[gmx-users] bash: /home/linux/installation/gromacs/bin/gmx_mpi: cannot execute binary file

[Mark Abraham]

Hi,

That shouldn't happen. Are you able to install and run other software
similarly?

I note that your gmx_mpi binary is quite old, and your cmake command
misspelled  -DCMAKE_INSTALL_PRIFFIX=$SOFT so perhaps you are simply not
doing what you think/say you are doing.

Mark

On Thu, Dec 1, 2016 at 10:56 AM Andrew Bostick <andrew.bostick1 at gmail.com>
wrote:

> Dear gromacs users,
>
> export SOFT=$HOME/installation
> export CPPFLAGS="-I$SOFT/include"
> export LDFLAGS="-L$SOFT/lib"
> export PATH="$PATH":$SOFT/bin
>
> tar xvf cmake-3.6.1.tar.gz
> cd ../cmake-3.6.1.
> ./configure --prefix=$SOFT
>
> make
> make install
>
>
>
> tar xvzf gromacs-5.1.3.tar.gz
>
> cd ../gromacs-5.1.3
>
> mkdir build
>
> cd build
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
> -DGMX_MPI=ON -DGMX_GPU=ON -DCMAKE_INSTALL_PRIFFIX=$SOFT
>
> make
>
> make check
>
> make install
>
> source /home/linux/installation/gromacs/bin/GMXRC
>
> *** The GMXRC file is as follows:
>
> # This is a convenience script to determine which
>
> # type of shell you have, and then run GMXRC.[csh|bash|zsh]
>
> # from the Gromacs binary directory.
>
> # If you only use one shell you can copy that GMXRC.* instead.
>
> # only csh/tcsh set the variable $shell (note: lower case!)
>
> # but check for the contents to be sure, since some environments may
>
> # set it also for other shells
>
> echo $shell | grep -q csh && goto CSH
>
> # if we got here, shell is bsh/bash/zsh/ksh
>
> . /home/linux/installation/gromacs/bin/GMXRC.bash
>
> return
>
> # csh/tcsh jump here
>
> CSH:
>
> source /home/linux/installation/gromacs/bin/GMXRC.csh
>
> ~
>
>
> ~
>
>
> ~
>
>
> ~
>
>
> ~
>
>
> "GMXRC" 18L, 594C
>
> I use following commands:
>
> source /home/linux/installation/gromacs/bin/GMXRC
>
> gmx_mpi
>
> But, I encountered with:
>
> bash: /home/linux/installation/gromacs/bin/gmx_mpi: cannot execute binary
> file
>
>
> In /home/linux/installation/gromacs/bin, I checked executablity of gmx_mpi
> file:
>
>
> -rwxr-xr-x 1 linux linux    3378 2016-07-13 05:56 demux.pl*
>
> -rwxr-xr-x 1 linux linux    149700 2016-07-14 16:12 gmx-completion.bash*
>
> -rwxr-xr-x 1 linux linux    41 2016-09-04 04:44
> gmx-completion-gmx_mpi.bash*
>
> -rwxr-xr-x 1 linux linux    275213 2016-09-04 04:44 gmx_mpi*
>
> -rwxr-xr-x 1 linux linux    594 2016-11-29 03:42 GMXRC*
>
> -rwxr-xr-x 1 linux linux    2758 2016-11-29 03:43 GMXRC.bash*
>
> -rwxr-xr-x 1 linux linux    2995 2016-09-04 02:53 GMXRC.csh*
>
> -rwxr-xr-x 1 linux linux    118 2016-09-04 02:53 GMXRC.zsh*
>
> -rwxr-xr-x 1 linux linux    8217 2016-07-13 05:56 xplor2gmx.pl*
>
>
> I used chmod 777 *.*. After that
>
> -rwxrwxrwx 1 linux linux   3378 2016-07-13 05:56 demux.pl*
>
> -rwxrwxrwx 1 linux linux 149700 2016-07-14 16:12 gmx-completion.bash*
>
> -rwxrwxrwx 1 linux linux     41 2016-09-04 04:44
> gmx-completion-gmx_mpi.bash*
>
> -rwxrwxrwx 1 linux linux 275213 2016-09-04 04:44 gmx_mpi*
>
> -rwxr-xr-x 1 linux linux    594 2016-11-29 03:42 GMXRC*
>
> -rwxrwxrwx 1 linux linux   2758 2016-11-29 03:43 GMXRC.bash*
>
> -rwxrwxrwx 1 linux linux   2995 2016-09-04 02:53 GMXRC.csh*
>
> -rwxrwxrwx 1 linux linux    118 2016-09-04 02:53 GMXRC.zsh*
>
> -rwxrwxrwx 1 linux linux   8217 2016-07-13 05:56 xplor2gmx.pl*
>
>
> After using the following commands:
>
> source /home/linux/installation/gromacs/bin/GMXRC
>
> gmx_mpi
>
> Again, I encountered with:
>
> bash: /home/linux/installation/gromacs/bin/gmx_mpi: cannot execute binary
> file
>
> Any help will be highly appreciated.
> --
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