[gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

[Mark Abraham]

Hi,

On Fri, Feb 12, 2016 at 1:42 PM Hardy, Adam <ah259 at hw.ac.uk> wrote:

> Hi Mark,
>
> I was able to compile GROMACS on Marenostrum, the cmake version is
> "2.6-patch 2".
>

That seems wildly unlikely. GROMACS has required CMake 2.8+ for quite a few
versions now.

On Fermi it failed, the cmake version is "2.8.8".
>

OK. I suggest you try a more recent version of CMake. I can build fine on
Vesta and Juqueen with e.g. 2.8.12.2, but haven't tried 2.8.8. Object
modules were a new feature in 2.8.8 (part of why we require that version)
and perhaps had some issues that have been resolved later.

This is not necassarily a fair comparison. I compiled using gnu on
> Marenostrum as I couldn't find the xl compiler oddly and wasn't feeling
> compelled to go looking for it.


Marenostrum isn't even BG/Q!


> I'm using xl on Fermi as using gnu is another problem all together:
>
> CMake Error at cmake/gmxManageSimd.cmake:390 (message):
>   Cannot compile the requested IBM QPX intrinsics.  If you are compiling
> for
>   BlueGene/Q with the XL compilers, use 'cmake ..
>   -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool
>   chain.
>
> Despite the correct file being specified and I can see the path set
> correctly in the CMakeCache.txt.
>

gcc's never been a supported compiler for GROMACS on BG/Q. Your reports
suggest that you were compiling GROMACS 4.5 on Marenostrum.

Mark


> Adam
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: 12 February 2016 12:06
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q
>
> Hi,
>
> Do the cmake versions differ?
>
> Mark
>
> On Fri, 12 Feb 2016 12:44 Hardy, Adam <ah259 at hw.ac.uk> wrote:
>
> > Dear all,
> >
> >
> > I'm having some difficulty compiling GROMACS 5.1.1 on a Bluegene/Q
> > machine. This is using the xl compiler.
> >
> >
> > I recieve the error:
> >
> >
> > ADD_LIBRARY for library mdrun_objlib is used with the MODULE option, but
> > the target platform supports only STATIC libraries. Building it STATIC
> > instead. This may lead to problems.
> > -- Configuring done
> > CMake Error at src/programs/CMakeLists.txt:45 (add_executable):
> >   Objects of target "mdrun_objlib" referenced but is not an OBJECT
> library.
> >
> > If I attempt to compile it, it fails:
> >
> > Linking CXX executable ../../bin/mdrun_mpi_d
> > CMakeFiles/mdrun.dir/mdrun_main.cpp.o:(.toc+0x0): undefined reference to
> > `gmx_mdrun(int, char**)'
> >
> > My cmake command is as follow:
> >
> > export
> CMAKE_PREFIX_PATH=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/lib/
> > export FLAGS="-O3 -qarch=qp -qtune=qp"
> > export
> FFTW_INC_DIR=/cineca/prod/libraries/fftw/3.3.3/bgq-xl--1.0/include/
> > export INSTALL_PRE=/fermi/home/userexternal/hbock000/gmx/
> >
> > cmake ../ -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=OFF -DGMX_X11=OFF
> > -DGMX_DOUBLE=ON \
> >           -DCMAKE_C_FLAGS="$FLAGS" -DCMAKE_CXX_FLAGS="$FLAGS"
> > -DGMX_BUILD_MDRUN_ONLY=ON  \
> >           -DFFTW_INCLUDE_DIR=$FFTW_INC_DIR \
> >           -DCMAKE_INSTALL_PREFIX=$INSTALL_PRE -DBUILD_SHARED_LIBS=off
> > -DGMX_BUILD_MDRUN_ONLY=ON\
> >           -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C
> > -DCMAKE_CXX_COMPILER=mpixlc -DCMAKE_C_COMPILER=mpixlcxx
> >
> >
> > I have managed to build for a similar BGQ machine without problems, but
> > I've no idea if this problem lies within GROMACS or with this machine.
> >
> >
> > Many thanks,
> >
> >
> > Adam
> >
> > ---------------------------------------
> >
> > Adam Hardy
> >
> > PhD Student
> >
> > Heriot Watt University
> >
> > Edinburgh Campus, Riccarton
> >
> > EH14 4AS
> >
> > +441314513074
> >
> > ah259 at hw.ac.uk
> >
> > ---------------------------------------
> > --
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