[gmx-developers] build libmd with additional libraries

[Mark Abraham]

On 7/12/2011 1:48 AM, Steyer, Michael wrote:
>
> I modified the gromacs-4.5.5/src/mdlib/ns.c file, there are different 
> libraries now used by ns.c.
>
> As ns.o will later be linked to libmd, I want to know where I can add 
> my additional includes and libraries.
>

libmd doesn't need or want to know about other libraries. For example it 
is dependent on libgmx, but construction of the libmd library files 
doesn't know when/if libgmx will ever exist.

Only at link time do the names have to get resolved. You can supply 
extra libraries to the configure line, e.g. something like ./configure 
LDFLAGS="-L/place/of/fancy/lib -lmyfancylib"

Mark

> I focused on the gromacs-4.5.5/src/mdlib/Makefile.am which will then 
> generate Makefile.in, using the autotools.
>
> The gromacs-4.5.5/src/mdlib/Makefile.am:
>
> -------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> ## Process this file with automake to produce Makefile.in
>
> # Note: Makefile is automatically generated from Makefile.in by the 
> configure
>
> # script, and Makefile.in is generated from Makefile.am by automake.
>
> AM_CPPFLAGS = -I$(top_srcdir)/include -DGMXLIBDIR=\"$(datadir)/top\"
>
> libmd at LIBSUFFIX@_la_LIBADD         = ../gmxlib/libgmx at LIBSUFFIX@.la
>
> libmd at LIBSUFFIX@_la_DEPENDENCIES   = ../gmxlib/libgmx at LIBSUFFIX@.la
>
> libmd at LIBSUFFIX@_la_LDFLAGS        = -no-undefined -version-info 
> @SHARED_VERSION_INFO@ $(FFT_LIBS) $(XML_LIBS) $(PT
>
> HREAD_LIBS)
>
> lib_LTLIBRARIES = libmd at LIBSUFFIX@.la
>
> pkgconfigdir = ${libdir}/pkgconfig
>
> pkgconfig_DATA = libmd at LIBSUFFIX@.pc
>
> EXTRA_DIST = libmd.pc.cmakein
>
> libmd at LIBSUFFIX@_la_SOURCES = \
>
>         calcmu.c        calcvir.c       constr.c        \
>
>         coupling.c      \
>
>         domdec.c        domdec_box.c    domdec_con.c    \
>
>         domdec_network.c domdec_setup.c domdec_top.c    \
>
>         ebin.c          \
>
>         edsam.c         ewald.c         \
>
>         force.c         forcerec.c      \
>
>         ghat.c          init.c          \
>
>     iteratedconstraints.c   md_support.c    \
>
>         mdatom.c        mdebin.c        minimize.c      \
>
>         mvxvf.c         ns.c            nlistheuristics.c    nsgrid.c   \
>
>         perf_est.c      genborn.c                       \
>
>         genborn_sse2_single.c                           \
>
>         genborn_sse2_single.h                           \
>
>         genborn_sse2_double.c                           \
>
>         genborn_sse2_double.h                           \
>
>         genborn_allvsall.c                              \
>
>         genborn_allvsall.h                              \
>
>         genborn_allvsall_sse2_single.c                  \
>
>         genborn_allvsall_sse2_single.h                  \
>
>         genborn_allvsall_sse2_double.c                  \
>
>         genborn_allvsall_sse2_double.h                  \
>
>         gmx_qhop_parm.c gmx_qhop_parm.h                 \
>
>         gmx_qhop_xml.c  gmx_qhop_xml.h                  \
>
>         groupcoord.c                    groupcoord.h    \
>
>         pme.c           pme_pp.c        pppm.c          \
>
>         partdec.c       pull.c          pullutil.c      \
>
>         rf_util.c       shakef.c        sim_util.c      \
>
>         shellfc.c       stat.c          \
>
>         tables.c        tgroup.c        tpi.c   \
>
>         update.c        vcm.c           vsite.c \
>
>         wall.c          wnblist.c       \
>
>         csettle.c       clincs.c        \
>
>         qmmm.c          gmx_fft.c       gmx_parallel_3dfft.c    \
>
>         fft5d.c         fft5d.h         \
>
>         gmx_wallcycle.c \
>
>         qm_gaussian.c   qm_mopac.c      qm_gamess.c             \
>
>         gmx_fft_fftw2.c gmx_fft_fftw3.c gmx_fft_fftpack.c       \
>
>         gmx_fft_mkl.c   qm_orca.c       mdebin_bar.c            \
>
> mdebin_bar.h
>
> LDADD = ../mdlib/libmd at LIBSUFFIX@.la ../gmxlib/libgmx at LIBSUFFIX@.la
>
> EXTRA_PROGRAMS = gmx_qhop_db_test
>
> gmx_qhop_db_test_LDADD = ../mdlib/libmd at LIBSUFFIX@.la 
> ../gmxlib/libgmx at LIBSUFFIX@.la ../kernel/libgmxpreprocess at LIB
>
> SUFFIX at .la
>
> # clean all libtool libraries, since the target names might have changed
>
> CLEANFILES     = *.la *~ \\\#*
>
> -------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> I tried to add my libraries to the "LDADD" as well as the 
> "libmd at LIBSUFFIX@_la_LDFLAGS" variables, without success.
>
> During linkage, I still get "gromacs-4.5.5/src/mdlib/.libs/libmd.so: 
> undefined reference to ..." errors.
>
> Which is the easiest way to add my required libraries to make them 
> part of libmd?
>
> Thanks and regards,
>
> Michael Steyer
>
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