[gmx-users] gromacs-5.0.4 installation problem

Fri May 8 04:15:03 CEST 2015

YAY :-) it is working, Do not know what was wrong but apparently something
was seriously messed up with cmake and compilers, removed cmake and gcc
gcc++ complier and gromacs, re-doing solved the problem.

*sudo apt-get update -y*
*sudo apt-get update**sudo apt-get install cmake*
Cheers
James

On Thu, May 7, 2015 at 7:45 PM, Roland Schulz <roland at utk.edu> wrote:

> Hi,
>
> please rerun cmake from an empty build directly and post both the full
> cmake output and the content of CMakeFiles/CMakeError.log.
>
> Roland
>
> On Thu, May 7, 2015 at 7:38 PM, James Lord <jjamesgreen110 at gmail.com>
> wrote:
>
> > Hi Mark,Szilard and Christopher,
> > Thanks for the comments,
> > apparently gcc 4.8.2 is there. Really can't understand why and what it is
> > complaining about,
> >
> > root at ubuntu:~/gromacs-5.0.4/build# gcc --version
> > gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2
> > Copyright (C) 2013 Free Software Foundation, Inc.
> > This is free software; see the source for copying conditions.  There is
> NO
> > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> PURPOSE.
> >
> >
> > So are you guys saying that a new installation might be better than
> messing
> > around with this?
> > Cheers
> > James
> >
> >
> >
> > On Thu, May 7, 2015 at 7:21 PM, Szilárd Páll <pall.szilard at gmail.com>
> > wrote:
> >
> > > Something is strange about that Ubuntu installation, gcc 4.8.2 should
> > > be the default.
> > > --
> > > Szilárd
> > >
> > >
> > > On Fri, May 8, 2015 at 12:10 AM, Mark Abraham <
> mark.j.abraham at gmail.com>
> > > wrote:
> > > > Hi,
> > > >
> > > > The error means you need a newer compiler in order to take advantage
> of
> > > > your hardware, e.g. the latest version of gcc you can get (which will
> > > > probably require you add a new PPA), though I am surprised that cmake
> > > found
> > > > a C++ compiler on 14.04 and then didn't find AVX support in it...
> > > something
> > > > seems strange.
> > > >
> > > > Mark
> > > >
> > > > On Thu, May 7, 2015 at 8:46 PM Christopher Neale <
> > > > chris.neale at alum.utoronto.ca> wrote:
> > > >
> > > >> Gromacs only notified you about turning off the GPU code, that was
> not
> > > an
> > > >> error. The error was the AVX vs. SSE4.1 problem. Not sure why you
> are
> > > >> getting that since I thought cmake would get these things straight.
> > > >>
> > > >> 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
> James
> > > >> Lord <jjamesgreen110 at gmail.com>
> > > >> Sent: 07 May 2015 14:05
> > > >> To: gmx-users at gromacs.org
> > > >> Subject: [gmx-users] gromacs-5.0.4 installation problem
> > > >>
> > > >> Hi all,
> > > >> I just installed a fresh ubuntu 14.04, and want to go ahead with
> > > >> gromacs-5.0.4 installation, I am constantly getting this annoying
> > > message,
> > > >> anyone can help?
> > > >>
> > > >> root at ubuntu:~/gromacs-5.0.4/build# cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > > >> -DREGRESSIONTEST_DOWNLOAD=ON
> > > >> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> > > >> acceleration
> > > >> CMake Error at cmake/gmxTestSimd.cmake:220 (message):
> > > >>   Cannot find AVX compiler flag.  Use a newer compiler, or choose
> > SSE4.1
> > > >> SIMD
> > > >>   (slower).
> > > >> Call Stack (most recent call first):
> > > >>   CMakeLists.txt:716 (gmx_test_simd)
> > > >>
> > > >>
> > > >> -- Configuring incomplete, errors occurred!
> > > >> See also
> "/home/james/gromacs-5.0.4/build/CMakeFiles/CMakeOutput.log".
> > > >> See also
> "/home/james/gromacs-5.0.4/build/CMakeFiles/CMakeError.log".
> > > >>
> > > >> After this I did
> > > >> sudo apt-get install nvidia-cuda-toolkit
> > > >> but still i am getting the same message
> > > >> Any comments?
> > > >> Cheers
> > > >> James
> > > >> --
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> > > >>
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