[gmx-developers] threads are now ON by default
Alexey Shvetsov
alexxyum at gmail.com
Fri Feb 12 21:21:03 CET 2010
On Пятница 12 февраля 2010 19:32:46 Sander Pronk wrote:
> Now that the last issues have been resolved with the threading code,
> thread-based parallelization has been turned on by default. To disable all
> the threading code, use
>
> --disable-threads.
>
> in configure, or turn the option GMX_THREADS off with ccmake.
>
> Running mdrun with just one thread (the default) is almost exactly the same
> as running it without threading code: the only thing that's different is
> that the few remaining global variables are protected by mutexes.
>
> Performance-wise mdrun runs very slightly faster with threads than with
> OpenMPI when Nthreads<=Ncores (and there is no other processes on the
> computer). When Nthreads>Ncores (or other processes are running), the
> thread code is much faster than OpenMPI, but the total runtime is still
> smaller than when Nthreads==Ncores.
>
> If there's any problems in getting things running, or with performance, I'd
> very much like to hear about it.
>
> Sander
Good news.
but looks like i get deadlock when running gromacs with 4 threads (intel core
i5 750) with md-vv integrator. I can share all input files. Same system with
almost same input parameters except integrator (md) runs fine with 4 threads
backtrace
0x00002b9c9fd9dd87 in sched_yield () at ../sysdeps/unix/syscall-template.S:82
82 ../sysdeps/unix/syscall-template.S: No such file or directory.
in ../sysdeps/unix/syscall-template.S
(gdb) bt
#0 0x00002b9c9fd9dd87 in sched_yield () at ../sysdeps/unix/syscall-
template.S:82
#1 0x00002b9c9f5aeb5d in tMPI_Gather (sendbuf=0x4, sendcount=<value optimized
out>, sendtype=<value optimized out>, recvbuf=<value optimized out>,
recvcount=<value optimized out>, recvtype=<value optimized out>, root=0,
comm=0xee2160)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/gmxlib/thread_mpi/gather.c:98
#2 0x00002b9c9f17885e in dd_gather (dd=<value optimized out>,
nbytes=1607464840, src=0x1290748, dest=0xffffffffffffffff)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/domdec_network.c:233
#3 0x00002b9c9f16f841 in dd_collect_cg (dd=<value optimized out>,
state_local=0x12d3600, lv=<value optimized out>, v=0x2b9cb4001010)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/domdec.c:1263
#4 dd_collect_vec (dd=<value optimized out>, state_local=0x12d3600, lv=<value
optimized out>, v=0x2b9cb4001010)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/domdec.c:1420
#5 0x00002b9c9f170df9 in dd_collect_state (dd=0x1287df0,
state_local=0x12d3600, state=0x2b9ca83782b0)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/domdec.c:1474
#6 0x00002b9c9f1d0b7b in write_traj (fplog=<value optimized out>,
cr=0x2b9ca8377ad0, fp_trn=<value optimized out>, bX=-1, bV=8, bF=0, fp_xtc=-1,
bXTC=0,
xtc_prec=1000, fn_cpt=0xee2490 "speptide.md.cpt", bCPT=1,
top_global=0x2b9ca83780b0, eIntegrator=10, simulation_part=1, step=14690,
t=29.379999999999999, state_local=0x12d3600, state_global=0x2b9ca83782b0,
f_local=0x12d8b00, f_global=0x2b9cb4c02010, n_xtc=0x7fff5fd02398,
x_xtc=0x7fff5fd02320) at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/stat.c:473
#7 0x0000000000414318 in do_md (fplog=<value optimized out>, cr=<value
optimized out>, nfile=<value optimized out>, fnm=<value optimized out>,
oenv=<value optimized out>, bVerbose=<value optimized out>, bCompact=1,
nstglobalcomm=1, vsite=0x0, constr=0x129b5d0, stepout=100, ir=0x2b9ca8377b40,
top_global=0x2b9ca83780b0, fcd=0x1287c60, state_global=0x2b9ca83782b0,
mdatoms=0x1296de0, nrnb=0x1290b90, wcycle=0x1290800, ed=0x0, fr=0x1291200,
repl_ex_nst=0, repl_ex_seed=-1, cpt_period=<value optimized out>,
max_hours=<value optimized out>, Flags=7168, runtime=0x7fff5fd02710)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/md.c:1943
#8 0x000000000040f155 in mdrunner (fplog=0xee1c50, cr=0x2b9ca8377ad0,
nfile=<value optimized out>, fnm=<value optimized out>, oenv=<value optimized
out>,
bVerbose=<value optimized out>, bCompact=1, nstglobalcomm=-1,
ddxyz=0x7fff5fd02844, dd_node_order=1, rdd=<value optimized out>,
rconstr=<value optimized out>, dddlb_opt=0x41f64d "auto", dlb_scale=<value
optimized out>, ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nstepout=100, resetstep=-1,
nmultisim=0, repl_ex_nst=0, repl_ex_seed=-1, pforce=<value optimized out>,
cpt_period=<value optimized out>, max_hours=<value optimized out>,
Flags=7168) at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/runner.c:669
#9 0x0000000000410168 in mdrunner_start_fn (arg=<value optimized out>)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/runner.c:170
#10 0x00002b9c9f5af8d4 in tMPI_Thread_starter (arg=<value optimized out>)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/gmxlib/thread_mpi/tmpi_init.c:360
#11 0x00002b9c9f5afc04 in tMPI_Init_fn (N=19466056, start_function=<value
optimized out>, arg=<value optimized out>)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/gmxlib/thread_mpi/tmpi_init.c:472
#12 0x000000000040ff19 in mdrunner_threads (nthreads=4, fplog=<value optimized
out>, cr=<value optimized out>, nfile=<value optimized out>,
fnm=<value optimized out>, oenv=<value optimized out>, bVerbose=1,
bCompact=1, nstglobalcomm=-1, ddxyz=0x7fff5fd04b10, dd_node_order=1,
rdd=<value optimized out>, rconstr=<value optimized out>,
dddlb_opt=0x41f64d "auto", dlb_scale=<value optimized out>, ddcsx=0x0,
ddcsy=0x0, ddcsz=0x0,
nstepout=100, resetstep=-1, nmultisim=0, repl_ex_nst=0, repl_ex_seed=-1,
pforce=<value optimized out>, cpt_period=<value optimized out>,
max_hours=<value optimized out>, Flags=7168) at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/runner.c:238
#13 0x0000000000419a1b in main (argc=6, argv=0x7fff5fd04ce8) at
/var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/mdrun.c:519
Current language: auto
The current source language is "auto; currently asm".
(gdb) up
#1 0x00002b9c9f5aeb5d in tMPI_Gather (sendbuf=0x4, sendcount=<value optimized
out>, sendtype=<value optimized out>, recvbuf=<value optimized out>,
recvcount=<value optimized out>, recvtype=<value optimized out>, root=0,
comm=0xee2160)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/gmxlib/thread_mpi/gather.c:98
98 TMPI_YIELD_WAIT(cur);
Current language: auto
The current source language is "auto; currently c".
(gdb) up
#2 0x00002b9c9f17885e in dd_gather (dd=<value optimized out>,
nbytes=1607464840, src=0x1290748, dest=0xffffffffffffffff)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/domdec_network.c:233
233 MPI_Gather(src,nbytes,MPI_BYTE,
(gdb) up
#3 0x00002b9c9f16f841 in dd_collect_cg (dd=<value optimized out>,
state_local=0x12d3600, lv=<value optimized out>, v=0x2b9cb4001010)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/domdec.c:1263
1263 dd_gather(dd,2*sizeof(int),buf2,ibuf);
(gdb) up
#4 dd_collect_vec (dd=<value optimized out>, state_local=0x12d3600, lv=<value
optimized out>, v=0x2b9cb4001010)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/domdec.c:1420
1420 dd_collect_cg(dd,state_local);
(gdb) up
#5 0x00002b9c9f170df9 in dd_collect_state (dd=0x1287df0,
state_local=0x12d3600, state=0x2b9ca83782b0)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/domdec.c:1474
1474 dd_collect_vec(dd,state_local,state_local->x,state-
>x);
(gdb) up
#6 0x00002b9c9f1d0b7b in write_traj (fplog=<value optimized out>,
cr=0x2b9ca8377ad0, fp_trn=<value optimized out>, bX=-1, bV=8, bF=0, fp_xtc=-1,
bXTC=0,
xtc_prec=1000, fn_cpt=0xee2490 "speptide.md.cpt", bCPT=1,
top_global=0x2b9ca83780b0, eIntegrator=10, simulation_part=1, step=14690,
t=29.379999999999999, state_local=0x12d3600, state_global=0x2b9ca83782b0,
f_local=0x12d8b00, f_global=0x2b9cb4c02010, n_xtc=0x7fff5fd02398,
x_xtc=0x7fff5fd02320) at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/mdlib/stat.c:473
473 dd_collect_state(cr->dd,state_local,state_global);
(gdb) up
#7 0x0000000000414318 in do_md (fplog=<value optimized out>, cr=<value
optimized out>, nfile=<value optimized out>, fnm=<value optimized out>,
oenv=<value optimized out>, bVerbose=<value optimized out>, bCompact=1,
nstglobalcomm=1, vsite=0x0, constr=0x129b5d0, stepout=100, ir=0x2b9ca8377b40,
top_global=0x2b9ca83780b0, fcd=0x1287c60, state_global=0x2b9ca83782b0,
mdatoms=0x1296de0, nrnb=0x1290b90, wcycle=0x1290800, ed=0x0, fr=0x1291200,
repl_ex_nst=0, repl_ex_seed=-1, cpt_period=<value optimized out>,
max_hours=<value optimized out>, Flags=7168, runtime=0x7fff5fd02710)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/md.c:1943
1943 write_traj(fplog,cr,fp_trn,bX,bV,bF,fp_xtc,bXTC,ir-
>xtcprec,
(gdb) up
#8 0x000000000040f155 in mdrunner (fplog=0xee1c50, cr=0x2b9ca8377ad0,
nfile=<value optimized out>, fnm=<value optimized out>, oenv=<value optimized
out>,
bVerbose=<value optimized out>, bCompact=1, nstglobalcomm=-1,
ddxyz=0x7fff5fd02844, dd_node_order=1, rdd=<value optimized out>,
rconstr=<value optimized out>, dddlb_opt=0x41f64d "auto", dlb_scale=<value
optimized out>, ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nstepout=100, resetstep=-1,
nmultisim=0, repl_ex_nst=0, repl_ex_seed=-1, pforce=<value optimized out>,
cpt_period=<value optimized out>, max_hours=<value optimized out>,
Flags=7168) at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/runner.c:669
669 integrator[inputrec->eI].func(fplog,cr,nfile,fnm,
(gdb) up
#9 0x0000000000410168 in mdrunner_start_fn (arg=<value optimized out>)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/runner.c:170
170 mda->ret=mdrunner(fplog, cr, mc.nfile, mc.fnm, mc.oenv,
mc.bVerbose,
(gdb) up
#10 0x00002b9c9f5af8d4 in tMPI_Thread_starter (arg=<value optimized out>)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/gmxlib/thread_mpi/tmpi_init.c:360
360 th->start_fn(th->start_arg);
(gdb) up
#11 0x00002b9c9f5afc04 in tMPI_Init_fn (N=19466056, start_function=<value
optimized out>, arg=<value optimized out>)
at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/gmxlib/thread_mpi/tmpi_init.c:472
472 tMPI_Start_threads(N, 0, 0, start_function, arg);
(gdb) up
#12 0x000000000040ff19 in mdrunner_threads (nthreads=4, fplog=<value optimized
out>, cr=<value optimized out>, nfile=<value optimized out>,
fnm=<value optimized out>, oenv=<value optimized out>, bVerbose=1,
bCompact=1, nstglobalcomm=-1, ddxyz=0x7fff5fd04b10, dd_node_order=1,
rdd=<value optimized out>, rconstr=<value optimized out>,
dddlb_opt=0x41f64d "auto", dlb_scale=<value optimized out>, ddcsx=0x0,
ddcsy=0x0, ddcsz=0x0,
nstepout=100, resetstep=-1, nmultisim=0, repl_ex_nst=0, repl_ex_seed=-1,
pforce=<value optimized out>, cpt_period=<value optimized out>,
max_hours=<value optimized out>, Flags=7168) at /var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/runner.c:238
238 tMPI_Init_fn(nthreads, mdrunner_start_fn, (void*)(&mda) );
(gdb) up
#13 0x0000000000419a1b in main (argc=6, argv=0x7fff5fd04ce8) at
/var/tmp/portage/sci-
chemistry/gromacs-9999/work/gromacs-9999/src/kernel/mdrun.c:519
519 rc = mdrunner_threads(nthreads,
(gdb) up
--
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
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