Alluded to this yesterday, GROMACS jobs don't finish on a SC. I have some information back from one of the admins there, they want me to post details etc so we can work out what is going on.
It looks like with my input data, GROMACS going into an infinite loop in the nb_kernel100_ia64_single subroutine. Can provide the tpr file assembled on the SC if / as required. GROMACS 4.0.3 on the SC was compiled with intel-cc v.11.0.069 with fftw v.2.1.5 on itanium ia64. Program works fine with generic kernel gmx_nb_generic_kernel but goes to infinite loop inside nb_kernel110_ia64_single. Double precision version works exactly the same way: fine with generic kernel, infinite loop in nb_kernel110_ia64_double. The details of the installation of double precision, single processor version: setenv CC icc setenv CFLAGS "-O3 -ip -ftz" setenv CPPFLAGS "-I$FFTWDIR/include" setenv CXX icpc setenv MPI icc setenv F77 ifort setenv FFLAGS "-O3 -ip -ftz" setenv LD ifort setenv LDFLAGS "-L$FFTWDIR/lib" ./configure --prefix=/opt/gromacs/4.0.3 --exec-prefix=/opt/gromacs/4.0.3 --disable-nice --disable-float --program-suffix=_d --with-fft=fftw2 gmake gmake install My md.mdp file for these runs is (yes, I need to update a few things in this, but want to make some comparisons between versions etc first): ; Run Control integrator = md ; simulation algorithm dt = 0.005 ; time step (ps) nsteps = 20000 ; # steps comm_mode = linear ; c.o.m. motion reset nstcomm = 1 ; steps for c.o.m. motion reset comm_grps = System ; groups for c.o.m. removal ; ; Output Control nstxout = 5000 ; write coordinates to .trr nstvout = 5000 ; write velocities to .trr nstlog = 800 ; write energies to .log nstenergy = 400 ; write energies to .edr nstxtcout = 800 ; write coordinates to .xtc ; ; Neightbour Searching nstlist = 10 ; update neighbour list ns_type = grid ; neighbour list method pbc = xyz ; periodic boundary conditions rlist = 1.0 ; cut-off for short-range neighbour (nm) ; ; Electrostatics and VdW coulombtype = cut-off ; type of coulomb interaction rcoulomb = 1.5 ; cut-off distance for coulomb (nm) epsilon_r = 1 ; dielectric constant vdwtype = cut-off ; type of VdW interaction rvdw = 1.0 ; cut-off for vdw (nm) DispCorr = EnerPres ; long range correction ; ; Temperature Coupling Tcoupl = berendsen ; type of temperature coupling tc-grps = System ; coupled groups tau_t = .05 ; T-coupling time constant (ps) ref_t = 310 ; reference temperature (K) ; ; Pressure Coupling Pcoupl = berendsen ; type of pressure coupling Pcoupltype = anisotropic ; pressure coupling geometry tau_p = 4.0 4.0 4.0 4.0 4.0 4.0 ; p-coupling time constant (ps) compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0 ; compressibiity ref_p = 1.0 1.0 1.0 0 0 0 ; reference pressure (bar) ; ; Velocity Generation gen_vel = no ; generate initial velocities ; ; Bonds constraints = all-bonds ; which bonds to contrain constraint_algorithm = lincs ; algorithm to use lincs_order = 8 ; highest order matrix expansion Catch ya, Dr Dallas Warren
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