[gmx-users] Build fails with AVX2_256 on Intel Xeon CPU E5-2680 v3

[Koji Tanaka]

Thanks Mark and Nicolas. I could figure it out.

The latest version of binutils made it work as suggested on this link.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-December/094481.html

Also, Nicolas, you need to be aware that once the build fails with the
error, you need to clean the src directory before you try it with the new
binutils. Otherwise, you will keep getting the same error.

Here's the link of binutils. https://www.gnu.org/software/binutils/

Bests,
Koji

On Sun, Jan 24, 2016 at 4:29 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> That shouldn't happen. What does the terminal output when you run cmake in
> a clean build tree?
>
> Mark
>
> On Sun, 24 Jan 2016 21:59 Nicolas Cheron <nicolas.cheron.boulot at gmail.com>
> wrote:
>
> > Hi,
> >
> > I have faced the same problem, with gcc 4.8.3, 4.9.1 and 5.2. I ended up
> > asking for SIMD=AVX_256. So I assume there is something else going wrong.
> >
> > Nicolas
> >
> > 2016-01-24 20:59 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> >
> > > Hi,
> > >
> > > Like the *5.1* installation instructions and that error suggest, you
> > need a
> > > recent compiler. The "stable" compilers in distros like centos are
> > merely a
> > > euphemism for outdated, if you want to run fast on new hardware.
> > >
> > > Mark
> > >
> > > On Sun, 24 Jan 2016 16:47 Koji Tanaka <kj.tanaka at gmail.com> wrote:
> > >
> > > > Hello Gromacs Community,
> > > >
> > > > I'm trying to build Gromacs with SIMD=AVX2_256 support, but it fails.
> > > > Instead, if I pick AVX_256, the build will finish okay.
> > > >
> > > > However, according to the documentation(
> > > > http://www.gromacs.org/Documentation/Installation_Instructions_5.0),
> > > > AVX2_256 is the right option for the Intel Xeon CPU E5-2680 v3
> > (Haswell).
> > > > Does anyone have the same problem?
> > > >
> > > > My environment is;
> > > > - CentOS 6.7
> > > > - Gromacs 5.1.1
> > > > - OpenMPI 1.10.1
> > > >
> > > > The error message is;
> > > > -------------------------------------------------------------------
> > > > CMake Error at cmake/gmxManageSimd.cmake:271 (message):
> > > >   Cannot find AVX2 compiler flag.  Use a newer compiler, or choose
> AVX
> > > SIMD
> > > >   (slower).
> > > > Call Stack (most recent call first):
> > > >   CMakeLists.txt:645 (gmx_manage_simd)
> > > >
> > > >
> > > > Also, I found the following error in build/CMakeFiles/CMakeError.log
> > > > -------------------------------------------------------------------
> > > > Run Build Command:/usr/bin/gmake "cmTryCompileExec1019102511/fast"
> > > > /usr/bin/gmake -f
> CMakeFiles/cmTryCompileExec1019102511.dir/build.make
> > > > CMakeFiles/cmTryCompileExec1019102511.dir/build
> > > > gmake[1]: Entering directory
> > > `/tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp'
> > > > /usr/bin/cmake -E cmake_progress_report
> > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/CMakeFiles 1
> > > > Building C object CMakeFiles/cmTryCompileExec1019102511.dir/src.c.o
> > > > /opt/openmpi/1.10.1/bin/mpicc   -Wundef -Wextra
> > > > -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith
> -Wall
> > > > -Wno-unused -Wunused-value -Wunused-p
> > > > arameter  -D_callconv___regcall   -o
> > > > CMakeFiles/cmTryCompileExec1019102511.dir/src.c.o   -c
> > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c
> > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c:1: error: expected
> > > ‘=’,
> > > > ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘f’
> > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c: In function
> ‘main’:
> > > > /tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp/src.c:1: warning:
> implicit
> > > > declaration of function ‘f’
> > > > gmake[1]: *** [CMakeFiles/cmTryCompileExec1019102511.dir/src.c.o]
> > Error 1
> > > > gmake[1]: Leaving directory
> > > `/tmp/gromacs-5.1.1/build/CMakeFiles/CMakeTmp'
> > > > gmake: *** [cmTryCompileExec1019102511/fast] Error 2
> > > >
> > > >
> > > > Any comment/suggestion would be appreciated!
> > > >
> > > > Thanks a lot,
> > > > Koji
> > > > --
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