Hi Wei
Thank you for your reply.
I tried your suggestion but I donīt think itīs running properly. In the qstat it says that it is running,
however the mdinfo output is empty and the results section of the file hpv.out is the following: (it doesnīt change
with time)
| # of SOLUTE degrees of freedom (RNDFP): 42414.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 42411. NUM_NOSHAKE = 0 CORRECTED RNDFP = 42411.
| TOTAL # of degrees of freedom (RNDF) = 42411.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8987E-11 at 2.875760
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 2500071
| TOTAL SIZE OF NONBOND LIST = 4359315
Thank you,
Susana
-----Original Message-----
From: amber-bounces.ambermd.org on behalf of Wei Zhang
Sent: Wed 4/29/2009 7:00 PM
To: AMBER Mailing List
Subject: Re: [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM)
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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed May 20 2009 - 13:26:23 PDT
