[gmx-users] cluster

[David van der Spoel]

Kushal Seth wrote:
> hi all !
> I am trying to run the following command -
> grompp -np 2  -v -f em.mdp -po emout-nowater -c
> binaryCR-Ochol-box-largeZ.pdb -p mytop-nowater1.top -o em-nowater.tpr
> 
> but i am encountering this problem,
> 
> 
> checking input for internal consistency...
> ...ling /usr/bin/cpp
> : No such file or directory
> cpp exit code: 32512

you don't have cpp in the expected place. check your mdp file and type 
which cpp to find where it is.


>  -I/usr/local/gromacs/share/gromacs/top  mytop-nowater1.top > gromppztCLJM'
> ' command is defined in the .mdp file
> processing topology...
> processing coordinates...
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: grompp.c, line: 427
> 
> Fatal error:
> number of coordinates in coordinate file ( 
> binaryCR-Ochol-box-largeZ.pdb, 10280)
>             does not match topology (mytop-nowater1.top, 0)
> 
> Plz help me on this.
> Thanks a lot in advance.
> 
>  
> On 4/2/06, *David van der Spoel* <spoel at xray.bmc.uu.se 
> <mailto:spoel at xray.bmc.uu.se>> wrote:
> 
>     Beniamino Sciacca wrote:
>      > thanks.
>      > but... another question: can i use a crossed network cable or a hub
>      > instead the switch?
>      > how can i say to gromacs to use both the pc?
>     Cross cable should work if you can convince your OS that you have
>     anetwork connection. search the website for running in parallel, e.g .
>     mpirun is a good keyword.
> 
> 
>      > thanks anymore, and sorry if the question isn't opportune enough
>      >
>      >
>      >
>      > David van der Spoel ha scritto:
>      >
>      >> Beniamino Sciacca wrote:
>      >>
>      >>> Hi!
>      >>> I've a laptop with centrino duo, and a desktop with AMD 64 X2.
>      >>> I've to work with my two pc in parallel. What have I to do?
>      >>> can i use a net cable?
>      >>
>      >> not really a gromacs question but anyway.
>      >> install the same OS on both (i.e. not 32 bit on the Intel and 64 bit
>      >> on the AMD). Install LAM, and then Gromacs.
>      >> Use network cables conected to a switch.
>      >>
>      >>
>      >>> thanks
>      >>> Beniamino
>      >>>
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> 
>     --
>     David.
>     ________________________________________________________________________
> 
>     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596,          75124 Uppsala, Sweden
>     phone:  46 18 471 4205          fax: 46 18 511 755
>     spoel at xray.bmc.uu.se
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
>     ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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