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.abra...@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 > <asinansag...@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 > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ali Sinan Saglam Graduate Student in Chemistry Chong Lab, Room 338, Eberly Hall University of Pittsburgh Pittsburgh, PA 15260 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
