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

Christopher Neale chris.neale at alum.utoronto.ca
Wed Nov 23 22:01:10 CET 2016 

All Hail Mark!

Seems as if -DGMX_PREFER_STATIC_LIBS=ON clobbers the incorporation of plugins, at least in gmx 5.1.2. Some output is below, but it seems to be that simple. Thanks a lot Mark!

## using -DGMX_PREFER_STATIC_LIBS=ON gives the following output to stdout/stderr at compile time
...
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Found PythonInterp: /usr/bin/python (found version "2.7.3")
...

## NOT using -DGMX_PREFER_STATIC_LIBS=ON gives the following output to stdout/stderr at compile time
## note the new line about VMD
...
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Found PythonInterp: /usr/bin/python (found version "2.7.3")
...
________________________________________
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 15:49:54
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Unable to compile plug-in support for gromacs 5.1.2

Hi,

Does a fresh build not preferring static libs help? Does the nohup.out
mention vmd?

Mark

On Wed, 23 Nov 2016 21:41 Christopher Neale <chris.neale at alum.utoronto.ca>
wrote:

> 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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