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

[Hardy, Adam]

Just to follow up on this, upgrading cmake from 2.8.8 (to 3.13 in this case) solved the problem.

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 Irina Kosheleva <ikoshelev at cars.uchicago.edu>
Sent: 12 February 2016 15:18
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

Hello Adam
For me alcf scientist suggested  to compile with:
Use xl compilers in your .soft environment.
cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX -DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include -DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a  -DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  -DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" -DCMAKE_INSTALL_PREFIX=
 It does not work for me because I have trouble compiling libxml2 library - suspect that come from Gromacs cmake command parsing-  but if you do not care - it may work for you.
Irina.
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Hardy, Adam
Sent: Friday, February 12, 2016 5:44 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] ADD_LIBRARY cmake error on Bluegene/Q

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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