On Tue, Sep 20, 2011 at 11:22 PM, Robert Konecny <rok.ucsd.edu> wrote:
> Hi Ken,
>
> you are right, there is a new function matvec() in the libFpbsa.a library
> which collides with the same named function in APBS. One solution is - as
> you are proposing - to rename all instances of matvec() in APBS. Other
> solution, perhaps simpler is to redefine matvec() in libapbs.a:
>
> cd $APBS_PREFIX/lib
> mv libapbs.a libapbs.a.bck
> objcopy --redefine-sym matvec_=matveci_ libapbs.a.bck libapbs.a
>
Good to note. I think the OP said something about renaming everything in
PBSA, though, not APBS. In any case, if it's easy enough to change things
in iAPBS, should it perhaps be done (or a note made of it in the install
process)?
Thanks!
Jason
>
> Thanks,
>
> Robert
>
>
> On Tue, Sep 20, 2011 at 05:05:00PM -0500, Kenneth Tussey wrote:
> > I finally got this to compile - I renamed every instance of matvec() in
> > the apbs source files to matvecc() to prevent the function collision
> > during linking. I am not sure what matvec() is doing in the apbs source
> > code, but I am relatively sure that matvec() in the amber code is the
> > routine for multiplying a matrix and a vector. I do not think that
> > renaming either function will cause a problem as long as every instance
> > of that function is renamed throughout the entire source code tree.
> >
> > I haven't tried it yet, but I imagine that running
> >
> > for i in $(find $AMBERHOME -name "*.f" -o -name "*.fh"); do \
> > grep " matvec(" $i && \
> > sed 's: matvec(: matvecc(:' > $i.new && \
> > mv $i.new $i;
> > done
> >
> > will replace every instance of the matvec() function in the amber code
> > with matvecc() name ( or whatever you want to use for this function),
> > and allow the code to compile.
> >
> > Here are the source files that appear to call matvec() -
> >
> > /opt/amber11/src/nmode/calink.f
> > /opt/amber11/AmberTools/src/pbsa/_jumps.f
> > /opt/amber11/AmberTools/src/pbsa/_irre32.f
> > /opt/amber11/AmberTools/src/pbsa/problem.f
> > /opt/amber11/AmberTools/src/pbsa/irre32.f
> > /opt/amber11/AmberTools/src/pbsa/_problem.f
> > /opt/amber11/AmberTools/src/pbsa/miniop.f
> > /opt/amber11/AmberTools/src/pbsa/jumps.f
> > /opt/amber11/AmberTools/src/pbsa/_irre31.f
> > /opt/amber11/AmberTools/src/pbsa/_miniop.f
> > /opt/amber11/AmberTools/src/pbsa/coed20.f
> > /opt/amber11/AmberTools/src/pbsa/_coed6.f
> > /opt/amber11/AmberTools/src/pbsa/irre31.f
> > /opt/amber11/AmberTools/src/pbsa/_coed20.f
> > /opt/amber11/AmberTools/src/pbsa/coed6.f
> >
> >
> > Hope this helps somebody compile sander.APBS in the future.
> >
> > Ken
> >
> >
> >
> >
> >
> >
> > On 09/20/2011 03:12 PM, Kenneth Tussey wrote:
> > > Hello,
> > >
> > > The patch did not seem to work :
> > >
> > > # patch -p0 -N < patch.apbs
> > > patching file src/sander/Makefile
> > > Hunk #1 FAILED at 305.
> > > 1 out of 1 hunk FAILED -- saving rejects to file
> src/sander/Makefile.rej
> > >
> > > But, I did read it , and assume the patch was just deleting the
> > > libFpbsa.a library from the Makefile. So I did that manually. Now, the
> > > final compilation, it seems, is missing critical definitions:
> > >
> > >
> > > gfortran -o sander.APBS 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 qmmm_module.o trace.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 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
> > > spatial_recip.o spatial_fft.o parms.o softcore.o mbar.o molecule.o
> > > xref.o dssp.o charmm.o qm_mm.o qm_ewald.o qm2_variable_solvent.o
> > > qmmm_qmtheorymodule.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/iAPBS-build/lib -liapbs -lapbsmainroutines
> > > -lapbs -lmaloc \
> > > /opt/amber11/lib/libsqm.a /opt/amber11/lib/arpack.a
> > > /opt/amber11/lib/lapack.a /opt/amber11/lib/blas.a \
> > > ../lib/nxtsec.o ../lib/sys.a mt19937.o ncsu-abmd-hooks.o
> > > ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar-math.o
> > > ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-colvar.o ncsu-constants.o
> > > ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.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-cv-LCOD.o
> > > ncsu-cv-COS_OF_DIHEDRAL.o ncsu-lexer.o ncsu-parser.o ncsu-pmd-hooks.o
> > > ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-smd-hooks.o
> > > ncsu-umbrella.o ncsu-utils.o ncsu-value.o
> > > /opt/amber11/lib/libnetcdf.a -DAPBS -lz
> > > sander.APBS.o: In function `sander_':
> > > _sander.APBS.f:(.text+0x401d): undefined reference to `pb_free_'
> > > runmin.o: In function `runmin_':
> > > _runmin.f:(.text+0x1b62): undefined reference to
> > > `__poisson_boltzmann_MOD_oution'
> > > _runmin.f:(.text+0x1b68): undefined reference to
> > > `__poisson_boltzmann_MOD_outwat'
> > > mdread.APBS.o: In function `mdread1_':
> > > _mdread.APBS.f:(.text+0x3986): undefined reference to `pb_read_'
> > > mdread.APBS.o: In function `mdread2_':
> > > _mdread.APBS.f:(.text+0xe763): undefined reference to `pb_init_'
> > > ene.o: In function `bond_':
> > > _ene.f:(.text+0x3c2): undefined reference to
> > > `__poisson_boltzmann_MOD_outflagorig'
> > > _ene.f:(.text+0x3c9): undefined reference to
> > > `__poisson_boltzmann_MOD_outflagorig'
> > > ene.o: In function `capwat_':
> > > _ene.f:(.text+0x357c): undefined reference to
> > > `__poisson_boltzmann_MOD_outflagorig'
> > > _ene.f:(.text+0x35a2): undefined reference to
> > > `__poisson_boltzmann_MOD_outflagorig'
> > > force.APBS.o: In function `force_':
> > > _force.APBS.f:(.text+0x1652): undefined reference to
> > > `__poisson_boltzmann_MOD_pb_force'
> > > _force.APBS.f:(.text+0x16f0): undefined reference to
> > > `__dispersion_cavity_MOD_npopt'
> > > _force.APBS.f:(.text+0x272e): undefined reference to
> > > `__dispersion_cavity_MOD_np_force'
> > > collect2: ld returned 1 exit status
> > > make: *** [sander.APBS] Error 1
> > >
> > >
> > >
> > > On 09/19/2011 05:22 PM, Jason Swails wrote:
> > >> Try applying the following patch that I attached
> > >>
> > >> go to AMBERHOME, and apply it via
> > >>
> > >> cd $AMBERHOME
> > >> patch -p0 -N< patch.apbs
> > >>
> > >> See if this works for you. If not, I will try building it myself and
> report
> > >> back.
> > >>
> > >> HTH,
> > >> Jason
> > >>
> > >> On Mon, Sep 19, 2011 at 4:47 PM, Kenneth Tussey
> > >> <tussey1.illinois.gmail.com>wrote:
> > >>
> > >>> When attempting to build sander.APBS as per the instructions on the
> > >>> iAPBS website, I get an error from having multiple definitions of
> > >>> matvec_. See code below. I have tried compiling with multiple
> versions
> > >>> of APBS 1.x.0, and they all seem to give the same error. Perhaps
> someone
> > >>> can shed some light on this? Thank you.
> > >>>
> > >>> Ken
> > >>>
> > >>> /make[1]: Leaving directory `/opt/amber11/AmberTools/src/arpack'
> > >>> ifort -o sander.APBS 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 qmmm_module.o trace.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
> > >>> 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 spatial_recip.o
> spatial_fft.o
> > >>> parms.o softcore.o mbar.o molecule.o xref.o dssp.o charmm.o qm_mm.o
> > >>> qm_ewald.o qm2_variable_solvent.o qmmm_qmtheorymodule.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/iAPBS-build/lib -liapbs
> -lapbsmainroutines
> > >>> -lapbs -lmaloc \
> > >>> /opt/amber11/lib/libsqm.a /opt/amber11/lib/libFpbsa.a
> > >>> /opt/amber11/lib/arpack.a -Wl,--start-group
> > >>>
> /usr/local/intel/composerxe-2011.4.191/mkl/lib/em64t/libmkl_intel_lp64.a
> > >>>
> /usr/local/intel/composerxe-2011.4.191/mkl/lib/em64t/libmkl_sequential.a
> > >>> /usr/local/intel/composerxe-2011.4.191/mkl/lib/em64t/libmkl_core.a
> > >>> -Wl,--end-group -lpthread -lsvml \
> > >>> ../lib/nxtsec.o ../lib/sys.a mt19937.o
> ncsu-abmd-hooks.o
> > >>> ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar-math.o
> > >>> ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-colvar.o ncsu-constants.o
> > >>> ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.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-cv-LCOD.o
> > >>> ncsu-cv-COS_OF_DIHEDRAL.o ncsu-lexer.o ncsu-parser.o ncsu-pmd-hooks.o
> > >>> ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-smd-hooks.o
> > >>> ncsu-umbrella.o ncsu-utils.o ncsu-value.o
> /opt/amber11/lib/libnetcdf.a
> > >>> -shared-intel -DAPBS
> > >>> /opt/amber11/lib/libFpbsa.a(miniop.o): In function `matvec_':
> > >>> _miniop.f:(.text+0xa80): multiple definition of `matvec_'
> > >>>
> > >>>
> /usr/local/iAPBS-build/lib/libapbs.a(matvecd.o):/usr/local/iAPBS-build/apbs-1.0.0-source/contrib/pmgZ/matvecd.f:38:
> > >>> first defined here
> > >>> /usr/local/iAPBS-build/lib/libiapbs.a(apbs_driver.o): In function
> > >>> `apbsdrv_':
> > >>> apbs_driver.c:(.text+0x1207): undefined reference to `loadPotMaps'
> > >>> make: *** [sander.APBS] Error 1/
> > >>>
> > >>> _______________________________________________
> > >>> 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
> > >
> >
> > _______________________________________________
> > 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
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Sep 20 2011 - 22:00:02 PDT
