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

Fri Feb 12 15:59:15 CET 2016

Sorry for the confusion, yes, find and replace Marenostrum with Juqeen for most of that last mail. Just got some PRACE test accounts and I got myself confused.

The 2.6 version of cmake was from Marenostum before I’d loaded the proper module.

Try again:

Fermi (failed build, xl compiler) - cmake 2.8.8
Juqeen (successful, gnu compiler?) - cmake 2.8.10.2

I had, clearly not really knowing what I was doing, specified gnu for Juqueen but this seems to be getting overridden somehow, I’ll look into that but whatever happened my build worked.

There’s no other version of cmake I can find but I’ll contact the helpdesk and see if they can make one available. If you have any other suggestions I’d love to hear them, otherwise thanks for your input.

Adam

On 12/02/2016, 13:50, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Mark Abraham" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of mark.j.abraham at gmail.com> wrote:

>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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