[gmx-users] 答复: Can't allocate memory problem
Szilárd Páll
pall.szilard at gmail.com
Fri Jul 18 20:57:17 CEST 2014
On Fri, Jul 18, 2014 at 8:25 PM, Yunlong Liu <yliu120 at jhmi.edu> wrote:
> Hi Mark,
>
> I post up my log file for the run here. Thank you.
>
> Log file opened on Wed Jul 16 11:26:51 2014
> Host: c442-403.stampede.tacc.utexas.edu pid: 31032 nodeid: 0 nnodes: 4
> GROMACS: mdrun_mpi_gpu, VERSION 5.0-rc1
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
> Gerrit Groenhof Christoph Junghans Peter Kasson 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 Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2014, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out 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: mdrun_mpi_gpu, VERSION 5.0-rc1
> Executable: /work/03002/yliu120/gromacs-5.0/mv2_mkl/bin/mdrun_mpi_gpu
> Library dir: /work/03002/yliu120/gromacs-5.0/mv2_mkl/share/gromacs/top
> Command line:
> mdrun_mpi_gpu -pin on -ntomp 8 -deffnm pi3k-wt-1 -gpu_id 00
>
> Gromacs version: VERSION 5.0-rc1
> Precision: single
> Memory model: 64 bit
> MPI library: MPI
> OpenMP support: enabled
> GPU support: enabled
> invsqrt routine: gmx_software_invsqrt(x)
> SIMD instructions: AVX_256
> FFT library: Intel MKL
> RDTSCP usage: enabled
> C++11 compilation: disabled
> TNG support: enabled
> Tracing support: disabled
> Built on: Wed Jun 4 13:59:17 CDT 2014
> Built by: xzhu216 at login1.stampede.tacc.utexas.edu [CMAKE]
> Build OS/arch: Linux 2.6.32-358.18.1.el6.x86_64 x86_64
> Build CPU vendor: GenuineIntel
> Build CPU brand: Intel(R) Xeon(R) CPU E5-2680 0 @ 2.70GHz
> Build CPU family: 6 Model: 45 Stepping: 7
> Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> C compiler: /opt/apps/intel/13/composer_xe_2013.2.146/bin/intel64/icc Intel 13.1.0.20130121
> C compiler flags: -mavx -fno-strict-aliasing -mkl=sequential -std=gnu99 -w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -ip -funroll-all-loops -alias-const -ansi-alias -O3 -DNDEBUG
> C++ compiler: /opt/apps/intel/13/composer_xe_2013.2.146/bin/intel64/icpc Intel 13.1.0.20130121
> C++ compiler flags: -mavx -fno-strict-aliasing -w3 -wd111 -wd177 -wd181 -wd193 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd1782 -ip -funroll-all-loops -alias-const -ansi-alias -O3 -DNDEBUG
> Boost version: 1.51.0 (external)
> CUDA compiler: /opt/apps/cuda/5.0/bin/nvcc 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 compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_35,code=compute_35;-use_fast_math;-ccbin=/opt/apps/intel/13/composer_xe_2013.2.146/bin/intel64/icc;;-Xcompiler;-gcc-version=450;; ;-mavx;-fno-strict-aliasing;-w3;-wd111;-wd177;-wd181;-wd193;-wd271;-wd304;-wd383;-wd424;-wd444;-wd522;-wd593;-wd869;-wd981;-wd1418;-wd1419;-wd1572;-wd1599;-wd2259;-wd2415;-wd2547;-wd2557;-wd3280;-wd3346;-wd1782;-ip;-funroll-all-loops;-alias-const;-ansi-alias;-O3;-DNDEBUG
> CUDA driver: 5.50
> CUDA runtime: 5.0
Tips: you will get better performance if you use: CUDA 5.5, gcc 4.8,
and fftw. The difference in total performance will depend on your
setup and could be anywhere between 0-15%.
>
>
> ++++ 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 --- -------- --------
>
>
> Number of CPUs detected (16) does not match the number reported by OpenMP (1).
> Consider setting the launch configuration manually!
Something is still not right here. This message means that the OpenMP
library reports that there is *one* core available (through
omp_get_num_procs). Please consult your job scheduler's documentation
because this could affect performance (my guess is that it doesn't).
>
> For optimal performance with a GPU nstlist (now 5) should be larger.
> The optimum depends on your CPU and GPU resources.
> You might want to try several nstlist values.
> Changing nstlist from 5 to 40, rlist from 1 to 1.093
>
> Input Parameters:
> integrator = md
> nsteps = 5000000
> init-step = 0
> cutoff-scheme = Verlet
> ns-type = Grid
> nstlist = 40
> ndelta = 2
> nstcomm = 100
> comm-mode = Linear
> nstlog = 10000
> nstxout = 10000
> nstvout = 10000
> nstfout = 0
> nstcalcenergy = 100
> nstenergy = 10000
> nstxout-compressed = 10000
> init-t = 0
> delta-t = 0.002
> x-compression-precision = 1000
> fourierspacing = 0.16
> nkx = 96
> nky = 96
> nkz = 96
> pme-order = 4
> ewald-rtol = 1e-05
> ewald-rtol-lj = 0.001
> ewald-geometry = 0
> epsilon-surface = 0
> optimize-fft = FALSE
> lj-pme-comb-rule = Geometric
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = TRUE
> bShakeSOR = FALSE
> etc = V-rescale
> bPrintNHChains = FALSE
> nsttcouple = 5
> epc = Parrinello-Rahman
> epctype = Isotropic
> nstpcouple = 5
> tau-p = 2
> 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]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-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-tolerance = 0.005
> rlist = 1.093
> rlistlong = 1.093
> nstcalclr = 5
> rtpi = 0.05
> coulombtype = PME
> coulomb-modifier = Potential-shift
> rcoulomb-switch = 0
> rcoulomb = 1
> vdwtype = Cut-off
> vdw-modifier = Potential-shift
> rvdw-switch = 0
> rvdw = 1
> epsilon-r = 1
> epsilon-rf = inf
> 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 = EnerPres
> 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
> interactiveMD = 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 = 645545913
> 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: 42998.7 429867
> ref-t: 310 310
> tau-t: 0.1 0.1
> anneal: No No
> ann-npoints: 0 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp-flags[ 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
> eSwapCoords = no
> bQMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> scalefactor = 1
> qm-opts:
> ngQM = 0
>
> Initializing Domain Decomposition on 4 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
> two-body bonded interactions: 0.429 nm, LJ-14, atoms 13175 13183
> multi-body bonded interactions: 0.489 nm, CMAP Dih., atoms 18312 18321
> Minimum cell size due to bonded interactions: 0.537 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.819 nm
> Estimated maximum distance required for P-LINCS: 0.819 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Using 0 separate PME nodes, as there are too few total
> nodes for efficient splitting
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 4 cells with a minimum initial size of 1.024 nm
> The maximum allowed number of cells is: X 11 Y 11 Z 10
> Domain decomposition grid 4 x 1 x 1, separate PME nodes 0
> PME domain decomposition: 4 x 1 x 1
> Domain decomposition nodeid 0, coordinates 0 0 0
>
> Using two step summing over 2 groups of on average 2.0 processes
>
> Using 4 MPI processes
> Using 8 OpenMP threads per MPI process
Try running with 4 ranks and 4 threads which avoids using
Hyperthreading and will probably improve performance.
> Detecting CPU SIMD instructions.
> Present hardware specification:
> Vendor: GenuineIntel
> Brand: Intel(R) Xeon(R) CPU E5-2680 0 @ 2.70GHz
> Family: 6 Model: 45 Stepping: 7
> Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> SIMD instructions most likely to fit this hardware: AVX_256
> SIMD instructions selected at GROMACS compile time: AVX_256
>
>
> 1 GPU detected on host c442-403.stampede.tacc.utexas.edu:
> #0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
>
> 1 GPU user-selected for this run.
> Mapping of GPUs to the 2 PP ranks in this node: #0, #0
>
> NOTE: You assigned a GPU to multiple MPI processes.
> 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 0.320163 nm for Ewald
> Cut-off's: NS: 1.093 Coulomb: 1 LJ: 1
> Long Range LJ corr.: <C6> 3.1875e-04
> System total charge: 1.000
> Generated table with 1046 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 1046 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 1046 data points for LJ12.
> Tabscale = 500 points/nm
> Generated table with 1046 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1046 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1046 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
>
> Using CUDA 8x8 non-bonded kernels
>
> Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
> Initialized non-bonded Ewald correction tables, spacing: 6.52e-04 size: 1536
>
>
> Overriding thread affinity set outside mdrun_mpi_gpu
>
> Pinning threads with an auto-selected logical core stride of 1
>
> Initializing Parallel LINear Constraint Solver
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess
> P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
> J. Chem. Theory Comput. 4 (2008) pp. 116-122
> -------- -------- --- Thank You --- -------- --------
>
> The number of constraints is 21852
> There are inter charge-group constraints,
> will communicate selected coordinates each lincs iteration
>
> ++++ 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 --- -------- --------
>
>
> Linking all bonded interactions to atoms
> There are 333337 inter charge-group exclusions,
> will use an extra communication step for exclusion forces for PME
>
> The initial number of communication pulses is: X 1
> The initial domain decomposition cell size is: X 3.06 nm
>
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 1.093 nm
> (the following are initial values, they could change due to box deformation)
> two-body bonded interactions (-rdd) 1.093 nm
> multi-body bonded interactions (-rdd) 1.093 nm
> atoms separated by up to 5 constraints (-rcon) 3.061 nm
>
> When dynamic load balancing gets turned on, these settings will change to:
> The maximum number of communication pulses is: X 1
> The minimum size for domain decomposition cells is 1.093 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.36
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 1.093 nm
> two-body bonded interactions (-rdd) 1.093 nm
> multi-body bonded interactions (-rdd) 1.093 nm
> atoms separated by up to 5 constraints (-rcon) 1.093 nm
>
>
> Making 1D domain decomposition grid 4 x 1 x 1, home cell index 0 0 0
>
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
>
> ++++ 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: 236549 Atoms
> Charge group distribution at step 0: 58642 59637 59750 58520
> Initial temperature: 310.644 K
>
> Started mdrun on node 0 Wed Jul 16 11:26:55 2014
> Step Time Lambda
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.07365e+04 2.95121e+04 3.01332e+03 -7.32021e+03 1.97198e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.01566e+05 4.01053e+05 -3.13304e+04 -3.70280e+06 2.22526e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01359e+06 6.13614e+05 -2.39998e+06 3.12141e+02 -2.18173e+02
> Pressure (bar) Constr. rmsd
> -3.47613e+01 3.40465e-05
>
> DD step 39 load imb.: force 16.2%
>
> step 80: timed with pme grid 96 96 96, coulomb cutoff 1.000: 1156.6 M-cycles
> step 160: timed with pme grid 80 80 80, coulomb cutoff 1.172: 1547.8 M-cycles
> step 240: timed with pme grid 96 96 96, coulomb cutoff 1.000: 1151.5 M-cycles
> step 320: timed with pme grid 84 84 84, coulomb cutoff 1.116: 1385.3 M-cycles
> optimal pme grid 96 96 96, coulomb cutoff 1.000
> DD step 9999 load imb.: force 12.0%
>
> Step Time Lambda
> 10000 20.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.04795e+04 2.99195e+04 2.92288e+03 -7.24773e+03 2.00091e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.01757e+05 4.01852e+05 -3.13182e+04 -3.70354e+06 2.21148e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01305e+06 6.07693e+05 -2.40536e+06 3.09129e+02 -2.18004e+02
> Pressure (bar) Constr. rmsd
> 4.97661e+01 3.21278e-05
>
> DD step 19999 load imb.: force 12.9%
>
> Step Time Lambda
> 20000 40.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.03101e+04 2.98583e+04 2.92319e+03 -7.24572e+03 1.98643e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02386e+05 4.04043e+05 -3.13265e+04 -3.70922e+06 2.22318e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01618e+06 6.10725e+05 -2.40545e+06 3.10671e+02 -2.18119e+02
> Pressure (bar) Constr. rmsd
> 5.25345e+01 3.19849e-05
>
> DD step 29999 load imb.: force 12.9%
>
> Step Time Lambda
> 30000 60.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.04086e+04 2.98208e+04 2.96232e+03 -7.36511e+03 1.97707e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02219e+05 4.04588e+05 -3.13898e+04 -3.70933e+06 2.18899e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01643e+06 6.09712e+05 -2.40671e+06 3.10156e+02 -2.19002e+02
> Pressure (bar) Constr. rmsd
> 1.69563e+01 3.28362e-05
>
> DD step 39999 load imb.: force 13.6%
>
> Step Time Lambda
> 40000 80.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.08454e+04 2.97168e+04 2.88905e+03 -7.38898e+03 1.97906e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.01724e+05 4.00249e+05 -3.13130e+04 -3.70497e+06 2.19180e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01654e+06 6.09973e+05 -2.40657e+06 3.10288e+02 -2.17931e+02
> Pressure (bar) Constr. rmsd
> -4.75665e+01 3.26365e-05
>
> DD step 49999 load imb.: force 15.1%
>
> Step Time Lambda
> 50000 100.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.05524e+04 2.96917e+04 2.93777e+03 -7.29600e+03 1.98992e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.01154e+05 4.02695e+05 -3.12880e+04 -3.70590e+06 2.18002e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01576e+06 6.07954e+05 -2.40780e+06 3.09262e+02 -2.17584e+02
> Pressure (bar) Constr. rmsd
> -7.76501e+00 3.21618e-05
>
> DD step 59999 load imb.: force 12.5%
>
> Step Time Lambda
> 60000 120.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.00781e+04 3.00110e+04 3.14274e+03 -7.37195e+03 2.00457e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02606e+05 4.01699e+05 -3.13388e+04 -3.70509e+06 2.19611e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01426e+06 6.09684e+05 -2.40458e+06 3.10142e+02 -2.18291e+02
> Pressure (bar) Constr. rmsd
> -3.63586e-01 3.19734e-05
>
> DD step 69999 load imb.: force 11.2%
>
> Step Time Lambda
> 70000 140.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.08759e+04 2.99581e+04 2.98187e+03 -7.47015e+03 1.97981e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02357e+05 4.01634e+05 -3.13895e+04 -3.70518e+06 2.19320e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01450e+06 6.10453e+05 -2.40404e+06 3.10533e+02 -2.18998e+02
> Pressure (bar) Constr. rmsd
> -5.49562e+01 3.32050e-05
>
> DD step 79999 load imb.: force 12.7%
>
> Step Time Lambda
> 80000 160.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.02476e+04 2.99203e+04 3.01794e+03 -7.41418e+03 1.99012e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02636e+05 3.99866e+05 -3.13105e+04 -3.70666e+06 2.17894e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01801e+06 6.10188e+05 -2.40782e+06 3.10398e+02 -2.17897e+02
> Pressure (bar) Constr. rmsd
> -7.82256e+01 3.22503e-05
>
> Writing checkpoint, step 84280 at Wed Jul 16 11:41:55 2014
>
>
> DD step 89999 load imb.: force 9.5%
>
> Step Time Lambda
> 90000 180.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.04253e+04 3.01029e+04 3.04981e+03 -7.29947e+03 1.98989e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02004e+05 4.03726e+05 -3.12806e+04 -3.70717e+06 2.20550e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01449e+06 6.08805e+05 -2.40568e+06 3.09694e+02 -2.17480e+02
> Pressure (bar) Constr. rmsd
> 2.29629e+01 3.23359e-05
>
> DD step 99999 load imb.: force 11.4%
>
> Step Time Lambda
> 100000 200.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.05809e+04 2.97365e+04 2.90575e+03 -7.46760e+03 2.00142e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02442e+05 4.02628e+05 -3.13276e+04 -3.70909e+06 2.19456e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01763e+06 6.09703e+05 -2.40793e+06 3.10151e+02 -2.18135e+02
> Pressure (bar) Constr. rmsd
> 2.61670e+01 3.23152e-05
>
> DD step 109999 load imb.: force 11.5%
>
> Step Time Lambda
> 110000 220.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.04489e+04 2.98261e+04 2.96408e+03 -7.46597e+03 1.99103e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.01929e+05 4.04057e+05 -3.13158e+04 -3.70812e+06 2.21537e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01561e+06 6.09714e+05 -2.40590e+06 3.10157e+02 -2.17970e+02
> Pressure (bar) Constr. rmsd
> 3.75535e+01 3.23884e-05
>
> DD step 119999 load imb.: force 13.4%
>
> Step Time Lambda
> 120000 240.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.02048e+04 2.96834e+04 2.99140e+03 -7.47253e+03 1.98509e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02924e+05 4.00695e+05 -3.13677e+04 -3.70737e+06 2.19556e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01790e+06 6.09085e+05 -2.40882e+06 3.09837e+02 -2.18693e+02
> Pressure (bar) Constr. rmsd
> -4.17847e+01 3.24539e-05
>
> DD step 129999 load imb.: force 13.9%
>
> Step Time Lambda
> 130000 260.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 4.99271e+04 2.98272e+04 2.93917e+03 -7.27635e+03 1.98999e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02518e+05 3.97726e+05 -3.13026e+04 -3.70217e+06 2.20807e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01583e+06 6.09694e+05 -2.40614e+06 3.10147e+02 -2.17788e+02
> Pressure (bar) Constr. rmsd
> -1.15382e+02 3.19481e-05
>
> DD step 139999 load imb.: force 10.1%
>
> Step Time Lambda
> 140000 280.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.03356e+04 2.97673e+04 2.87730e+03 -7.47602e+03 1.97827e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02578e+05 4.02705e+05 -3.12475e+04 -3.70659e+06 2.19426e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01532e+06 6.06119e+05 -2.40920e+06 3.08328e+02 -2.17021e+02
> Pressure (bar) Constr. rmsd
> -4.87389e+01 3.29943e-05
>
> DD step 149999 load imb.: force 12.0%
>
> Step Time Lambda
> 150000 300.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.01586e+04 2.98972e+04 2.97697e+03 -7.38809e+03 1.99546e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02136e+05 4.04987e+05 -3.13378e+04 -3.71164e+06 2.18617e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01840e+06 6.08594e+05 -2.40980e+06 3.09587e+02 -2.18277e+02
> Pressure (bar) Constr. rmsd
> 4.10102e+01 3.20743e-05
>
> DD step 159999 load imb.: force 11.6%
>
> Step Time Lambda
> 160000 320.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.02983e+04 2.99181e+04 2.94672e+03 -7.49915e+03 1.99437e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.03281e+05 4.00190e+05 -3.12908e+04 -3.70493e+06 2.23782e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01477e+06 6.09016e+05 -2.40575e+06 3.09802e+02 -2.17623e+02
> Pressure (bar) Constr. rmsd
> -6.39499e+01 3.24603e-05
>
> Writing checkpoint, step 168560 at Wed Jul 16 11:56:56 2014
>
>
> DD step 169999 load imb.: force 12.3%
>
> Step Time Lambda
> 170000 340.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 4.96860e+04 2.97866e+04 2.87484e+03 -7.42084e+03 1.98346e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.03200e+05 4.05459e+05 -3.13545e+04 -3.71085e+06 2.20106e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01677e+06 6.08386e+05 -2.40839e+06 3.09481e+02 -2.18509e+02
> Pressure (bar) Constr. rmsd
> 7.35129e+01 3.22101e-05
>
> DD step 179999 load imb.: force 12.5%
>probably
> Step Time Lambda
> 180000 360.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.01938e+04 2.98005e+04 3.12308e+03 -7.44680e+03 1.97367e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.02109e+05 4.02954e+05 -3.12995e+04 -3.70869e+06 2.20544e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01747e+06 6.08815e+05 -2.40865e+06 3.09700e+02 -2.17744e+02
> Pressure (bar) Constr. rmsd
> -1.15302e+01 3.22109e-05
>
> DD step 189999 load imb.: force 13.4%
>
> Step Time Lambda
> 190000 380.00000 0.00000
>
> Energies (kJ/mol)
> U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14
> 5.07811e+04 2.99541e+04 2.98628e+03 -7.39091e+03 1.97456e+04
> Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> 2.01761e+05 4.03922e+05 -3.13225e+04 -3.71005e+06 2.19542e+04
> Potential Kinetic En. Total Energy Temperature Pres. DC (bar)
> -3.01766e+06 6.10133e+05 -2.40753e+06 3.10370e+02 -2.18064e+02
> Pressure (bar) Constr. rmsd
> -2.96181e+01 3.28160e-05
>
> If you want to see the full log file, please give me an email address that I could send it to.
Pastebin?
Cheers,
Sz.
> Thank you.
> Yunlong
>
> ________________________________________
> 发件人: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> 代表 Mark Abraham <mark.j.abraham at gmail.com>
> 发送时间: 2014年7月18日 23:52
> 收件人: Discussion list for GROMACS users
> 主题: Re: [gmx-users] Can't allocate memory problem
>
> Hi,
>
> That's highly unusual, and suggests you are doing something highly unusual,
> like trying to run on huge numbers of threads, or very large numbers of
> bonded interactions. How are you setting up to call mdrun, and what is in
> your tpr?
>
> Mark
> On Jul 17, 2014 10:13 PM, "Yunlong Liu" <yliu120 at jhmi.edu> wrote:
>
>> Hi,
>>
>>
>> I am currently experiencing a "Can't allocate memory" problem on Gromacs
>> 4.6.5 with GPU acceleration.
>>
>> Actually, I am running my simulations on Stampede/TACC supercomputers with
>> their GPU queue. My first experience is when the simulation length longer
>> than 10 ns, the system starts to throw out the "Can't allocate memory"
>> problem as follows:
>>
>>
>> Fatal error:
>> Not enough memory. Failed to realloc 1403808 bytes for f_t->f,
>> f_t->f=0xa912a010
>> (called from file
>> /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c,
>> line 3840)
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> "These Gromacs Guys Really Rock" (P.J. Meulenhoff)
>> : Cannot allocate memory
>> Error on node 0, will try to stop all the nodes
>> Halting parallel program mdrun_mpi_gpu on CPU 0 out of 4
>>
>> -------------------------------------------------------
>> Program mdrun_mpi_gpu, VERSION 4.6.5
>> Source code file:
>> /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/smalloc.c,
>> line: 241
>>
>> Fatal error:
>> Not enough memory. Failed to realloc 1403808 bytes for f_t->f,
>> f_t->f=0xaa516e90
>> (called from file
>> /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c,
>> line 3840)
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> Recently, this error occurs even I run a short NVT equilibrium. This
>> problem also exists when I use Gromacs 5.0 with GPU acceleration. I looked
>> up the Gromacs errors website to check the reasons for this. But it seems
>> that none of those reasons will fit in this situation. I use a very good
>> computer, the Stampede and I run short simulations. And I know gromacs use
>> nanometers as unit. I tried all the solutions that I can figure out but the
>> problem becomes more severe.
>>
>> Is there anybody that has an idea on solving this issue?
>>
>> Thank you.
>>
>> Yunlong
>>
>>
>>
>>
>>
>>
>>
>>
>> Davis Yunlong Liu
>>
>> BCMB - Second Year PhD Candidate
>>
>> School of Medicine
>>
>> The Johns Hopkins University
>>
>> E-mail: yliu120 at jhmi.edu<mailto:yliu120 at jhmi.edu>
>> --
>> Gromacs Users mailing list
>>
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>>
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