Hi Susana,
There are two test cases under that directory: Run.amoeba and
Run.amoeba_sol. Can you
try to run sander using the output of the other one: Run.amoeba_sol?
The command should
be:
$AMBERHOME/exe/sander -O -i mdin -c hpv.xyz -p hpv.prmtop.save -o
hpv.out
Sincerely,
Wei
On Apr 29, 2009, at 12:45 PM, Tomasio, Susana wrote:
>
> Hi all!!
>
> I'm still stuck with the same problem! I am just trying to run the
> amoeba test and I can't run sander.
> I don't understand where does the file 'inpcrd' that is on
> $AMBERHOME/amber10/test/sleap/amoeba come from!
> After passing the Run.amoeba test this is the error that I get when
> I try to run sander:
>
> The command that I am using is the following:
>
> $AMBERHOME/exe/sander.MPI -O -i mdin -o jac.out -c jac.xyz -p
> jac_2.prmtop -r jac.rst -x jac.mdcr
>
> bash: mc: line 1: syntax error: unexpected end of file
> -bash: error importing function definition for `mc'
> [node11:18813] MPI_ABORT invoked on rank 0 in communicator
> MPI_COMM_WORLD with errorcode 1
> bash: mc: line 1: syntax error: unexpected end of file
> -bash: error importing function definition for `mc'
> [node11:18813] MPI_ABORT invoked on rank 0 in communicator
> MPI_COMM_WORLD with errorcode 1
> forrtl: error (78): process killed (SIGTERM)
> Image PC Routine Line
> Source
> libpthread.so.0 00002AD2F7C53C00 Unknown Unknown
> Unknown
> libopen-pal.so.0 00002AD2F720194C Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6D99784 Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6DF9ED5 Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6DFAABB Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6DF46CA Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6DAE4AA Unknown Unknown
> Unknown
> libmpi_f77.so.0 00002AD2F6C31BC4 Unknown Unknown
> Unknown
> sander.MPI 00000000004F1863 Unknown Unknown
> Unknown
> sander.MPI 00000000004EEAC6 Unknown Unknown
> Unknown
> sander.MPI 000000000043FE22 Unknown Unknown
> Unknown
> libc.so.6 00002AD2F7D7C184 Unknown Unknown
> Unknown
> sander.MPI 000000000043FD69 Unknown Unknown
> Unknown
>
> Image PC Routine Line
> Source
> libpthread.so.0 00002AD2F7C53C00 Unknown Unknown
> Unknown
> libopen-pal.so.0 00002AD2F720194C Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6D99784 Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6DF9ED5 Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6DFAABB Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6DF46CA Unknown Unknown
> Unknown
> libmpi.so.0 00002AD2F6DAE4AA Unknown Unknown
> Unknown
> libmpi_f77.so.0 00002AD2F6C31BC4 Unknown Unknown
> Unknown
> sander.MPI 00000000004F1863 Unknown Unknown
> Unknown
> sander.MPI 00000000004EEAC6 Unknown Unknown
> Unknown
> sander.MPI 000000000043FE22 Unknown Unknown
> Unknown
> libc.so.6 00002AD2F7D7C184 Unknown Unknown
> Unknown
> sander.MPI 000000000043FD69 Unknown Unknown
> Unknown
>
> Does anyone can help me please?
>
> Thank you,
>
> Susana
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed May 20 2009 - 13:25:16 PDT
