[gmx-users] GPU low performance
Szilárd Páll
pall.szilard at gmail.com
Fri Feb 20 01:25:16 CET 2015
Please consult the manual an wiki.
--
Szilárd
On Thu, Feb 19, 2015 at 6:44 PM, Carmen Di Giovanni <cdigiova at unina.it> wrote:
>
> Szilard,
> about:
>
> Fatal error
> 1) Setting the number of thread-MPI threads is only supported with
> thread-MPI
> and Gromacs was compiled without thread-MPI
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> The error is quite clearly explains that you're trying to use mdrun's
> built-in thread-MPI parallelization, but you have a binary that does
> not support it. Use the MPI launching syntax instead.
>
> Can you help me about the MPI launching syntax? What is the suitable
> command ?
A previous poster has already pointed you to the "Acceleration and
parallelization" page which, I believe describes the matter in detail.
>
>
> 2) Have you looked at the the performance table at the end of the log?
> You are wasting a large amount of runtime calculating energies every
> step and this overhead comes in multiple places in the code - one of
> them being the non-timed code parts which typically take <3%.
>
>
> As can I reduce runtime to calculate the energies every step?
> I must to modify something in mdp file ?
This is discussed throughly in the manual, you should be looking for
the nstcalcenergy option.
>
> Thank you in advance
>
> Carmen
> --
> Carmen Di Giovanni, PhD
> Dept. of Pharmaceutical and Toxicological Chemistry
> "Drug Discovery Lab"
> University of Naples "Federico II"
> Via D. Montesano, 49
> 80131 Naples
> Tel.: ++39 081 678623
> Fax: ++39 081 678100
> Email: cdigiova at unina.it
>
>
>
> Quoting Szilárd Páll <pall.szilard at gmail.com>:
>
>> On Thu, Feb 19, 2015 at 11:32 AM, Carmen Di Giovanni <cdigiova at unina.it>
>> wrote:
>>>
>>> Dear Szilárd,
>>>
>>> 1) the output of command nvidia-smi -ac 2600,758 is
>>>
>>> [root at localhost test_gpu]# nvidia-smi -ac 2600,758
>>> Applications clocks set to "(MEM 2600, SM 758)" for GPU 0000:03:00.0
>>>
>>> Warning: persistence mode is disabled on this device. This settings will
>>> go
>>> back to default as soon as driver unloads (e.g. last application like
>>> nvidia-smi or cuda application terminates). Run with [--help | -h] switch
>>> to
>>> get more information on how to enable persistence mode.
>>
>>
>> run nvidia-smi -pm 1 if you want to avoid that.
>>
>>> Setting applications clocks is not supported for GPU 0000:82:00.0.
>>> Treating as warning and moving on.
>>> All done.
>>>
>>> ----------------------------------------------------------------------------
>>> 2) I decreased nlists to 20
>>> However when I do the command:
>>> gmx_mpi mdrun -deffnm nvt -ntmpi 8 -gpu_id 00001111
>>> give me a fatal error:
>>>
>>> GROMACS: gmx mdrun, VERSION 5.0
>>> Executable: /opt/SW/gromacs-5.0/build/mpi-cuda/bin/gmx_mpi
>>> Library dir: /opt/SW/gromacs-5.0/share/top
>>> Command line:
>>> gmx_mpi mdrun -deffnm nvt -ntmpi 8 -gpu_id 00001111
>>>
>>>
>>> Back Off! I just backed up nvt.log to ./#nvt.log.8#
>>> Reading file nvt.tpr, VERSION 5.0 (single precision)
>>> Changing nstlist from 10 to 40, rlist from 1 to 1.097
>>>
>>>
>>> -------------------------------------------------------
>>> Program gmx_mpi, VERSION 5.0
>>> Source code file: /opt/SW/gromacs-5.0/src/programs/mdrun/runner.c, line:
>>> 876
>>>
>>> Fatal error:
>>> Setting the number of thread-MPI threads is only supported with
>>> thread-MPI
>>> and Gromacs was compiled without thread-MPI
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>
>>
>> The error is quite clearly explains that you're trying to use mdrun's
>> built-in thread-MPI parallelization, but you have a binary that does
>> not support it. Use the MPI launching syntax instead.
>>
>>> Halting program gmx_mpi
>>>
>>> gcq#223: "Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron
>>> Bradshaw)
>>>
>>>
>>> --------------------------------------------------------------------------
>>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>> with errorcode -1.
>>>
>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> You may or may not see output from other processes, depending on
>>> exactly when Open MPI kills them.
>>> -------------------------------------------------------------------------
>>>
>>>
>>> 4) I don't understand as I can reduce the "Rest" time
>>
>>
>> Have you looked at the the performance table at the end of the log?
>> You are wasting a large amount of runtime calculating energies every
>> step and this overhead comes in multiple places in the code - one of
>> them being the non-timed code parts which typically take <3%.
>>
>> Cheers,
>> --
>> Szilard
>>
>>
>>>
>>> Carmen
>>>
>>>
>>>
>>> --
>>> Carmen Di Giovanni, PhD
>>> Dept. of Pharmaceutical and Toxicological Chemistry
>>> "Drug Discovery Lab"
>>> University of Naples "Federico II"
>>> Via D. Montesano, 49
>>> 80131 Naples
>>> Tel.: ++39 081 678623
>>> Fax: ++39 081 678100
>>> Email: cdigiova at unina.it
>>>
>>>
>>>
>>> Quoting Szilárd Páll <pall.szilard at gmail.com>:
>>>
>>>> Please keep the mails on the list.
>>>>
>>>> On Wed, Feb 18, 2015 at 6:32 PM, Carmen Di Giovanni <cdigiova at unina.it>
>>>> wrote:
>>>>>
>>>>>
>>>>> nvidia-smi -q -g 0
>>>>>
>>>>> ==============NVSMI LOG==============
>>>>>
>>>>> Timestamp : Wed Feb 18 18:30:01 2015
>>>>> Driver Version : 340.24
>>>>>
>>>>> Attached GPUs : 2
>>>>> GPU 0000:03:00.0
>>>>> Product Name : Tesla K20c
>>>>
>>>>
>>>> [...
>>>>>
>>>>>
>>>>> Clocks
>>>>> Graphics : 705 MHz
>>>>> SM : 705 MHz
>>>>> Memory : 2600 MHz
>>>>> Applications Clocks
>>>>> Graphics : 705 MHz
>>>>> Memory : 2600 MHz
>>>>> Default Applications Clocks
>>>>> Graphics : 705 MHz
>>>>> Memory : 2600 MHz
>>>>> Max Clocks
>>>>> Graphics : 758 MHz
>>>>> SM : 758 MHz
>>>>> Memory : 2600 MHz
>>>>
>>>>
>>>>
>>>> This is the relevant part I was looking for. The Tesla K20c supports
>>>> setting a so-called application clock which is essentially means that
>>>> you can bump its clock frequency using the NVDIA management tool
>>>> nvidia-smi from the default 705 MHz to 758 MHz.
>>>>
>>>> Use the command:
>>>> nvidia-smi -ac 2600,758
>>>>
>>>> This should give you another 7% or so (I didn't remember the correct
>>>> max clock before, that's why I guessing 5%).
>>>>
>>>> Cheers,
>>>> Szilard
>>>>
>>>>> Clock Policy
>>>>> Auto Boost : N/A
>>>>> Auto Boost Default : N/A
>>>>> Compute Processes
>>>>> Process ID : 19441
>>>>> Name : gmx_mpi
>>>>> Used GPU Memory : 110 MiB
>>>>>
>>>>> [carmendigi at localhost test_gpu]$
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Carmen Di Giovanni, PhD
>>>>> Dept. of Pharmaceutical and Toxicological Chemistry
>>>>> "Drug Discovery Lab"
>>>>> University of Naples "Federico II"
>>>>> Via D. Montesano, 49
>>>>> 80131 Naples
>>>>> Tel.: ++39 081 678623
>>>>> Fax: ++39 081 678100
>>>>> Email: cdigiova at unina.it
>>>>>
>>>>>
>>>>>
>>>>> Quoting Szilárd Páll <pall.szilard at gmail.com>:
>>>>>
>>>>>> As I suggested above please use pastebin.com or similar!
>>>>>> --
>>>>>> Szilárd
>>>>>>
>>>>>>
>>>>>> On Wed, Feb 18, 2015 at 6:09 PM, Carmen Di Giovanni
>>>>>> <cdigiova at unina.it>
>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dear Szilàrd, it's not possible attach the full log file in the forum
>>>>>>> mail
>>>>>>> because it is too big.
>>>>>>> I send it by your private mail address.
>>>>>>> Thank you in advance
>>>>>>> Carmen
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Carmen Di Giovanni, PhD
>>>>>>> Dept. of Pharmaceutical and Toxicological Chemistry
>>>>>>> "Drug Discovery Lab"
>>>>>>> University of Naples "Federico II"
>>>>>>> Via D. Montesano, 49
>>>>>>> 80131 Naples
>>>>>>> Tel.: ++39 081 678623
>>>>>>> Fax: ++39 081 678100
>>>>>>> Email: cdigiova at unina.it
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Quoting Szilárd Páll <pall.szilard at gmail.com>:
>>>>>>>
>>>>>>>> We need a *full* log file, not parts of it!
>>>>>>>>
>>>>>>>> You can try running with "-ntomp 16 -pin on" - it may be a bit
>>>>>>>> faster
>>>>>>>> not not use HyperThreading.
>>>>>>>> --
>>>>>>>> Szilárd
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Feb 18, 2015 at 5:20 PM, Carmen Di Giovanni
>>>>>>>> <cdigiova at unina.it>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Justin,
>>>>>>>>> the problem is evident for all calculations.
>>>>>>>>> This is the log file of a recent run:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --------------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>> Log file opened on Mon Dec 22 16:28:00 2014
>>>>>>>>> Host: localhost.localdomain pid: 8378 rank ID: 0 number of
>>>>>>>>> ranks:
>>>>>>>>> 1
>>>>>>>>> GROMACS: gmx mdrun, VERSION 5.0
>>>>>>>>>
>>>>>>>>> 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: gmx mdrun, VERSION 5.0
>>>>>>>>> Executable: /opt/SW/gromacs-5.0/build/mpi-cuda/bin/gmx_mpi
>>>>>>>>> Library dir: /opt/SW/gromacs-5.0/share/top
>>>>>>>>> Command line:
>>>>>>>>> gmx_mpi mdrun -deffnm prod_20ns
>>>>>>>>>
>>>>>>>>> Gromacs version: VERSION 5.0
>>>>>>>>> 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: fftw-3.3.3-sse2
>>>>>>>>> RDTSCP usage: enabled
>>>>>>>>> C++11 compilation: disabled
>>>>>>>>> TNG support: enabled
>>>>>>>>> Tracing support: disabled
>>>>>>>>> Built on: Thu Jul 31 18:30:37 CEST 2014
>>>>>>>>> Built by: root at localhost.localdomain [CMAKE]
>>>>>>>>> Build OS/arch: Linux 2.6.32-431.el6.x86_64 x86_64
>>>>>>>>> Build CPU vendor: GenuineIntel
>>>>>>>>> Build CPU brand: Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
>>>>>>>>> Build CPU family: 6 Model: 62 Stepping: 4
>>>>>>>>> Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt
>>>>>>>>> lahf_lm
>>>>>>>>> mmx
>>>>>>>>> msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
>>>>>>>>> sse2
>>>>>>>>> sse3
>>>>>>>>> sse4.1 sse4.2 ssse3 tdt x2apic
>>>>>>>>> C compiler: /usr/bin/cc GNU 4.4.7
>>>>>>>>> C compiler flags: -mavx -Wno-maybe-uninitialized -Wextra
>>>>>>>>> -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith
>>>>>>>>> -Wall
>>>>>>>>> -Wno-unused -Wunused-value -Wunused-parameter
>>>>>>>>> -fomit-frame-pointer
>>>>>>>>> -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG
>>>>>>>>> C++ compiler: /usr/bin/c++ GNU 4.4.7
>>>>>>>>> C++ compiler flags: -mavx -Wextra
>>>>>>>>> -Wno-missing-field-initializers
>>>>>>>>> -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer
>>>>>>>>> -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG
>>>>>>>>> Boost version: 1.55.0 (internal)
>>>>>>>>> CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda
>>>>>>>>> compiler
>>>>>>>>> driver;Copyright (c) 2005-2013 NVIDIA Corporation;Built on
>>>>>>>>> Thu_Mar_13_11:58:58_PDT_2014;Cuda compilation tools, release 6.0,
>>>>>>>>> V6.0.1
>>>>>>>>> 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;-Xcompiler;-fPIC
>>>>>>>>> ;
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ;-mavx;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-fomit-frame-pointer;-funroll-all-loops;-Wno-array-bounds;-O3;-DNDEBUG
>>>>>>>>> CUDA driver: 6.50
>>>>>>>>> CUDA runtime: 6.0
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ++++ 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 --- -------- --------
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> For optimal performance with a GPU nstlist (now 10) should be
>>>>>>>>> larger.
>>>>>>>>> The optimum depends on your CPU and GPU resources.
>>>>>>>>> You might want to try several nstlist values.
>>>>>>>>> Changing nstlist from 10 to 40, rlist from 1.2 to 1.285
>>>>>>>>>
>>>>>>>>> Input Parameters:
>>>>>>>>> integrator = md
>>>>>>>>> tinit = 0
>>>>>>>>> dt = 0.002
>>>>>>>>> nsteps = 10000000
>>>>>>>>> init-step = 0
>>>>>>>>> simulation-part = 1
>>>>>>>>> comm-mode = Linear
>>>>>>>>> nstcomm = 1
>>>>>>>>> bd-fric = 0
>>>>>>>>> ld-seed = 1993
>>>>>>>>> emtol = 10
>>>>>>>>> emstep = 0.01
>>>>>>>>> niter = 20
>>>>>>>>> fcstep = 0
>>>>>>>>> nstcgsteep = 1000
>>>>>>>>> nbfgscorr = 10
>>>>>>>>> rtpi = 0.05
>>>>>>>>> nstxout = 2500
>>>>>>>>> nstvout = 2500
>>>>>>>>> nstfout = 0
>>>>>>>>> nstlog = 2500
>>>>>>>>> nstcalcenergy = 1
>>>>>>>>> nstenergy = 2500
>>>>>>>>> nstxout-compressed = 500
>>>>>>>>> compressed-x-precision = 1000
>>>>>>>>> cutoff-scheme = Verlet
>>>>>>>>> nstlist = 40
>>>>>>>>> ns-type = Grid
>>>>>>>>> pbc = xyz
>>>>>>>>> periodic-molecules = FALSE
>>>>>>>>> verlet-buffer-tolerance = 0.005
>>>>>>>>> rlist = 1.285
>>>>>>>>> rlistlong = 1.285
>>>>>>>>> nstcalclr = 10
>>>>>>>>> coulombtype = PME
>>>>>>>>> coulomb-modifier = Potential-shift
>>>>>>>>> rcoulomb-switch = 0
>>>>>>>>> rcoulomb = 1.2
>>>>>>>>> epsilon-r = 1
>>>>>>>>> epsilon-rf = 1
>>>>>>>>> vdw-type = Cut-off
>>>>>>>>> vdw-modifier = Potential-shift
>>>>>>>>> rvdw-switch = 0
>>>>>>>>> rvdw = 1.2
>>>>>>>>> DispCorr = No
>>>>>>>>> table-extension = 1
>>>>>>>>> fourierspacing = 0.135
>>>>>>>>> fourier-nx = 128
>>>>>>>>> fourier-ny = 128
>>>>>>>>> fourier-nz = 128
>>>>>>>>> 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 = 2
>>>>>>>>> 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 = 2.092
>>>>>>>>> tcoupl = V-rescale
>>>>>>>>> nsttcouple = 10
>>>>>>>>> nh-chain-length = 0
>>>>>>>>> print-nose-hoover-chain-variables = FALSE
>>>>>>>>> pcoupl = No
>>>>>>>>> pcoupltype = Semiisotropic
>>>>>>>>> nstpcouple = -1
>>>>>>>>> tau-p = 0.5
>>>>>>>>> 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 = no
>>>>>>>>> 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
>>>>>>>>> adress = FALSE
>>>>>>>>> userint1 = 0
>>>>>>>>> userint2 = 0
>>>>>>>>> userint3 = 0
>>>>>>>>> userint4 = 0
>>>>>>>>> userreal1 = 0
>>>>>>>>> userreal2 = 0
>>>>>>>>> userreal3 = 0
>>>>>>>>> userreal4 = 0
>>>>>>>>> grpopts:
>>>>>>>>> nrdf: 869226
>>>>>>>>> ref-t: 300
>>>>>>>>> tau-t: 0.1
>>>>>>>>> annealing: No
>>>>>>>>> annealing-npoints: 0
>>>>>>>>> acc: 0 0 0
>>>>>>>>> nfreeze: N N N
>>>>>>>>> energygrp-flags[ 0]: 0
>>>>>>>>> Using 1 MPI process
>>>>>>>>> Using 32 OpenMP threads
>>>>>>>>>
>>>>>>>>> Detecting CPU SIMD instructions.
>>>>>>>>> Present hardware specification:
>>>>>>>>> Vendor: GenuineIntel
>>>>>>>>> Brand: Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
>>>>>>>>> Family: 6 Model: 62 Stepping: 4
>>>>>>>>> Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr
>>>>>>>>> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2 GPUs detected on host localhost.localdomain:
>>>>>>>>> #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: yes, stat:
>>>>>>>>> compatible
>>>>>>>>> #1: NVIDIA GeForce GTX 650, compute cap.: 3.0, ECC: no, stat:
>>>>>>>>> compatible
>>>>>>>>>
>>>>>>>>> 1 GPU auto-selected for this run.
>>>>>>>>> Mapping of GPU to the 1 PP rank in this node: #0
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> NOTE: potentially sub-optimal launch configuration, gmx_mpi started
>>>>>>>>> with
>>>>>>>>> less
>>>>>>>>> PP MPI process per node than GPUs available.
>>>>>>>>> Each PP MPI process can use only one GPU, 1 GPU per node will
>>>>>>>>> be
>>>>>>>>> used.
>>>>>>>>>
>>>>>>>>> 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: 1.285 Coulomb: 1.2 LJ: 1.2
>>>>>>>>> System total charge: -0.012
>>>>>>>>> Generated table with 1142 data points for Ewald.
>>>>>>>>> Tabscale = 500 points/nm
>>>>>>>>> Generated table with 1142 data points for LJ6.
>>>>>>>>> Tabscale = 500 points/nm
>>>>>>>>> Generated table with 1142 data points for LJ12.
>>>>>>>>> Tabscale = 500 points/nm
>>>>>>>>> Generated table with 1142 data points for 1-4 COUL.
>>>>>>>>> Tabscale = 500 points/nm
>>>>>>>>> Generated table with 1142 data points for 1-4 LJ6.
>>>>>>>>> Tabscale = 500 points/nm
>>>>>>>>> Generated table with 1142 data points for 1-4 LJ12.
>>>>>>>>> Tabscale = 500 points/nm
>>>>>>>>>
>>>>>>>>> Using CUDA 8x8 non-bonded kernels
>>>>>>>>>
>>>>>>>>> Potential shift: LJ r^-12: -1.122e-01 r^-6: -3.349e-01, Ewald
>>>>>>>>> -1.000e-05
>>>>>>>>> Initialized non-bonded Ewald correction tables, spacing: 7.82e-04
>>>>>>>>> size:
>>>>>>>>> 1536
>>>>>>>>>
>>>>>>>>> Removing pbc first time
>>>>>>>>> Pinning threads with an auto-selected 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 5913
>>>>>>>>>
>>>>>>>>> ++++ 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: 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: 434658 Atoms
>>>>>>>>>
>>>>>>>>> Constraining the starting coordinates (step 0)
>>>>>>>>>
>>>>>>>>> Constraining the coordinates at t0-dt (step 0)
>>>>>>>>> RMS relative constraint deviation after constraining: 3.67e-05
>>>>>>>>> Initial temperature: 300.5 K
>>>>>>>>>
>>>>>>>>> Started mdrun on rank 0 Mon Dec 22 16:28:01 2014
>>>>>>>>> Step Time Lambda
>>>>>>>>> 0 0.00000 0.00000
>>>>>>>>>
>>>>>>>>> Energies (kJ/mol)
>>>>>>>>> G96Angle Proper Dih. Improper Dih. LJ-14
>>>>>>>>> Coulomb-14
>>>>>>>>> 9.74139e+03 4.34956e+03 2.97359e+03 -1.93107e+02
>>>>>>>>> 8.05534e+04
>>>>>>>>> LJ (SR) Coulomb (SR) Coul. recip. Potential
>>>>>>>>> Kinetic
>>>>>>>>> En.
>>>>>>>>> 1.01340e+06 -7.13271e+06 2.01361e+04 -6.00175e+06
>>>>>>>>> 1.09887e+06
>>>>>>>>> Total Energy Conserved En. Temperature Pressure (bar)
>>>>>>>>> Constr.
>>>>>>>>> rmsd
>>>>>>>>> -4.90288e+06 -4.90288e+06 3.04092e+02 1.70897e+02
>>>>>>>>> 2.16683e-05
>>>>>>>>>
>>>>>>>>> step 80: timed with pme grid 128 128 128, coulomb cutoff 1.200:
>>>>>>>>> 6279.0
>>>>>>>>> M-cycles
>>>>>>>>> step 160: timed with pme grid 112 112 112, coulomb cutoff 1.306:
>>>>>>>>> 6962.2
>>>>>>>>> M-cycles
>>>>>>>>> step 240: timed with pme grid 100 100 100, coulomb cutoff 1.463:
>>>>>>>>> 8406.5
>>>>>>>>> M-cycles
>>>>>>>>> step 320: timed with pme grid 128 128 128, coulomb cutoff 1.200:
>>>>>>>>> 6424.0
>>>>>>>>> M-cycles
>>>>>>>>> step 400: timed with pme grid 120 120 120, coulomb cutoff 1.219:
>>>>>>>>> 6369.1
>>>>>>>>> M-cycles
>>>>>>>>> step 480: timed with pme grid 112 112 112, coulomb cutoff 1.306:
>>>>>>>>> 7309.0
>>>>>>>>> M-cycles
>>>>>>>>> step 560: timed with pme grid 108 108 108, coulomb cutoff 1.355:
>>>>>>>>> 7521.2
>>>>>>>>> M-cycles
>>>>>>>>> step 640: timed with pme grid 104 104 104, coulomb cutoff 1.407:
>>>>>>>>> 8369.8
>>>>>>>>> M-cycles
>>>>>>>>> optimal pme grid 128 128 128, coulomb cutoff 1.200
>>>>>>>>> Step Time Lambda
>>>>>>>>> 2500 5.00000 0.00000
>>>>>>>>>
>>>>>>>>> Energies (kJ/mol)
>>>>>>>>> G96Angle Proper Dih. Improper Dih. LJ-14
>>>>>>>>> Coulomb-14
>>>>>>>>> 9.72545e+03 4.33046e+03 2.98087e+03 -1.95794e+02
>>>>>>>>> 8.05967e+04
>>>>>>>>> LJ (SR) Coulomb (SR) Coul. recip. Potential
>>>>>>>>> Kinetic
>>>>>>>>> En.
>>>>>>>>> 1.01293e+06 -7.13110e+06 2.01689e+04 -6.00057e+06
>>>>>>>>> 1.08489e+06
>>>>>>>>> Total Energy Conserved En. Temperature Pressure (bar)
>>>>>>>>> Constr.
>>>>>>>>> rmsd
>>>>>>>>> -4.91567e+06 -4.90300e+06 3.00225e+02 1.36173e+02
>>>>>>>>> 2.25998e-05
>>>>>>>>>
>>>>>>>>> Step Time Lambda
>>>>>>>>> 5000 10.00000 0.00000
>>>>>>>>>
>>>>>>>>> ............
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thank you in advance
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Carmen Di Giovanni, PhD
>>>>>>>>> Dept. of Pharmaceutical and Toxicological Chemistry
>>>>>>>>> "Drug Discovery Lab"
>>>>>>>>> University of Naples "Federico II"
>>>>>>>>> Via D. Montesano, 49
>>>>>>>>> 80131 Naples
>>>>>>>>> Tel.: ++39 081 678623
>>>>>>>>> Fax: ++39 081 678100
>>>>>>>>> Email: cdigiova at unina.it
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Quoting Justin Lemkul <jalemkul at vt.edu>:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 2/18/15 11:09 AM, Barnett, James W wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> What's your exact command?
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> A full .log file would be even better; it would tell us everything
>>>>>>>>>> we
>>>>>>>>>> need
>>>>>>>>>> to know :)
>>>>>>>>>>
>>>>>>>>>> -Justin
>>>>>>>>>>
>>>>>>>>>>> Have you reviewed this page:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>>>>>>>>>>>
>>>>>>>>>>> James "Wes" Barnett
>>>>>>>>>>> Ph.D. Candidate
>>>>>>>>>>> Chemical and Biomolecular Engineering
>>>>>>>>>>>
>>>>>>>>>>> Tulane University
>>>>>>>>>>> Boggs Center for Energy and Biotechnology, Room 341-B
>>>>>>>>>>>
>>>>>>>>>>> ________________________________________
>>>>>>>>>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>>>>>>>>>>> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
>>>>>>>>>>> Carmen
>>>>>>>>>>> Di
>>>>>>>>>>> Giovanni <cdigiova at unina.it>
>>>>>>>>>>> Sent: Wednesday, February 18, 2015 10:06 AM
>>>>>>>>>>> To: gromacs.org_gmx-users at maillist.sys.kth.se
>>>>>>>>>>> Subject: Re: [gmx-users] GPU low performance
>>>>>>>>>>>
>>>>>>>>>>> I post the message of a md run :
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Force evaluation time GPU/CPU: 40.974 ms/24.437 ms = 1.677
>>>>>>>>>>> For optimal performance this ratio should be close to 1!
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> NOTE: The GPU has >20% more load than the CPU. This imbalance
>>>>>>>>>>> causes
>>>>>>>>>>> performance loss, consider using a shorter cut-off and a
>>>>>>>>>>> finer
>>>>>>>>>>> PME
>>>>>>>>>>> grid.
>>>>>>>>>>>
>>>>>>>>>>> As can I solved this problem ?
>>>>>>>>>>> Thank you in advance
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Carmen Di Giovanni, PhD
>>>>>>>>>>> Dept. of Pharmaceutical and Toxicological Chemistry
>>>>>>>>>>> "Drug Discovery Lab"
>>>>>>>>>>> University of Naples "Federico II"
>>>>>>>>>>> Via D. Montesano, 49
>>>>>>>>>>> 80131 Naples
>>>>>>>>>>> Tel.: ++39 081 678623
>>>>>>>>>>> Fax: ++39 081 678100
>>>>>>>>>>> Email: cdigiova at unina.it
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Quoting Justin Lemkul <jalemkul at vt.edu>:
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On 2/18/15 10:30 AM, Carmen Di Giovanni wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Daear all,
>>>>>>>>>>>>> I'm working on a machine with an INVIDIA Teska K20.
>>>>>>>>>>>>> After a minimization on a protein of 1925 atoms this is the
>>>>>>>>>>>>> mesage:
>>>>>>>>>>>>>
>>>>>>>>>>>>> Force evaluation time GPU/CPU: 2.923 ms/116.774 ms = 0.025
>>>>>>>>>>>>> For optimal performance this ratio should be close to 1!
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Minimization is a poor indicator of performance. Do a real MD
>>>>>>>>>>>> run.
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> NOTE: The GPU has >25% less load than the CPU. This imbalance
>>>>>>>>>>>>> causes
>>>>>>>>>>>>> performance loss.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Core t (s) Wall t (s) (%)
>>>>>>>>>>>>> Time: 3289.010 205.891 1597.4
>>>>>>>>>>>>> (steps/hour)
>>>>>>>>>>>>> Performance: 8480.2
>>>>>>>>>>>>> Finished mdrun on rank 0 Wed Feb 18 15:50:06 2015
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Cai I improve the performance?
>>>>>>>>>>>>> At the moment in the forum I didn't full informations to solve
>>>>>>>>>>>>> this
>>>>>>>>>>>>> problem.
>>>>>>>>>>>>> In attachment there is the log. file
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> The list does not accept attachments. If you wish to share a
>>>>>>>>>>>> file,
>>>>>>>>>>>> upload it to a file-sharing service and provide a URL. The full
>>>>>>>>>>>> .log is quite important for understanding your hardware,
>>>>>>>>>>>> optimizations, and seeing full details of the performance
>>>>>>>>>>>> breakdown.
>>>>>>>>>>>> But again, base your assessment on MD, not EM.
>>>>>>>>>>>>
>>>>>>>>>>>> -Justin
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>> ==================================================
>>>>>>>>>>>>
>>>>>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>>>>>>>
>>>>>>>>>>>> Department of Pharmaceutical Sciences
>>>>>>>>>>>> School of Pharmacy
>>>>>>>>>>>> Health Sciences Facility II, Room 629
>>>>>>>>>>>> University of Maryland, Baltimore
>>>>>>>>>>>> 20 Penn St.
>>>>>>>>>>>> Baltimore, MD 21201
>>>>>>>>>>>>
>>>>>>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>>>>>>>
>>>>>>>>>>>> ==================================================
>>>>>>>>>>>> --
>>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>>>
>>>>>>>>>>>> * Please search the archive at
>>>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>>>>>>>>>>> before
>>>>>>>>>>>> posting!
>>>>>>>>>>>>
>>>>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>>>
>>>>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>>>>>
>>>>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>>>>>> or send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>>
>>>>>>>>>>> * Please search the archive at
>>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>>>>>>>>>> before
>>>>>>>>>>> posting!
>>>>>>>>>>>
>>>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>>
>>>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>>>>
>>>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>>>>> or
>>>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> ==================================================
>>>>>>>>>>
>>>>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>>>>>
>>>>>>>>>> Department of Pharmaceutical Sciences
>>>>>>>>>> School of Pharmacy
>>>>>>>>>> Health Sciences Facility II, Room 629
>>>>>>>>>> University of Maryland, Baltimore
>>>>>>>>>> 20 Penn St.
>>>>>>>>>> Baltimore, MD 21201
>>>>>>>>>>
>>>>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>>>>>
>>>>>>>>>> ==================================================
>>>>>>>>>> --
>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at
>>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>>>> posting!
>>>>>>>>>>
>>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>>
>>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>>>> or
>>>>>>>>>> send
>>>>>>>>>> a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>
>>>>>>>>> * Please search the archive at
>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>>> posting!
>>>>>>>>>
>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>>
>>>>>>>>> * For (un)subscribe requests visit
>>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>>> or
>>>>>>>>> send a
>>>>>>>>> mail to gmx-users-request at gromacs.org.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Gromacs Users mailing list
>>>>>>>>
>>>>>>>> * Please search the archive at
>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>>> posting!
>>>>>>>>
>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>
>>>>>>>> * For (un)subscribe requests visit
>>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>>> or
>>>>>>>> send
>>>>>>>> a mail to gmx-users-request at gromacs.org.
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>
>
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