -1 Step Time 0 0.00000 Energies (kJ/mol) Bond U-B Proper Dih. LJ-14 Coulomb-14 2.69888e+05 1.89001e+06 7.80833e+05 8.45283e+04 -3.65185e+06 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Drude Bond -1.45270e+06 -8.49501e+04 5.42092e+05 1.32971e+04 2.14485e+09 Aniso. Polariz. Thole Pol. Potential Pres. DC (bar) Pressure (bar) 0.00000e+00 -3.11925e+04 2.14321e+09 0.00000e+00 -2.66510e+02 DD step 0 load imb.: force 3.9% pme mesh/force 0.937 ``` Step Time 1 1.00000 ``` Energies (kJ/mol) Bond U-B Proper Dih. LJ-14 Coulomb-14 2.70014e+05 1.88976e+06 7.80830e+05 8.45242e+04 -3.65202e+06 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Drude Bond -1.45270e+06 -8.49501e+04 5.42039e+05 1.33733e+04 2.14062e+09 Aniso. Polariz. Thole Pol. Potential Pres. DC (bar) Pressure (bar) 0.00000e+00 -3.12481e+04 2.13898e+09 0.00000e+00 -2.66510e+02 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [December 2, 2020, 11:12am UTC](https://gromacs.bioexcel.eu/t/gromacs-drude/1180/2 "2020-12-02T11:12:21Z")
The Drude implementation does not currently support domain decomposition, only OpenMP parallelization and single-domain GPU. The DD code relevant to Drude is being rewritten.