[gmx-users] cudaStreamSynchronize failed
Szilárd Páll
szilard.pall at cbr.su.se
Fri May 10 17:58:16 CEST 2013
Hi,
Such an issue typically indicates a GPU kernel crash. This can be
caused by a large variety of factors from program bug to GPU hardware
problem. To do a simple check for the former please run with the CUDA
memory checker, e.g:
/usr/local/cuda/bin/cuda-memcheck mdrun [...]
Additionally, as your GPU is a consumer card, potentially running
factory-overclocked, there is a chance of it exhibiting memory errors.
To check for this, run a memory testing tool
(http://sourceforge.net/projects/cudagpumemtest is pretty good)
preferably at least for a few hours and to make sure that it's not
some machine overheating problem, I'd also run GROMACS on the CPU only
on 6 threads next to cudamemtest.
Cheers,
--
Szilárd
On Tue, May 7, 2013 at 2:08 PM, Cintia C. Vequi-Suplicy
<cintia at if.usp.br> wrote:
> Hello,
>
> I am running a bilayer simulation with Gromacs4.6.1.
> I have just bought the GPU card and I am doing some tests with a DPPC
> bilayer simulation.
>
> But I am always getting the same error:
> -------------------------------------------------------
> Program mdrun, VERSION 4.6.1
> Source code file:
> /home/cintia/Downloads/gromacs-4.6.1/src/mdlib/nbnxn_cuda/nbnxn_cuda.cu,
> line: 565
>
> Fatal error:
> cudaStreamSynchronize failed in cu_blockwait_nb: unspecified launch failure
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> I saw that someone posted a similar error here before, but I was not able to
> understand the solution for it.
> Can anyone help?
>
> Below is the .log file with the details of the hardware and the system.
>
> Thank you in advance,
> Cíntia
>
>
> Log file opened on Mon May 6 21:19:32 2013
> Host: titan2 pid: 12346 nodeid: 0 nnodes: 1
> Gromacs version: VERSION 4.6.1
> Precision: single
> Memory model: 64 bit
> MPI library: thread_mpi
> OpenMP support: enabled
> GPU support: enabled
> invsqrt routine: gmx_software_invsqrt(x)
> CPU acceleration: SSE4.1
> FFT library: fftw-3.3.2-sse2
> Large file support: enabled
> RDTSCP usage: enabled
> Built on: Sex Mai 3 16:52:44 BRT 2013
> Built by: root at titan2 [CMAKE]
> Build OS/arch: Linux 3.8.0-19-generic x86_64
> Build CPU vendor: GenuineIntel
> Build CPU brand: Intel(R) Core(TM) i7 CPU 870 @ 2.93GHz
> Build CPU family: 6 Model: 30 Stepping: 5
> Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc
> pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
> C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3
> C compiler flags: -msse4.1 -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer
> -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
> C++ compiler: /usr/bin/c++ GNU c++ (Ubuntu/Linaro 4.7.3-1ubuntu1)
> 4.7.3
> C++ compiler flags: -msse4.1 -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer
> -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG
> CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c)
> 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda
> compilation tools, release 5.0, V0.2.1221
> CUDA driver: 5.50
> CUDA runtime: 5.0
>
>
> :-) G R O M A C S (-:
>
> God Rules Over Mankind, Animals, Cosmos and Such
>
> :-) VERSION 4.6.1 (-:
>
> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
> Herman J.C. Berendsen, Aldert van Buuren, PÃĪr Bjelkmar,
> Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans,
> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
> Berk Hess, David van der Spoel, and Erik Lindahl.
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2012,2013, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> This program 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.
>
> :-) mdrun (-:
>
>
> ++++ 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 --- -------- --------
>
> Input Parameters:
> integrator = md
> nsteps = 50000000
> init-step = 0
> cutoff-scheme = Verlet
> ns_type = Grid
> nstlist = 40
> ndelta = 2
> nstcomm = 100
> comm-mode = Linear
> nstlog = 2000
> nstxout = 2000
> nstvout = 2000
> nstfout = 0
> nstcalcenergy = 40
> nstenergy = 2000
> nstxtcout = 2000
> init-t = 0
> delta-t = 0.002
> xtcprec = 2000
> fourierspacing = 0.12
> nkx = 96
> nky = 96
> nkz = 120
> pme-order = 4
> ewald-rtol = 1e-05
> ewald-geometry = 0
> epsilon-surface = 0
> optimize-fft = FALSE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = V-rescale
> bPrintNHChains = FALSE
> nsttcouple = 40
> epc = Berendsen
> epctype = Semiisotropic
> nstpcouple = 40
> tau-p = 0.5
> ref-p (3x3):
> ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
> ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
> ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> compress (3x3):
> compress[ 0]={ 4.51000e-05, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 4.51000e-05, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.51000e-05}
> 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
> verlet-buffer-drift = 0.005
> rlist = 1.385
> rlistlong = 1.385
> nstcalclr = 40
> rtpi = 0.05
> coulombtype = PME
> coulomb-modifier = Potential-shift
> rcoulomb-switch = 0
> rcoulomb = 1.3
> vdwtype = Cut-off
> vdw-modifier = Potential-shift
> rvdw-switch = 0
> rvdw = 1.3
> epsilon-r = 1
> epsilon-rf = 66
> tabext = 1
> implicit-solvent = No
> gb-algorithm = Still
> gb-epsilon-solvent = 80
> nstgbradii = 1
> rgbradii = 1
> 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
> DispCorr = No
> bSimTemp = FALSE
> free-energy = no
> nwall = 0
> wall-type = 9-3
> wall-atomtype[0] = -1
> wall-atomtype[1] = -1
> wall-density[0] = 0
> wall-density[1] = 0
> wall-ewald-zfac = 3
> pull = no
> rotation = FALSE
> disre = No
> disre-weighting = Conservative
> disre-mixed = FALSE
> dr-fc = 1000
> dr-tau = 0
> nstdisreout = 100
> orires-fc = 0
> orires-tau = 0
> nstorireout = 100
> dihre-fc = 0
> em-stepsize = 0.01
> em-tol = 10
> niter = 20
> fc-stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> shake-tol = 0.0001
> lincs-order = 4
> lincs-warnangle = 30
> lincs-iter = 1
> bd-fric = 0
> ld-seed = 1993
> cos-accel = 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}
> adress = FALSE
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 51709 169941
> ref-t: 296 296
> tau-t: 0.4 0.4
> anneal: No No
> ann-npoints: 0 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp-flags[ 0]: 0 0
> energygrp-flags[ 1]: 0 0
> efield-x:
> n = 0
> efield-xt:
> n = 0
> efield-y:
> n = 0
> efield-yt:
> n = 0
> efield-z:
> n = 0
> efield-zt:
> n = 0
> bQMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> scalefactor = 1
> qm-opts:
> ngQM = 0
> Using 1 MPI thread
> Using 8 OpenMP threads
>
> Detecting CPU-specific acceleration.
> Present hardware specification:
> Vendor: GenuineIntel
> Brand: Intel(R) Core(TM) i7 CPU 870 @ 2.93GHz
> Family: 6 Model: 30 Stepping: 5
> Features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pdcm
> popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
> Acceleration most likely to fit this hardware: SSE4.1
> Acceleration selected at GROMACS compile time: SSE4.1
>
>
> 1 GPU detected:
> #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC: no, stat:
> compatible
>
> 1 GPU auto-selected for this run: #0
>
> Will do PME sum in reciprocal space.
>
> ++++ 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 0.416211 nm for Ewald
> Cut-off's: NS: 1.385 Coulomb: 1.3 LJ: 1.3
> System total charge: -0.000
> Generated table with 1192 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 1192 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 1192 data points for LJ12.
> Tabscale = 500 points/nm
> Generated table with 1192 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1192 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1192 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
>
> Using CUDA 8x8 non-bonded kernels
>
>
> NOTE: With GPUs, reporting energy group contributions is not supported
>
> Potential shift: LJ r^-12: 0.043 r^-6 0.207, Ewald 1.000e-05
> Initialized non-bonded Ewald correction tables, spacing: 8.47e-04 size: 1536
>
> Removing pbc first time
> Pinning threads with a logical core stride of 1
>
> Initializing LINear Constraint Solver
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
> LINCS: A Linear Constraint Solver for molecular simulations
> J. Comp. Chem. 18 (1997) pp. 1463-1472
> -------- -------- --- Thank You --- -------- --------
>
> The number of constraints is 25088
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> S. Miyamoto and P. A. Kollman
> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
> Water Models
> J. Comp. Chem. 13 (1992) pp. 952-962
> -------- -------- --- Thank You --- -------- --------
>
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: Other
> 1: SOL
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> G. Bussi, D. Donadio and M. Parrinello
> Canonical sampling through velocity rescaling
> J. Chem. Phys. 126 (2007) pp. 014101
> -------- -------- --- Thank You --- -------- --------
>
> There are: 110572 Atoms
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
> RMS relative constraint deviation after constraining: 9.68e-06
> Initial temperature: 297.425 K
>
> Started mdrun on node 0 Mon May 6 21:19:33 2013
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 4.06051e+04 3.40234e+04 1.67362e+03 -1.49709e+04 1.26501e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.84039e+04 -1.74059e+06 9.01597e+03 -1.49534e+06 2.74174e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22117e+06 2.97544e+02 -1.51178e+01 5.64838e-06
>
> step 80: timed with pme grid 96 96 120, coulomb cutoff 1.300: 2932.9
> M-cycles
> step 160: timed with pme grid 80 84 108, coulomb cutoff 1.402: 2333.3
> M-cycles
> step 240: timed with pme grid 72 72 96, coulomb cutoff 1.561: 2516.6
> M-cycles
> step 320: timed with pme grid 64 64 80, coulomb cutoff 1.840: 3431.2
> M-cycles
> step 400: timed with pme grid 96 96 112, coulomb cutoff 1.314: 2684.6
> M-cycles
> step 480: timed with pme grid 96 96 108, coulomb cutoff 1.363: 2610.2
> M-cycles
> step 560: timed with pme grid 80 84 108, coulomb cutoff 1.402: 2330.4
> M-cycles
> step 640: timed with pme grid 80 80 104, coulomb cutoff 1.415: 2149.0
> M-cycles
> step 720: timed with pme grid 80 80 100, coulomb cutoff 1.472: 2282.5
> M-cycles
> step 800: timed with pme grid 80 80 96, coulomb cutoff 1.533: 2440.7
> M-cycles
> step 880: timed with pme grid 64 64 96, coulomb cutoff 1.757: 3136.5
> M-cycles
> optimal pme grid 80 80 104, coulomb cutoff 1.415
> Step Time Lambda
> 2000 4.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.75222e+04 3.41983e+04 1.56252e+03 -1.48124e+04 1.26605e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.86561e+04 -1.74134e+06 4.80517e+03 -1.50280e+06 2.74079e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22872e+06 2.97442e+02 1.11946e+02 4.97038e-06
>
> Step Time Lambda
> 4000 8.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.77735e+04 3.40478e+04 1.55007e+03 -1.44974e+04 1.26617e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.99255e+04 -1.74150e+06 4.64326e+03 -1.50144e+06 2.72655e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22879e+06 2.95896e+02 1.20289e+01 4.96588e-06
>
> Step Time Lambda
> 6000 12.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.81221e+04 3.39915e+04 1.59676e+03 -1.47521e+04 1.26560e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.81554e+04 -1.73932e+06 4.75281e+03 -1.50089e+06 2.71166e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22973e+06 2.94281e+02 3.46273e+01 4.89748e-06
>
> Step Time Lambda
> 8000 16.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.78257e+04 3.35386e+04 1.57203e+03 -1.45192e+04 1.26689e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.83318e+04 -1.73972e+06 4.61104e+03 -1.50167e+06 2.73747e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22792e+06 2.97081e+02 9.03051e+01 4.89449e-06
>
> Step Time Lambda
> 10000 20.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.74885e+04 3.37616e+04 1.56529e+03 -1.46381e+04 1.26331e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.59409e+04 -1.73768e+06 4.63791e+03 -1.50260e+06 2.72735e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22986e+06 2.95982e+02 -1.14181e+02 4.95959e-06
>
> Step Time Lambda
> 12000 24.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.78367e+04 3.40592e+04 1.55085e+03 -1.47973e+04 1.26719e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.93389e+04 -1.74059e+06 4.64703e+03 -1.50124e+06 2.72343e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22890e+06 2.95557e+02 1.33158e+02 4.89296e-06
>
> Step Time Lambda
> 14000 28.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.77797e+04 3.44968e+04 1.63869e+03 -1.47180e+04 1.26373e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.83450e+04 -1.74028e+06 4.61777e+03 -1.50175e+06 2.72387e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22936e+06 2.95605e+02 6.12269e+00 4.98597e-06
>
> Step Time Lambda
> 16000 32.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.75292e+04 3.36058e+04 1.67502e+03 -1.43040e+04 1.26396e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 5.04003e+04 -1.74248e+06 4.70094e+03 -1.50248e+06 2.72324e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.23015e+06 2.95537e+02 1.64334e+02 4.97314e-06
>
> Step Time Lambda
> 18000 36.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.81658e+04 3.40675e+04 1.57609e+03 -1.45716e+04 1.26521e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 5.16244e+04 -1.74247e+06 4.68621e+03 -1.50040e+06 2.71938e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22846e+06 2.95118e+02 1.24742e+02 4.97458e-06
>
> Step Time Lambda
> 20000 40.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.79139e+04 3.35854e+04 1.53764e+03 -1.45186e+04 1.26644e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.93214e+04 -1.74182e+06 4.73934e+03 -1.50259e+06 2.73360e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22923e+06 2.96661e+02 5.05927e+01 4.86786e-06
>
> Step Time Lambda
> 22000 44.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.76891e+04 3.47562e+04 1.65573e+03 -1.45616e+04 1.26527e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.92753e+04 -1.74023e+06 4.73983e+03 -1.50014e+06 2.72006e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22814e+06 2.95191e+02 -6.57924e+00 4.96477e-06
>
> Step Time Lambda
> 24000 48.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.76193e+04 3.44905e+04 1.55150e+03 -1.46070e+04 1.26559e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.90591e+04 -1.73865e+06 4.68991e+03 -1.49929e+06 2.72635e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22666e+06 2.95874e+02 -1.64041e+01 4.93705e-06
>
> Step Time Lambda
> 26000 52.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.79457e+04 3.39780e+04 1.60300e+03 -1.44765e+04 1.26544e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.76575e+04 -1.74067e+06 4.61449e+03 -1.50280e+06 2.73512e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22929e+06 2.96826e+02 -1.92726e+01 4.97294e-06
>
> Step Time Lambda
> 28000 56.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.79846e+04 3.43774e+04 1.55924e+03 -1.44129e+04 1.26602e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.98360e+04 -1.74239e+06 4.60775e+03 -1.50183e+06 2.73156e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22868e+06 2.96440e+02 1.20466e+02 4.83686e-06
>
> Step Time Lambda
> 30000 60.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.79217e+04 3.40808e+04 1.66489e+03 -1.46594e+04 1.26586e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.83414e+04 -1.73951e+06 4.58175e+03 -1.50099e+06 2.73058e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22794e+06 2.96333e+02 -7.79706e+01 4.93017e-06
>
> Step Time Lambda
> 32000 64.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.81304e+04 3.40636e+04 1.62792e+03 -1.46462e+04 1.26630e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.84920e+04 -1.74024e+06 4.61553e+03 -1.50133e+06 2.73041e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22829e+06 2.96315e+02 -4.93505e+01 5.00846e-06
>
> Step Time Lambda
> 34000 68.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.83906e+04 3.35932e+04 1.54746e+03 -1.46102e+04 1.26587e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.65123e+04 -1.73669e+06 4.66940e+03 -1.50000e+06 2.72370e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22763e+06 2.95587e+02 3.49948e+01 4.84548e-06
>
> Step Time Lambda
> 36000 72.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.79808e+04 3.39248e+04 1.65090e+03 -1.45744e+04 1.26665e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.81267e+04 -1.73795e+06 4.67039e+03 -1.49951e+06 2.71574e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22793e+06 2.94723e+02 -2.77373e+00 5.00708e-06
>
> Step Time Lambda
> 38000 76.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.76108e+04 3.39492e+04 1.61483e+03 -1.46447e+04 1.26405e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.86239e+04 -1.74192e+06 4.64354e+03 -1.50372e+06 2.72468e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.23125e+06 2.95694e+02 -3.46091e+01 4.83479e-06
>
> Step Time Lambda
> 40000 80.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.75317e+04 3.42019e+04 1.62794e+03 -1.45424e+04 1.26466e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.96389e+04 -1.74253e+06 4.68602e+03 -1.50292e+06 2.72934e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22999e+06 2.96198e+02 3.22313e+01 5.02197e-06
>
> Step Time Lambda
> 42000 84.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.80765e+04 3.42050e+04 1.52647e+03 -1.45472e+04 1.26425e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.95822e+04 -1.74110e+06 4.69777e+03 -1.50113e+06 2.72607e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22852e+06 2.95843e+02 -1.13640e+01 4.92608e-06
>
> Step Time Lambda
> 44000 88.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.78492e+04 3.40960e+04 1.63704e+03 -1.45698e+04 1.26346e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.75518e+04 -1.73985e+06 4.59341e+03 -1.50234e+06 2.72002e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.23034e+06 2.95187e+02 -8.41246e+01 5.03544e-06
>
> Step Time Lambda
> 46000 92.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.77658e+04 3.42858e+04 1.67298e+03 -1.47786e+04 1.26686e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.93716e+04 -1.74306e+06 4.61603e+03 -1.50344e+06 2.74380e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22906e+06 2.97768e+02 -2.28804e+01 4.95687e-06
>
> Step Time Lambda
> 48000 96.00000 0.00000
>
> Energies (kJ/mol)
> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
> 3.82197e+04 3.34201e+04 1.57555e+03 -1.46122e+04 1.26530e+05
> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
> 4.77465e+04 -1.73781e+06 4.69134e+03 -1.50024e+06 2.72870e+05
> Total Energy Temperature Pressure (bar) Constr. rmsd
> -1.22737e+06 2.96129e+02 2.47163e+01 4.86327e-06
>
> Writing checkpoint, step 48640 at Mon May 6 21:34:34 2013
>
>
> Step Time Lambda
> 50000 100.00000 0.00000
>
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.6.1
> Source code file:
> /home/cintia/Downloads/gromacs-4.6.1/src/mdlib/nbnxn_cuda/nbnxn_cuda.cu,
> line: 565
>
> Fatal error:
> cudaStreamSynchronize failed in cu_blockwait_nb: unspecified launch failure
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "O My God, They Killed Kenny !" (South Park)
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users
mailing list