[gmx-users] 答复: Can't allocate memory problem
Yunlong Liu
yliu120 at jhmi.edu
Fri Jul 18 20:29:25 CEST 2014
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
++++ 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!
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
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%
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.
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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