On 12/07/2011 4:51 AM, Justin A. Lemkul wrote:
Hi All,
I'm having a strange problem with some implicit solvent systems and
I'm wondering if anyone's experienced the same problem or if I've
stumbled upon a bug. I'm testing some methodology with a robust
system (everyone's favorite, 1AKI lysozyme). Running simulations with
finite cutoffs works fine (in serial or parallel using DD), but if I
try to call the all-vs-all kernels (e.g. infinite cutoffs), the
simulations instantly crash (at step 0) with LINCS warnings. Running
in serial, however, produces perfectly stable trajectories using
all-vs-all, but the simulations are very slow.
The effects are independent of integrator (tested sd and md) and
hardware/compilers. The problem is reproducible on two very different
systems:
1. x86_64 via OpenMPI 1.4.2 and compiled with cmake with gcc-4.3.4
2. Mac OSX with threads and compiled via autoconf with gcc-4.4.4
All force fields that I've tested (OPLS-AA, CHARMM27, and AMBER03)
give the same result.
The problem is present in version 4.5.4 and the most current
release-4-5-patches. My .mdp file and a gdb backtrace are provided at
the end of this message.
Is there anything else to try, or should I just file a redmine issue
with a .tpr file?
Judging by the .mdp file, I have similar systems working just fine in
parallel. If you upload the .tpr to Redmine, I'll try it out.
Mark
-Justin
=== .mdp file ===
constraints = all-bonds
integrator = sd
dt = 0.002 ; ps !
nsteps = 50000 ; 100 ps
nstlist = 0
ns_type = simple ; grid also fails
rlist = 0
coulombtype = cut-off
vdwtype = cut-off
rcoulomb = 0
rvdw = 0
pbc = no
epsilon_rf = 0
rgbradii = 0
comm_mode = angular
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78.3
sa_surface_tension = 2.25936
nstxout = 0
nstfout = 0
nstvout = 0
nstxtcout = 500
nstlog = 500
nstcalcenergy = -1
nstenergy = 500
tc_grps = system
tau_t = 1.0
ref_t = 298
gen_vel = yes
gen_temp = 298
gen_seed = 1023
=== debug output ===
(following the usual LINCS warnings)
(gdb) up
#1 0x002cf045 in pbc_rvec_sub (pbc=0x0, xi=0x62fae58, xj=0xf954c55c,
dx=0xbfffc1cc) at genborn.c:106
106 rvec_sub(xi,xj,dx);
(gdb) up
#2 0x002d36c0 in gb_bonds_tab (x=0x39000, f=0xdfe000,
fshift=0x1033e00, charge=0x10d3e00, p_gbtabscale=0x1032028,
invsqrta=0x105e000, dvda=0x1060000, GBtab=0xb35010, idef=0x1092600,
epsilon_r=1, gb_epsilon_solvent=78.3000031, facel=137.161057, pbc=0x0,
graph=0x0) at genborn.c:1373
1373 ki = pbc_rvec_sub(pbc,x[ai],x[aj],dx);
(gdb) up
#3 0x002d4829 in calc_gb_forces (cr=0x903890, md=0x905580,
born=0x905370, top=0x1092600, atype=0x1092b1c, x=0x39000, f=0xdfe000,
fr=0x1031e00, idef=0x1092600, gb_algorithm=2, sa_algorithm=0,
nrnb=0x1031000, bRad=1, pbc=0xbfffc5dc, graph=0x0, enerd=0x9070b0) at
genborn.c:1680
1680 enerd->term[F_GBPOL] += gb_bonds_tab(x,f,fr->fshift,
md->chargeA,&(fr->gbtabscale),
(gdb) up
#4 0x002a4ee1 in do_force_lowlevel (fplog=0xa07d94c0, step=0,
fr=0x1031e00, ir=0x1001a00, idef=0x1092600, cr=0x903890,
nrnb=0x1031000, wcycle=0x904f30, md=0x905580, opts=0x1001c84,
x=0x39000, hist=0x907f50, f=0xdfe000, enerd=0x9070b0, fcd=0x904e10,
mtop=0x900c00, top=0x1092600, born=0x905370, atype=0x1092b1c,
bBornRadii=1, box=0x907e40, lambda=0, graph=0x0, excl=0x1092b44,
mu_tot=0x1031e70, flags=501, cycles_pme=0xbfffc914) at force.c:267
267 calc_gb_forces(cr,md,born,top,atype,x,f,fr,idef,
(gdb) up
#5 0x003373d5 in do_force (fplog=0xa07d94c0, cr=0x903890,
inputrec=0x1001a00, step=0, nrnb=0x1031000, wcycle=0x904f30,
top=0x1092600, mtop=0x900c00, groups=0x900c70, box=0x907e40,
x=0x39000, hist=0x907f50, f=0xdfe000, vir_force=0xbfffd4d4,
mdatoms=0x905580, enerd=0x9070b0, fcd=0x904e10, lambda=0, graph=0x0,
fr=0x1031e00, vsite=0x0, mu_tot=0xbfffd434, t=0, field=0x0, ed=0x0,
bBornRadii=1, flags=501) at sim_util.c:725
725 do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
(gdb) up
#6 0x000173cc in do_md (fplog=0xa07d94c0, cr=0x903890, nfile=28,
fnm=0xbfffed60, oenv=0x900500, bVerbose=1, bCompact=1,
nstglobalcomm=10, vsite=0x0, constr=0x905400, stepout=100,
ir=0x1001a00, top_global=0x900c00, fcd=0x904e10,
state_global=0x900d20, mdatoms=0x905580, nrnb=0x1031000,
wcycle=0x904f30, ed=0x0, fr=0x1031e00, repl_ex_nst=0, repl_ex_seed=-1,
cpt_period=15, max_hours=-1, deviceOptions=0x24214 "", Flags=7680,
runtime=0xbfffd758) at md.c:1015
1015
do_force(fplog,cr,ir,step,nrnb,wcycle,top,top_global,groups,
(gdb) up
#7 0x00013210 in mdrunner (nthreads_requested=2, fplog=0xa07d94c0,
cr=0x903890, nfile=28, fnm=0xbfffed60, oenv=0x900500, bVerbose=1,
bCompact=1, nstglobalcomm=-1, ddxyz=0xbfffea10, dd_node_order=1,
rdd=0, rconstr=0, dddlb_opt=0x2756f "auto", dlb_scale=0.800000012,
ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nstepout=100, resetstep=-1,
nmultisim=0, repl_ex_nst=0, repl_ex_seed=-1, pforce=-1, cpt_period=15,
max_hours=-1, deviceOptions=0x24214 "", Flags=7680) at runner.c:811
811 integrator[inputrec->eI].func(fplog,cr,nfile,fnm,
(gdb) up
#8 0x0001cb7b in main (argc=7, argv=0xbffff3c8) at mdrun.c:662
662 rc = mdrunner(nthreads,
fplog,cr,NFILE,fnm,oenv,bVerbose,bCompact,
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