[gmx-users] Unable to compile plug-in support for gromacs 5.1.2

Mark Abraham mark.j.abraham at gmail.com
Wed Nov 23 21:33:23 CET 2016 

Hi,

Offhand the first error is inexplicable, but the first is that the linker
flags aren't set up right. However I do think we fixed that at some
stage...

Mark

On Wed, 23 Nov 2016 21:23 Christopher Neale <chris.neale at alum.utoronto.ca>
wrote:

> I've now also tried gromacs 4.6.7 and though I was not able to compile
> with plugin support, I did get more error messages there.
>
> Compiling gromacs 4.6.7 in the same way, I still see this output during
> compilation:
>
> -- Checking for dlopen
> -- Performing Test HAVE_DLOPEN
> -- Performing Test HAVE_DLOPEN - Success
> -- Checking for dlopen - found
>
> However, in gmx4.6.7 (but not 5.1.2) compilation, I get the errors:
>
> [ 55%] Building C object
> share/template/CMakeFiles/template.dir/template.c.o
> [ 55%] Linking C executable template
> ../../src/gmxlib/libgmx.a(vmddlopen.c.o): In function `vmddlopen':
> vmddlopen.c:(.text+0x6): undefined reference to `dlopen'
> ../../src/gmxlib/libgmx.a(vmddlopen.c.o): In function `vmddlerror':
> vmddlopen.c:(.text+0x11): undefined reference to `dlerror'
> ../../src/gmxlib/libgmx.a(vmddlopen.c.o): In function `vmddlsym':
> vmddlopen.c:(.text+0x21): undefined reference to `dlsym'
> ../../src/gmxlib/libgmx.a(vmddlopen.c.o): In function `vmddlclose':
> vmddlopen.c:(.text+0x31): undefined reference to `dlclose'
> collect2: ld returned 1 exit status
> make[2]: *** [share/template/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs....
>
>
> ### But I do have dlfcn.h in a standard location that should get picked up
> by an #include statement:
>
> $ ls /usr/include/dlfcn.h
> /usr/include/dlfcn.h
>
> Still, I tried exporting CMAKE_INCLUDE_PATH=/usr/include and compiled
> again (clean build directory) but got the same problem (and same thing if I
> used -DCMAKE_INCLUDE_PATH=/usr/include as a cmake argument).
>
> Thanks again for any help,
> Chris.
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of
> Christopher Neale <chris.neale at alum.utoronto.ca>
> Sent: 23 November 2016 13:23:52
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Unable to compile plug-in support for gromacs 5.1.2
>
> This sender failed our fraud detection checks and may not be who they
> appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
>
> Dear Users:
>
> I tried to compile gromacs 5.1.2 with plugin support, but upon running gmx
> trjconv I get the following error message indicating that plugin support
> was not actually included:
>
> $ /scratch/cneale/exe/GROMACS/exec/gromacs-5.1.2/serial_plugins/bin/gmx
> trjconv -f MD1.mdcrd.nc -s EM.gro  -o a.xtc
>
> <... snip ...>
>
> Fatal error:
> Not supported in read_first_frame: MD1.mdcrd.nc. Please make sure that
> the file is a trajectory.
> GROMACS is not compiled with plug-in support. Thus it cannot read
> non-GROMACS trajectory formats using the VMD plug-ins.
> Please compile with plug-in support if you want to read non-GROMACS
> trajectory formats.
>
>
>
> ### compilation was via nohup ./cn_compile.sh , where the contents of that
> compilation script are:
> mkdir -p ../../../exec/gromacs-5.1.2/serial_plugins
> export FFTW_LOCATION=/scratch/cneale/exe/FFTW/fftw-3.3.4/exec
> /scratch/cneale/exe/CMAKE/cmake-3.5.1-Linux-x86_64/bin/cmake
> ../../../source/gromacs-5.1.2/ \
>       -DCMAKE_PREFIX_PATH=$FFTW_LOCATION \
>
> -DCMAKE_INSTALL_PREFIX=$(pwd)/../../../exec/gromacs-5.1.2/serial_plugins \
>       -DGMX_X11=OFF \
>       -DGMX_MPI=OFF \
>       -DCMAKE_CXX_COMPILER=g++ \
>       -DCMAKE_C_COMPILER=gcc \
>       -DGMX_PREFER_STATIC_LIBS=ON \
>       -DGMX_GPU=OFF \
>       -DGMX_USE_PLUGINS=ON \
>
> -DGMX_VMD_PLUGIN_PATH=/scratch/cneale/exe/vmd-1.9.2/plugins/LINUXAMD64/molfile
> make -j 8
> make install -j 8
>
>
>
> ### I also tried adding the following preliminary command, but it made no
> difference:
> export
> VMD_PLUGIN_PATH=/scratch/cneale/exe/vmd-1.9.2/plugins/LINUXAMD64/molfile
>
> Also, including -DGMX_LOAD_PLUGINS=ON to the cmake command did not help
> either.
>
>
> ### Here is some further information that might be useful based on the
> other posts I saw on this topic:
>
> $ grep PLUG CMakeCache.txt
> GMX_LOAD_PLUGINS:BOOL=ON
> GMX_USE_PLUGINS:UNINITIALIZED=ON
>
> GMX_VMD_PLUGIN_PATH:UNINITIALIZED=/scratch/cneale/exe/vmd-1.9.2/plugins/LINUXAMD64/molfile
> //ADVANCED property for variable: GMX_LOAD_PLUGINS
> GMX_LOAD_PLUGINS-ADVANCED:INTERNAL=1
>
> $ grep DLOPEN CMakeCache.txt
> HAVE_DLOPEN:INTERNAL=1
>
> $ grep HAVE_DLOPEN nohup.out
> -- Performing Test HAVE_DLOPEN
> -- Performing Test HAVE_DLOPEN - Success
>
> $ ls /scratch/cneale/exe/vmd-1.9.2/plugins/LINUXAMD64/molfile
> abinitplugin.so    brixplugin.so  dcdplugin.so     fs4plugin.so
> jsplugin.so      molemeshplugin.so  pbeqplugin.so      rst7plugin.so
>   vaspchgcarplugin.so   webpdbplugin.so
> avsplugin.so       carplugin.so   dlpolyplugin.so  gamessplugin.so
>  lammpsplugin.so  msmsplugin.so      pdbplugin.so       situsplugin.so
>    vaspoutcarplugin.so   xbgfplugin.so
> babelplugin.so     ccp4plugin.so  dmsplugin.so     graspplugin.so
> maeffplugin.so   namdbinplugin.so   phiplugin.so       spiderplugin.so
>   vaspparchgplugin.so   xsfplugin.so
> basissetplugin.so  corplugin.so   dsn6plugin.so    grdplugin.so
> mapplugin.so     netcdfplugin.so    pltplugin.so       stlplugin.so
>    vaspposcarplugin.so   xyzplugin.so
> bgfplugin.so       cpmdplugin.so  dtrplugin.so     gridplugin.so
>  mdfplugin.so     offplugin.so       pqrplugin.so       tinkerplugin.so
>     vaspxdatcarplugin.so
> binposplugin.so    crdplugin.so   dxplugin.so      gromacsplugin.so
> mol2plugin.so    parm7plugin.so     psfplugin.so       uhbdplugin.so
>   vaspxmlplugin.so
> biomoccaplugin.so  cubeplugin.so  edmplugin.so     hoomdplugin.so
> moldenplugin.so  parmplugin.so     raster3dplugin.so
> vasp5xdatcarplugin.so  vtfplugin.so
>
>
> Thank you for your advice on this compilation with plugins,
> Chris.
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