Hi,
you need to get the latest APBS code from the git repository as described
here
http://mccammon.ucsd.edu/iapbs/doc/amber.html#_building_iapbs_interface,
you can't use the official 1.4 tarball.
Best,
Robert
On Thu, Sep 05, 2013 at 11:52:42PM +0530, Asmita Gupta wrote:
> yes...i think with the new combined APBS-iAPBS version 1.4..the
> configuration step using cmake fails..i am getting the following messages...
>
> while running
>
> cmake -DCMAKE_INSTALL_PREFIX:PATH=${APBS_PREFIX} -DENABLE_QUIET=ON \
> -DBUILD_TOOLS=OFF -DENABLE_PYTHON=OFF -DENABLE_OPENMP=OFF \
> -DENABLE_iAPBS=ON -DBUILD_WRAPPER=ON -DENABLE_MPI=OFF ..
>
> =============================
> CMake Warning at CMakeLists.txt:193 (message):
> Liberty library not found
>
> CMake Warning at CMakeLists.txt:237 (message):
> The socket library was not found
>
> CMake Warning at CMakeLists.txt:259 (message):
> The thread library was not found
>
> CMake Warning at CMakeLists.txt:369 (message):
> Did not find fetk
>
> CMake Warning at CMakeLists.txt:383 (message):
> External maloc headers not found.
> ==========================
>
> with older version, this message was not there and build was successful..
>
> Thanks
>
>
> On Thu, Sep 5, 2013 at 11:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > OK, it seems that you're missing 2 libraries, libapbs_routines.a and
> > libiapbs.a. I would suggest retrying step 2.2 in
> > http://mccammon.ucsd.edu/iapbs/doc/amber.html#_building_iapbs_interface
> > and make sure the build completes successfully. It may be helpful to
> > redirect stderr to a file during the build so you can more easily find
> > error messages.
> >
> > -Dan
> >
> >
> > On Thu, Sep 5, 2013 at 11:40 AM, Asmita Gupta <asmita4des.gmail.com>
> > wrote:
> > > it gives:
> > >
> > > libapbs_generic.so libapbs_mg.so libapbs_pmgc.so libmaloc.so
> > >
> > >
> > > On Thu, Sep 5, 2013 at 11:03 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> > >
> > >> Hi,
> > >>
> > >> What is the result of 'ls $APBS_LIBDIR'?
> > >>
> > >> -Dan
> > >>
> > >> On Thu, Sep 5, 2013 at 11:25 AM, Asmita Gupta <asmita4des.gmail.com>
> > >> wrote:
> > >> > Hi..
> > >> >
> > >> > I tried to do what you suggested...but now the error message is
> > >> changed...i
> > >> > am getting some missing library routines notice..
> > >> >
> > >> > ================================================
> > >> > gfortran -DBINTRAJ -DAPBS -ffree-form -I../../AmberTools/src/pbsa
> > >> > -I../../AmberTools/src/sqm -I../../AmberTools/src/rism -I../../include
> > >> > -I/usr/local/softs/iapbs_build/amber12/include
> > >> > -I/usr/local/softs/iapbs_build/amber12/include -DAPBS -DAPBS -o
> > >> > sander.APBS file_io_dat.APBS.o apbs_vars.APBS.o apbs.APBS.o
> > constants.o
> > >> > state.o memory_module.o stack.o nose_hoover.o nose_hoover_vars.o
> > >> > nose_hoover_init.o trace.o rmsgrd.o lmod.o rand2.o lmodC.o xminC.o
> > >> decomp.o
> > >> > icosasurf.o egb.o remd.o findmask.o relax_mat.o nmr.o multitmd.o
> > >> > multisander.o sander.APBS.o trajene.o cshf.o nmrcal.o mtmdcall.o
> > pearsn.o
> > >> > printe.APBS.o runmin.o rdparm.o mdread.APBS.o locmem.o runmd.o
> > getcor.o
> > >> > degcnt.o decnvh.o fastwt.o parallel.o shake.o ene.o mdwrit.o minrit.o
> > >> set.o
> > >> > dynlib.APBS.o mdfil.o nmlsrc.o ew_force.o ew_setup.o ew_box.o
> > >> ew_bspline.o
> > >> > ew_fft.o nonbond_list.o short_ene.o ew_recip.o pcshift.o align.o csa.o
> > >> > rfree.o rgroup.o amopen.o debug.o ew_recip_reg.o ew_handle_dips.o
> > >> > ew_dipole_recip.o mexit.o new_time.o extra_pts.o thermo_int.o matinv.o
> > >> > assert.o mmtsb.o mmtsb_client.o erfcfun.o constantph.o prn_dipoles.o
> > >> ips.o
> > >> > sglds.o iwrap2.o emap.o amoeba_valence.o amoeba_multipoles.o
> > >> amoeba_recip.o
> > >> > amoeba_interface.o amoeba_direct.o amoeba_mdin.o amoeba_adjust.o
> > >> > amoeba_self.o amoeba_vdw.o amoeba_induced.o amoeba_runmd.o bintraj.o
> > >> > binrestart.o spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o
> > >> > linear_response.o molecule.o xref.o dssp.o charmm.o crg_reloc.o
> > >> > sander_lib.o amd.o qm_mm.o qm_ewald.o qmmm_vsolv.o qm2_extern_module.o
> > >> > qm2_extern_adf_module.o qm2_read_adf_results.o KFReader.o ArrayList.o
> > >> > qm2_extern_gms_module.o qm2_extern_tc_module.o qm2_extern_gau_module.o
> > >> > qm2_extern_orc_module.o qm2_extern_nw_module.o qmmm_adaptive_module.o
> > >> > prn_qmmm_dipole.o \
> > >> > pimd_vars.o pimd_force.o pimd_init.o cmd_vars.o
> > >> cmd_matrix.o
> > >> > lscivr_vars.o lsc_init.o lsc_xp.o force.APBS.o \
> > >> > -L/usr/local/softs/iapbs_build/lib -liapbs
> > -lapbs_routines
> > >> > -lapbs_mg -lapbs_generic -lapbs_pmgc -lmaloc -lz \
> > >> > -L/usr/local/softs/iapbs_build/amber12/lib -lsqm
> > -lFpbsa \
> > >> > ../lib/nxtsec.o ../lib/sys.a ncsu-abmd-hooks.o
> > >> > ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar.o
> > >> > ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o
> > >> ncsu-constants.o
> > >> > ncsu-cv-ANGLE.o ncsu-cv-COM_ANGLE.o ncsu-cv-COM_DISTANCE.o
> > >> > ncsu-cv-COM_TORSION.o ncsu-cv-COS_OF_DIHEDRAL.o ncsu-cv-DISTANCE.o
> > >> > ncsu-cv-HANDEDNESS.o ncsu-cv-LCOD.o ncsu-cv-MULTI_RMSD.o
> > >> > ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o ncsu-cv-R_OF_GYRATION.o
> > >> > ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o ncsu-pmd-hooks.o
> > ncsu-rmsd.o
> > >> > ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-cv-PCA.o ncsu-read-pca.o
> > >> > ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o mt19937.o
> > >> > /usr/local/softs/iapbs_build/amber12/lib/libnetcdf.a \
> > >> > -larpack -llapack -lblas \
> > >> > -DAPBS -DAPBS
> > >> > /usr/bin/ld: cannot find -liapbs
> > >> > /usr/bin/ld: cannot find -lapbs_routines
> > >> > collect2: error: ld returned 1 exit status
> > >> > make: *** [sander.APBS] Error 1
> > >> > =============================================
> > >> >
> > >> > P.S. : i have created APBS_LIBDIR and APBS_LIBS variables as
> > mentioned in
> > >> > the link below:
> > >> >
> > http://mccammon.ucsd.edu/iapbs/doc/amber.html#_building_iapbs_interface
> > >> >
> > >> > Thanks
> > >> >
> > >> >
> > >> > On Thu, Sep 5, 2013 at 9:27 PM, Jason Swails <jason.swails.gmail.com>
> > >> wrote:
> > >> >
> > >> >> On Thu, Sep 5, 2013 at 11:27 AM, Asmita Gupta <asmita4des.gmail.com>
> > >> >> wrote:
> > >> >>
> > >> >> > yes, i did that
> > >> >> >
> > >> >> > make clean
> > >> >> > make depend
> > >> >> > make -e AMBERBUILDFLAGS="-DAPBS" sander.APBS
> > >> >> >
> > >> >>
> > >> >> Try:
> > >> >>
> > >> >> make -C $AMBERHOME clean
> > >> >> make depend
> > >> >> make -e AMBERBUILDFLAGS="-DAPBS" sander.APBS
> > >> >>
> > >> >> instead and see if that works.
> > >> >>
> > >> >>
> > >> >>
> > >> >> >
> > >> >> > and then i ended up with the error
> > >> >> >
> > >> >> >
> > >> >> > On Thu, Sep 5, 2013 at 7:51 PM, Daniel Roe <daniel.r.roe.gmail.com
> > >
> > >> >> wrote:
> > >> >> >
> > >> >> > > Hi,
> > >> >> > >
> > >> >> > > On Thu, Sep 5, 2013 at 12:35 AM, Asmita Gupta <
> > asmita4des.gmail.com
> > >> >
> > >> >> > > wrote:
> > >> >> > > > Fatal Error: Wrong module version '0' (expected '9') for file
> > >> >> > >
> > >> >> > > Did you 'make clean' first?
> > >> >> > >
> > >> >> > > -Dan
> > >> >> > >
> > >> >> > > --
> > >> >> > > -------------------------
> > >> >> > > Daniel R. Roe, PhD
> > >> >> > > Department of Medicinal Chemistry
> > >> >> > > University of Utah
> > >> >> > > 30 South 2000 East, Room 201
> > >> >> > > Salt Lake City, UT 84112-5820
> > >> >> > > http://home.chpc.utah.edu/~cheatham/
> > >> >> > > (801) 587-9652
> > >> >> > > (801) 585-9119 (Fax)
> > >> >> > >
> > >> >> > > _______________________________________________
> > >> >> > > AMBER mailing list
> > >> >> > > AMBER.ambermd.org
> > >> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> > >
> > >> >> > _______________________________________________
> > >> >> > AMBER mailing list
> > >> >> > AMBER.ambermd.org
> > >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >
> > >> >>
> > >> >>
> > >> >>
> > >> >> --
> > >> >> Jason M. Swails
> > >> >> BioMaPS,
> > >> >> Rutgers University
> > >> >> Postdoctoral Researcher
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
> > >> >> AMBER.ambermd.org
> > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >>
> > >>
> > >> --
> > >> -------------------------
> > >> Daniel R. Roe, PhD
> > >> Department of Medicinal Chemistry
> > >> University of Utah
> > >> 30 South 2000 East, Room 201
> > >> Salt Lake City, UT 84112-5820
> > >> http://home.chpc.utah.edu/~cheatham/
> > >> (801) 587-9652
> > >> (801) 585-9119 (Fax)
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-9119 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Sep 05 2013 - 12:00:02 PDT
