Hi, everyone of gmx-users, I met a problem when I use the ‘particle decomposition’ option in a NTP MD simulation of Engrailed Homeodomain (En) in CL- neutralized water box. It just crashed with an error “Fatal error in PMPI_Bcast: Other MPI error, error stack: …..”. However, I’ve tried the ‘domain decomposition’ and everything is ok! I use the Gromacs 4.05 and 4.07, the MPI lib is mpich2-1.2.1p1. The system box size is 5.386(nm)3. The MDP file list as below:
######################################################## title = En ;cpp = /lib/cpp ;include = -I../top define = integrator = md dt = 0.002 nsteps = 3000000 nstxout = 500 nstvout = 500 nstlog = 250 nstenergy = 250 nstxtcout = 500 comm-mode = Linear nstcomm = 1 ;xtc_grps = Protein energygrps = protein non-protein nstlist = 10 ns_type = grid pbc = xyz ;default xyz ;periodic_molecules = yes ;default no rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes tcoupl = v-rescale tc_grps = protein non-protein tau_t = 0.1 0.1 ref_t = 298 298 Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 298 gen_seed = 173529 constraints = hbonds lincs_order = 10 ######################################################## When I conduct MD using “nohup mpiexec -np 2 mdrun_dmpi -s 11_Trun.tpr -g 12_NTPmd.log -o 12_NTPmd.trr -c 12_NTPmd.pdb -e 12_NTPmd_ener.edr -cpo 12_NTPstate.cpt &”, everything is OK. Since the system doesn’t support more than 2 processes under ‘domain decomposition’ option, it took me about 30 days to calculate a 6ns trajectory. Then I decide to use the ‘particle decomposition’ option. The command line is “nohup mpiexec -np 6 mdrun_dmpi -pd -s 11_Trun.tpr -g 12_NTPmd.log -o 12_NTPmd.trr -c 12_NTPmd.pdb -e 12_NTPmd_ener.edr -cpo 12_NTPstate.cpt &”. And I got the crash in the nohup file like below: #################### Fatal error in PMPI_Bcast: Other MPI error, error stack: PMPI_Bcast(1302)......................: MPI_Bcast(buf=0x8fedeb0, count=60720, MPI_BYTE, root=0, MPI_COMM_WORLD) failed MPIR_Bcast(998).......................: MPIR_Bcast_scatter_ring_allgather(842): MPIR_Bcast_binomial(187)..............: MPIC_Send(41).........................: MPIC_Wait(513)........................: MPIDI_CH3I_Progress(150)..............: MPID_nem_mpich2_blocking_recv(948)....: MPID_nem_tcp_connpoll(1720)...........: state_commrdy_handler(1561)...........: MPID_nem_tcp_send_queued(127).........: writev to socket failed - Bad address rank 0 in job 25 cluster.cn_52655 caused collective abort of all ranks exit status of rank 0: killed by signal 9 #################### And the ends of the log file list as below: #################### …….. …….. …….. …….. bQMMM = FALSE QMconstraints = 0 QMMMscheme = 0 scalefactor = 1 qm_opts: ngQM = 0 #################### I’ve search the gmx-users mail list and tried to adjust the md parameters, and no solution was found. The "mpiexec -np x" option doesn't work except when x=1. I did found that when the whole En protein is constrained using position restraints (define = -DPOSRES), the ‘particle decomposition’ option works. However this is not the kind of MD I want to conduct. Could anyone help me about this problem? And I also want to know how can I accelerate this kind of MD (long time simulation of small system) using Gromacs? Thinks a lot! (Further information about the simulated system: The system has one En protein (54 residues, 629 atoms), total 4848 spce waters, and 7 Cl- used to neutralize the system. The system has been minimized first. A 20ps MD is also performed for the waters and ions before EM.)
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