[gmx-users] Cannot find "gmx_mpi" when installing gromacs 5.0

[朱文鹏]

Dear Mark,

Thank you for your response. But I can install gromacs 4.6.5 successfully
with the same permission.

I will still contact the administrator of the cluster. Do you have idea
what permissions I should ask them for if I need to install 5.0? Any files
or directories, or any permissions to execute files?

I don't think it is good for gromacs installation to access some parts
needing higher permissions. After all, most of users who need to install
gromacs onto cluster are not administrators.

Best,
Jason


>Date: Thu, 28 Aug 2014 08:45:40 +0200
>From: Mark Abraham <mark.j.abraham at gmail.com>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Cannot find "gmx_mpi" when installing gromacs
        5.0
>Message-ID:
        <CAMNuMAQmqGKJdL7RgzfM4uA4OVXsPo5r98EvUmm5ZucP1oJCxA at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8

>I'd guess your permissions on some part of
>/users/yli/gromacs-5.0/exec/bin/gmx_mpi
>are such that you can't access.

>Mark


On Thu, Aug 28, 2014 at 4:06 AM, ??? <jasonzhu925 at gmail.com> wrote:

> Dear all,
>
> I am trying to install gromacs 5.0 by cmake on my cluster. But an error
> occurs when I "make install".
>
> The "module list" for environment is given as below:
> mvapich2/2.0rc1-intel
> cmake/2.8.12.2
> intel/2013.1.106
> fftw/3.3.2
>
> And the sequence of commands to execute is:
> -------------------------------------------------------
> cmake ../ \
> -DCMAKE_C_COMPILER=mpicc \
> -DCMAKE_CXX_COMPILER=mpicxx \
> -DGMX_X11=OFF \
> -DGMX_MPI=ON \
> -DCMAKE_INSTALL_PREFIX=/users/yli/gromacs-5.0/exec \
> -DCMAKE_INCLUDE_PATH=/gpfs/runtime/opt/fftw/3.3.2/include \
> -DCMAKE_LIBRARY_PATH=/gpfs/runtime/opt/fftw/3.3.2/lib/libfftw3f.a
>
> make
>
> make install
> -------------------------------------------------------
>
> Configuration and "make" finished successfully. There are no errors or
> warnings on the first two steps. However, an error shows up at the final
> step of "make install" as below:
> ---------------------------
> ..........
> -- Up-to-date:
>
> /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/
analysismodule.h
> -- Up-to-date:
>
> /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/
analysissettings.h
> -- Up-to-date:
>
> /users/yli/gromacs-5.0/exec/include/gromacs/trajectoryanalysis/
cmdlinerunner.h
> CMake Error at src/programs/cmake_install.cmake:42 (FILE):
>   file INSTALL cannot find "/users/yli/gromacs-5.0/exec/bin/gmx_mpi".
> Call Stack (most recent call first):
>   src/cmake_install.cmake:40 (INCLUDE)
>   cmake_install.cmake:49 (INCLUDE)
>
>
> make: *** [install] Error 1
> ---------------------------
>
> And the executable file "gmx_mpi" cannot be found anywhere. It is the
first
> time I install the version 5.0. The same installation and environments
work
> for the version 4.6.5. I am wondering if anyone has the same problems when
> installing gromacs 5.0. I would appreciate it if you have any suggestion
to
> my installation.
>
> Thank you very much.
>
> Best,
> Jason