[gmx-developers] Branches w/working OpenCL support
Roland Schulz
roland at utk.edu
Thu Jun 18 23:31:58 CEST 2015
On Thu, Jun 18, 2015 at 5:12 PM, Mirco Wahab <
mirco.wahab at chemie.tu-freiberg.de> wrote:
> Hi Mark,
>
> On 17.06.2015 23:31, Mark Abraham wrote:
> > I've solved three correctness issues with the OpenCL implementation now,
> > and NPT on AMD looks quite nice. Can you please try the code at
> > https://gerrit.gromacs.org/#/c/4314/26 and let us know if the situation
> > is improved?
>
> I tried but could not really compile under VS-2013/MSVC-18. The problem
> is, as is already stated in a comment, the macro expansion into an
> alignment declaration, which is not supported by MSVC:
>
This is weird. Because it works for me with VS-2013. Do you have the latest
Update (2013 Update 4)?
Roland
>
> [basedefinitions.h]
> 244:
> #if defined(_MSC_VER) && (_MSC_VER >= 1700 || defined(__ICL))
> # define GMX_ALIGNMENT 1
> # define GMX_ALIGNED(type, alignment)
> __declspec(align(alignment*sizeof(type))) type
> #elif defined(__GNUC__) || defined(__clang__)
> # define GMX_ALIGNMENT 1
> ...
>
>
> I then changed the "(alignment*sizeof(type))" expression
> into "32" which would be probably the value it's been
> expanded to:
> # define GMX_ALIGNED(type, alignment) __declspec(align(32)) type
> but tested other values (16, 64).
>
> I'm not sure this is the show-stopper, but any trial yielded the
> same result. mdrun segfaults immediately after initializing
> independent of the input file (but working fine in nb=cpu mode).
>
> I'm attaching the log file here.
>
> regards,
>
> M.
>
>
>
> --------------------- 8< [crashed md.log w/gpu] ------------------------
> Log file opened on Thu Jun 18 23:09:02 2015
> Host: DENEB pid: 4884 rank ID: 0 number of ranks: 1
> :-) GROMACS - gmx mdrun, VERSION 5.1-beta1-dev (-:
>
> 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 Anca Hamuraru Vincent
> Hindriksen
> Dimitrios Karkoulis 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
> Teemu Virolainen 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) 2001-2015, 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 5.1-beta1-dev
> Executable: D:\GromacsCL\bin\gmx.exe
> Data prefix: D:\GromacsCL
> Command line:
> gmx mdrun -v
>
> GROMACS version: VERSION 5.1-beta1-dev
> Precision: single
> Memory model: 64 bit
> MPI library: thread_mpi
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support: enabled
> OpenCL support: enabled
> invsqrt routine: gmx_software_invsqrt(x)
> SIMD instructions: SSE2
> FFT library: fftw3
> RDTSCP usage: enabled
> C++11 compilation: disabled
> TNG support: enabled
> Tracing support: disabled
> Built on: Unknown date
> Built by: Anonymous at unknown [CMAKE]
> Build OS/arch: Windows-6.2 AMD64
> Build CPU vendor: AuthenticAMD
> Build CPU brand: AMD Phenom(tm) II X6 1090T Processor
> Build CPU family: 16 Model: 10 Stepping: 0
> Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm misalignsse mmx
> msr nonstop_tsc pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a
> C compiler: C:/Program Files (x86)/Microsoft Visual Studio
> 12.0/VC/bin/x86_amd64/cl.exe MSVC 18.0.31101.0
> C compiler flags: /DWIN32 /D_WINDOWS /W3 /MD /O2 /Ob2 /D NDEBUG
> C++ compiler: C:/Program Files (x86)/Microsoft Visual Studio
> 12.0/VC/bin/x86_amd64/cl.exe MSVC 18.0.31101.0
> C++ compiler flags: /DWIN32 /D_WINDOWS /W3 /GR /EHsc /wd4800
> /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090 /MD /O2 /Ob2 /D
> NDEBUG
> Boost version: 1.57.0 (external)
> OpenCL include dir: C:/Program Files (x86)/AMD APP SDK/3.0-0-Beta/include
> OpenCL library: C:/Program Files (x86)/AMD APP
> SDK/3.0-0-Beta/lib/x86_64/OpenCL.lib
> OpenCL version: 2.0
>
>
> Running on 1 node with total 6 cores, 6 hardware threads, 1 compatible GPU
> Hardware detected:
> CPU info:
> Vendor: AuthenticAMD
> Brand: AMD Phenom(tm) II X6 1090T Processor
> Family: 16 model: 10 stepping: 0
> CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm misalignsse mmx
> msr nonstop_tsc pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a
> SIMD instructions most likely to fit this hardware: SSE2
> SIMD instructions selected at GROMACS compile time: SSE2
> GPU info:
> Number of GPUs detected: 1
> #0: name: Pitcairn, vendor: Advanced Micro Devices, Inc., device
> version: OpenCL 1.2 AMD-APP (1642.5), stat: compatible
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
> molecular simulation
> J. Chem. Theory Comput. 4 (2008) pp. 435-447
> -------- -------- --- Thank You --- -------- --------
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
> Berendsen
> GROMACS: Fast, Flexible and Free
> J. Comp. Chem. 26 (2005) pp. 1701-1719
> -------- -------- --- Thank You --- -------- --------
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> E. Lindahl and B. Hess and D. van der Spoel
> GROMACS 3.0: A package for molecular simulation and trajectory analysis
> J. Mol. Mod. 7 (2001) pp. 306-317
> -------- -------- --- Thank You --- -------- --------
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
> GROMACS: A message-passing parallel molecular dynamics implementation
> Comp. Phys. Comm. 91 (1995) pp. 43-56
> -------- -------- --- Thank You --- -------- --------
>
> Input Parameters:
> integrator = md
> tinit = 0
> dt = 0.001
> nsteps = 100000
> init-step = 0
> simulation-part = 1
> comm-mode = Linear
> nstcomm = 100
> bd-fric = 0
> ld-seed = 665864
> emtol = 10
> emstep = 0.01
> niter = 20
> fcstep = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> rtpi = 0.05
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 100
> nstcalcenergy = 100
> nstenergy = 1000
> nstxout-compressed = 100
> compressed-x-precision = 1000
> cutoff-scheme = Verlet
> nstlist = 25
> ns-type = Grid
> pbc = xyz
> periodic-molecules = FALSE
> verlet-buffer-tolerance = 0.005
> rlist = 1.097
> rlistlong = 1.097
> nstcalclr = 25
> coulombtype = Reaction-Field
> coulomb-modifier = Potential-shift
> rcoulomb-switch = 0
> rcoulomb = 1
> epsilon-r = 1
> epsilon-rf = inf
> vdw-type = Cut-off
> vdw-modifier = Potential-shift
> rvdw-switch = 0
> rvdw = 1
> DispCorr = No
> table-extension = 1
> fourierspacing = 0.16
> fourier-nx = 0
> fourier-ny = 0
> fourier-nz = 0
> pme-order = 4
> ewald-rtol = 1e-005
> ewald-rtol-lj = 0.001
> lj-pme-comb-rule = Geometric
> ewald-geometry = 0
> epsilon-surface = 0
> implicit-solvent = No
> gb-algorithm = Still
> nstgbradii = 1
> rgbradii = 1
> gb-epsilon-solvent = 80
> gb-saltconc = 0
> gb-obc-alpha = 1
> gb-obc-beta = 0.8
> gb-obc-gamma = 4.85
> gb-dielectric-offset = 0.009
> sa-algorithm = Ace-approximation
> sa-surface-tension = 2.05016
> tcoupl = V-rescale
> nsttcouple = 25
> nh-chain-length = 0
> print-nose-hoover-chain-variables = FALSE
> pcoupl = No
> pcoupltype = Isotropic
> nstpcouple = -1
> tau-p = 2
> compressibility (3x3):
> compressibility[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000}
> compressibility[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000}
> compressibility[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000}
> ref-p (3x3):
> ref-p[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000}
> ref-p[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000}
> ref-p[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000}
> refcoord-scaling = No
> posres-com (3):
> posres-com[0]=0.00000e+000
> posres-com[1]=0.00000e+000
> posres-com[2]=0.00000e+000
> posres-comB (3):
> posres-comB[0]=0.00000e+000
> posres-comB[1]=0.00000e+000
> posres-comB[2]=0.00000e+000
> QMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> MMChargeScaleFactor = 1
> qm-opts:
> ngQM = 0
> constraint-algorithm = Lincs
> continuation = FALSE
> Shake-SOR = FALSE
> shake-tol = 0.0001
> lincs-order = 4
> lincs-iter = 1
> lincs-warnangle = 30
> nwall = 0
> wall-type = 9-3
> wall-r-linpot = -1
> wall-atomtype[0] = -1
> wall-atomtype[1] = -1
> wall-density[0] = 0
> wall-density[1] = 0
> wall-ewald-zfac = 3
> pull = FALSE
> rotation = FALSE
> interactiveMD = FALSE
> disre = No
> disre-weighting = Conservative
> disre-mixed = FALSE
> dr-fc = 1000
> dr-tau = 0
> nstdisreout = 100
> orire-fc = 0
> orire-tau = 0
> nstorireout = 100
> free-energy = no
> cos-acceleration = 0
> deform (3x3):
> deform[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000}
> deform[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000}
> deform[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000}
> 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: 17493
> ref-t: 300
> tau-t: 0.2
> annealing: No
> annealing-npoints: 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp-flags[ 0]: 0
>
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