Re: Amber forcefield in namd simulation in parallel version

From: Santanu Santra (santop420_at_gmail.com)
Date: Fri Dec 02 2016 - 00:05:35 CST

Hi to all,
    I have created prmtop file in xleap and then minimize my protein in
serial version (CPU) , then it was working, but after that when I started
to rescale in HPC (Parellel version) it is writing few lines in output file
and some error came like that above .
  For reference I am sending the configuration file and prmtop file.
     If anyone can suggest anything, this will be highly appreciated.
 Thanks in advance.

On Fri, Dec 2, 2016 at 10:30 AM, Santanu Santra <santop420_at_gmail.com> wrote:

> I have created prmtop file in xleap and then minimize my protein in serial
> version (CPU) , then it was working, but after that when I started to
> rescale in HPC (Parellel version) it is writing few lines in output file
> and some error came like that above:
>
> Reading parm file (protein_test.prmtop) ..
> PARM file in AMBER 7 format
> FATAL ERROR: Failed to read AMBER parm file!
> [0] Stack Traceback:
> [0:0] _Z8NAMD_diePKc+0x72 [0x4f11a2]
> [0:1] _ZN9NamdState14configListInitEP10ConfigList+0xee4 [0x942cb4]
> [0:2] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x42d [0x9c28fd]
> [0:3] TclInvokeStringCommand+0x88 [0xbc5b98]
> [0:4] [0xbc87b7]
> [0:5] [0xbc9bd2]
> [0:6] Tcl_EvalEx+0x16 [0xbca3f6]
> [0:7] Tcl_FSEvalFileEx+0x151 [0xc2c5a1]
> [0:8] Tcl_EvalFile+0x2e [0xc2c75e]
> [0:9] _ZN9ScriptTcl4loadEPc+0xf [0x9c166f]
> [0:10] main+0x425 [0x4f5995]
> [0:11] __libc_start_main+0xfd [0x36c361ed1d]
> [0:12] [0x4f0a39]
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 9 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.
>
>
> On Thu, Dec 1, 2016 at 7:28 PM, Norman Geist <norman.geist_at_uni-greifswald--001a1139821c0374250542a6ba57--
--001a1139821c03742a0542a6ba59--

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