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
>
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Received on Tue Sep 20 2011 - 15:30:02 PDT
