[gmx-users] AVX libraries with GMX4.6.3
Mark Abraham
mark.j.abraham at gmail.com
Fri Aug 30 20:32:18 CEST 2013
ewald_rtol of 1e-9 is a very long way from the normal range of values,
and your other electrostatics settings seem pretty normal. I'd expect
these results to be of doubtful value, but I am surprised to see
that/if there is a marked different with acceleration type. I suggest
you try a normal simulation protocol and see how you go.
Mark
On Fri, Aug 30, 2013 at 7:31 PM, Ali Sinan Saglam
<asinansaglam at gmail.com> wrote:
> 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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