[gmx-users] build nuance in gmx5 (avoiding "file INSTALL cannot find gmx")

[Christopher Neale]

Dear Szilárd:

I report it only because it is allowed in gmx4 builds (or at least it works, I am not sure whether or not is it "allowed").

I move the source because I often have many modified source trees that I rename to keep things straight.

The quick and dirty method that you cite presumes that one has root access, which is very unlikely on the places that most simulations are run. 

The http://www.gromacs.org/Documentation/Installation_Instructions_5.0#typical-gromacs-installation section below that does have a note about "-DCMAKE_INSTALL_PREFIX=xxx to install GROMACS to a non-standard location (default /usr/local/gromacs)" but that gives no suggestions on how to use it and based on my experience I presume that "-DCMAKE_INSTALL_PREFIX=$(pwd)" would give a similar error if applied to the "quick and dirty" method. 

My intention is not to try to get gromacs to change the build procedure. Just to report something that worked once that no longer works and to include a snippit from the relevant error message so that it is searchable.

Thank you,
Chris.

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Szilárd Páll <pall.szilard at gmail.com>
Sent: 21 May 2015 11:24
To: Discussion list for GROMACS users
Cc: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] build nuance in gmx5 (avoiding "file INSTALL cannot find gmx")

You can't install into the build tree, AFAIK that's not allowed!
Install into a clean target directory instead.

Also, you "mkdir source; mv * source" step is just weird. Why move the
source around? Instead you can simply create a build directory - this
can even be in the source tree just as the uiqck and dirty install
steps suggest:
http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation

--
Szilárd


On Thu, May 21, 2015 at 5:11 PM, Christopher Neale
<chris.neale at alum.utoronto.ca> wrote:
> Dear Users:
>
> This is just a note about compiling gromacs 5 so that the solution can be found by others if they need it.
>
> I used to compile gromacs like this:
>
> download and unpack tarball
> cd gromacs-5.0.5
> mkdir source
> mv * source
> mkdir exec
> cd exec
> ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd)
>
> However, that no longer works. What happens is that "make" creates ./bin/gmx and then "make install" removes ./bin/gmx and then complains that it does not exist:
>
> CMake Error at src/programs/cmake_install.cmake:42 (file):
>   file INSTALL cannot find
>   "/project2/p/pomes/cneale/GPC/exe/intel/gromacs-5.0.5/exec/bin/gmx".
> Call Stack (most recent call first):
>   src/cmake_install.cmake:40 (include)
>   cmake_install.cmake:48 (include)
>
> My solution was to build in a separate directory from either the source or the executable:
> download and unpack tarball
> cd gromacs-5.0.5
> mkdir source
> mv * source
> mkdir exec build
> cd build
> ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd)/../exec
>
> Perhaps this is standard practice. Anyway, my original procedure works for gmx4.6.7 but not gmx5.0.5 so I thought I would report it.
>
> Note that this is separate from the issue that some have reported where a CMAKE_INSTALL_PREFIX using $(pwd) did not install but using the explicit path worked (I tested the explicit paths and got the same error that I report above).
>
> Chris.
>
>
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