[gmx-users] AVX libraries with GMX4.6.3
Ali Sinan Saglam
asinansaglam at gmail.com
Fri Aug 30 19:31:26 CEST 2013
Hi Mark,
I have tried GCC 4.7.1, 4.7.2 and ICC 13 (with and without MKL, my
colleague also tried double precision) compilers, all showed the same
behavior.
I will add the .mdp file I have used but the problem consists for all input
files my colleagues tried (they had their own input files, independent to
me). For example the first graph is Barnase - Barstar in a large box
(~100,000 atoms, explicit tip3p waters, neutralized and a small amount of
salt, roughly 60-70 atoms of NaCl) and the mdp file used was;
;##################################################### INTEGRATOR
######################################################
integrator = md ; Molecular
dynamics
dt = 0.002 ; Timestep (ps)
nsteps = 500000 ; Simulation
duration (timesteps)
nstcomm = 1000 ; Center of
mass motion removal interval (timesteps)
comm-grps = system ; Remove center
of mass motion of system
;###################################################### ENSEMBLE
#######################################################
Pcoupl = no ; Disable
barostat
tcoupl = no ; Disable
thermostat
;################################################ BONDED INTERACTIONS
##################################################
constraints = hbonds ; Disable
constraints
constraint_algorithm = LINCS ; Constrain
bonds using LINCS
lincs_iter = 1 ; Number of
LINCS iterations
;############################################### NONBONDED INTERACTIONS
################################################
coulombtype = PME ; Switch/PME
long-range electrostatics
fourierspacing = 0.1
pme_order = 4
ewald_rtol = 0.000000001
pbc = xyz ; Periodic
boundary condition
rcoulomb = 1.00 ; Short-range
electrostatic cutoff (nm)
;rcoulomb_switch = 0.9 ; Short-range
electrostatic switch cutoff (nm)
vdwtype = Switch ; Switch van
der Waals interactions
rvdw = 0.9 ; Van der Waals
cutoff (nm)
rvdw_switch = 0.8 ; Van der Waals
switch cutoff (nm)
DispCorr = EnerPres ; Long-range
dispersion correction to energy and pressure
ns_type = grid ; Update
neighbor list using grid
nstlist = 10 ; Neighbor list
update interval (timesteps)
rlist = 1.00 ; Neighbor list
cut-off (nm)
continuation = yes
;####################################################### OUTPUT
########################################################
nstlog = 500 ; Energy log
output interval (timesteps)
nstenergy = 500000 ; Energy output
interval (timesteps)
nstxout = 500000 ;
Full-resolution trajectory output interval (timesteps)
nstvout = 500000 ;
Full-resolution velocity output interval (timesteps)
nstfout = 500000 ;
Full-resolution force output interval (timesteps)
nstxtcout = 500 ;
Reduced-resolution trajectory output interval (timesteps)
xtc-precision = 10000 ;
Reduced-resolution trajectory output precision
While the second graph is for EG5 (~130,000 atoms I believe, I don't have
the exact number but I remember that it's a bigger system than mine, same
water model). I'm unsure what my 3rd colleague tested but had similar
results (his system heated to 400+K) and we didn't share any input files.
All conserved energy fine with SSE instruction set (my results were losing
energy with 1.1kcal/mol.ps)
Best,
Ali Sinan Saglam
On Fri, Aug 30, 2013 at 12:03 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> With what compiler? (e.g. consult mdrun -version) There are many known
> bugs in early point versions of each minor release of gcc, for
> example. This is why the installation instructions stress getting the
> latest version of your compiler.
>
> Otherwise, what is your .mdp file and simulation system contents?
>
> Mark
>
> On Fri, Aug 30, 2013 at 5:48 PM, Ali Sinan Saglam
> <asinansaglam at gmail.com> wrote:
> > Hi,
> >
> > I have been running some energy conservation tests with GMX4.6.3 and had
> > encountered some issues when using the AVX-256 instruction set.
> >
> > I first noticed that my systems were freezing on a cluster that uses
> > Sandy-bridge CPUs and did not on a different cluster using SSE. After
> > realizing that the problems were not in my configuration and setup I
> > started compiling multiple copies of Gromacs and saw that only the
> AVX-256
> > compiled binaries showed this behavior.
> >
> > After a few colleagues reproduced the same results, I'm now pretty sure
> > this is the case. Two colleagues started completely independently and
> > reproduced the same behavior on 2 different clusters and 2 desktop
> machines
> > (all sandy-brige, in all cases AVX yielded really weird temperatures,
> > sometimes exponential freezing sometimes heating etc.).
> >
> > Gromacs was compiled with -DGMX_CPU_ACCELERATION=AVX or =SSE4.1 (or any
> > version of SSE) and that was the only difference between the two
> binaries.
> > The method of simulation was exactly the same outside of the mdrun that
> was
> > used. The temperature results from my simulations can be seen here;
> > https://www.dropbox.com/s/ul7g0fb4il17wxm/avx_sse_temp.png
> > Another example with a different person reproducing the results;
> > https://www.dropbox.com/s/x7mr3kcgmvd78ie/adam_avx_sse_temp.png
> >
> > Cmake command was;
> > cmake SOURCE -DGMX_BUILD_OWN_FFTW=on -DGMX_OPENMM=off -DGMX_MPI=off
> > -DGMX_GPU=off -DGMX_THREAD_MPI=on -DGMX_CPU_ACCELERATION=AVX (or SSE4.1)
> > (also tried THREAD_MPI=off, similar results)
> >
> > Also all builds passed regression tests.
> >
> > I just wondered if this is a known problem or are we making a mistake
> while
> > compiling?
> >
> > Best,
> > Ali Sinan Saglam
> > --
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--
Ali Sinan Saglam
Graduate Student in Chemistry
Chong Lab, Room 338, Eberly Hall
University of Pittsburgh
Pittsburgh, PA 15260
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