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-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher > On Mar 21, 2016, at 5:46 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote: > > No, because replicas must be run in multisander/multipmemd mode! > >> On Mon, Mar 21, 2016 at 10:36 AM, Bin ZOU <zoubin1025.gmail.com> wrote: >> >> Hi Elisa, >> >> You can just use pmemd, not the MPI version, to have a try and maybe you >> can see what is wrong >> >> On Mon, Mar 21, 2016 at 5:08 PM, Elisa Pieri <elisa.pieri90.gmail.com> >> wrote: >> >>> Ah yes, I forgot to mention it.. the mdout files are empty. Just like the >>> cpouts and the logfiles. >>> >>> Any idea? >>> >>> Thanks, Elisa >>> >>> On Fri, Mar 18, 2016 at 7:46 PM, Jason Swails <jason.swails.gmail.com> >>> wrote: >>> >>>> On Fri, Mar 18, 2016 at 6:05 AM, Elisa Pieri <elisa.pieri90.gmail.com> >>>> wrote: >>>> >>>>> Dear all, >>>>> >>>>> I was perfectly able to run pH-REMD in explicit solvent, while I have >>>>> problems in Implicit solvent. When I execute the command: >>>>> >>>>> mpirun -n 16 pmemd.MPI -ng 8 -groupfile dio.grpfile >>>>> >>>>> I get this error: >>>>> >>>>> Running multipmemd version of pmemd Amber12 >>>>> Total processors = 16 >>>>> Number of groups = 8 >> -------------------------------------------------------------------------- >>>>> MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD >>>>> with errorcode 1. >>>>> >>>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>> You may or may not see output from other processes, depending on >>>>> exactly when Open MPI kills them. >> -------------------------------------------------------------------------- >> -------------------------------------------------------------------------- >>>>> mpirun has exited due to process rank 3 with PID 6576 on >>>>> node agachon exiting improperly. There are two reasons this could >>> occur: >>>>> >>>>> 1. this process did not call "init" before exiting, but others in >>>>> the job did. This can cause a job to hang indefinitely while it waits >>>>> for all processes to call "init". By rule, if one process calls >> "init", >>>>> then ALL processes must call "init" prior to termination. >>>>> >>>>> 2. this process called "init", but exited without calling "finalize". >>>>> By rule, all processes that call "init" MUST call "finalize" prior to >>>>> exiting or it will be considered an "abnormal termination" >>>>> >>>>> This may have caused other processes in the application to be >>>>> terminated by signals sent by mpirun (as reported here). >>>>> >>>>> The groupfile has 8 items repeating the unity: >>>>> >>>>> # pH 08 >>>>> -O -i ph08.mdin -p 3lzt.parm7 -c 3lzt.equil.rst7 -cpin >> 3lzt.equil.cpin >>> -o >>>>> 3lzt.ph08.mdout -cpout 3lzt.ph08.cpout -cprestrt 3lzt.ph08.cpin -r >>>>> 3lzt.ph08.rst7 -inf 3lzt.ph08.mdinfo -rem 4 -remlog rem.ph.log -x >>>>> 3lzt.ph08.nc >>>>> >>>>> (of course, the pH changes from item to item). This is (one of) the >>>> input: >>>>> >>>>> REM for CpH >>>>> &cntrl >>>>> icnstph=1, dt=0.002, ioutfm=1, ntxo=2, >>>>> nstlim=100, ig=-1, ntb=0, numexchg=10000, >>>>> ntwr=10000, ntwx=1000, irest=1, >>>>> cut=30, ntcnstph=5, ntpr=1000, >>>>> ntx=5, solvph=8, saltcon=0.1, ntt=3, >>>>> ntc=2, ntf=2, gamma_ln=5.0, igb=2, >>>>> tempi=300, temp0=300, nrespa=1, >>>>> tol=0.000001, >>>>> / >>>>> >>>>> I don't understand where this error comes from. Can you help me? >>>> >>>> The error message you sent is another one of those "something went >>> wrong" >>>> error messages -- but it gives no details about the "what" went wrong. >>>> Look for error messages in some of the mdout files -- those will be >> more >>>> informative. >>>> >>>> HTH, >>>> Jason >>>> >>>> -- >>>> Jason M. Swails >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> >> -- >> Regards, >> ZOU, Bin >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Mar 21 2016 - 08:00:04 PDT