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

Christopher Neale chris.neale at alum.utoronto.ca
Wed Nov 23 21:40:50 CET 2016 

Thanks Mark. I was hoping that the 4.6.7 error message would help me to understand why the 5.1.2 compilation is succeeding but the plugins are not linked.

Can anybody confirm that gromacs 5.1.2 can be built with the VMD plugins to process non-gromacs trajectory files?

Thank you,
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 Mark Abraham <mark.j.abraham at gmail.com>
Sent: 23 November 2016 15:33:09
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Unable to compile plug-in support for gromacs 5.1.2

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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