[gmx-developers] threads are now ON by default
Michael Shirts
mrshirts at gmail.com
Fri Feb 12 22:23:51 CET 2010
Hi, Alexey-
Thanks for tracking this down. md-vv is still getting the kinks
worked out. Is this in the same place as the bug you were seeing a
couple of days ago, or a different place?
Sander, perhaps if you could check for non-threadsafeness (looks like
its in write_traj) since you're a bit more familiar -- if you can't
see it quickly, please let me know, and I'll try to track it down!
Best,
Michael
> Date: Fri, 12 Feb 2010 23:21:03 +0300
> From: Alexey Shvetsov <alexxyum at gmail.com>
> Subject: Re: [gmx-developers] threads are now ON by default
> To: Discussion list for GROMACS development
> <gmx-developers at gromacs.org>
> Message-ID: <201002122321.15014.alexxyum at gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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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