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?
Elisa
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Received on Fri Mar 18 2016 - 06:30:04 PDT
