Hi, On Fri, Feb 12, 2016 at 1:42 PM Hardy, Adam <[email protected]> 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: [email protected] < > [email protected]> on behalf of Mark > Abraham <[email protected]> > Sent: 12 February 2016 12:06 > To: [email protected] > 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 <[email protected]> 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 > > > > [email protected] > > > > --------------------------------------- > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to [email protected]. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
