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

Irina Kosheleva ikoshelev at cars.uchicago.edu
Fri Feb 12 16:18:48 CET 2016

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.
-----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/

          -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 Hardy

PhD Student

Heriot Watt University

Edinburgh Campus, Riccarton

EH14 4AS


ah259 at hw.ac.uk

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