My guess is that you had a leftover libnetcdf.a file from your first
installation attempt with gcc-4.1.2 (maybe?).
Your modified configure2 looks fine to me. Try installing again, but run
"make clean uninstall" first (just to make sure you get rid of everything).
HTH,
Jason
On Wed, May 30, 2012 at 6:25 AM, Kevin Parkes <Kevin.Parkes.medivir.com>wrote:
> Jason,
>
> Modified configure 2 attached.
>
> Thanks
>
> Kevin
>
> Dr K E B Parkes
> Director Computational Chemistry & Structural Biology
> Medivir AB
> Tel +44 (0)1799 532102
> Mob +44 (0)7920 053412
> Fax +44 (0)1799 532101
>
>
> > -----Original Message-----
> > From: Jason Swails [mailto:jason.swails.gmail.com]
> > Sent: 30 May 2012 14:05
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Amber 12 on x86_64 CentOS 5
> >
> > Can you attach your modified configure2 file?
> >
> > On Wed, May 30, 2012 at 5:48 AM, Kevin Parkes
> > <Kevin.Parkes.medivir.com>wrote:
> >
> > > Hi,
> > >
> > > I'm trying to compile Amber12 in serial with fftw3 support on an
> > > x86_64 workstation running CentOS 5.8.
> > >
> > > Unfortunately on CentOS 5 gcc is only at 4.1.2 although there is a
> > > preview version of gcc version 4.4.6. I've tried
> > installing this and
> > > editing
> > > AmberTools/src/configure2 so that gcc, gfortran and g++ all
> > point to
> > > the
> > > 4.4.6 installation and then ./configure gnu runs without
> > complaint but
> > > 'make install' fails at this point:
> > >
> > > gfortran44 -DBINTRAJ -ffree-form -I../../AmberTools/src/pbsa
> > > -I../../AmberTools/src/sqm -I../../AmberTools/src/rism
> > -I../../include
> > > -I/usr/local/medivir/amber/amber12/include
> > > -I/usr/local/medivir/amber/amber12/include -o sander
> > file_io_dat.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.o
> > trajene.o cshf.o
> > > nmrcal.o mtmdcall.o pearsn.o printe.o runmin.o rdparm.o
> > sander_lib.o
> > > mdread.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.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 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.o
> > -L/usr/local/medivir/amber/am
> > > 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 \
> > > -lFpbsa ../../AmberTools/src/lib/nxtsec.o \
> > > ../../AmberTools/src/lib/sys.a
> > > -L/usr/local/medivir/amber/amber12/lib -lnetcdf \
> > > -larpack -llapack -lblas \
> > >
> > > /usr/local/medivir/amber/amber12/lib/libnetcdf.a(netcdf.o): In
> > > function
> > > `__netcdf_MOD_nf90_inq_libvers':
> > > netcdf.f90:(.text+0x1a): undefined reference to `nf_inq_libvers_'
> > > /usr/local/medivir/amber/amber12/lib/libnetcdf.a(netcdf.o): In
> > > function
> > > `__netcdf_MOD_nf90_strerror':
> > > netcdf.f90:(.text+0x5a): undefined reference to `nf_strerror_'
> > > /usr/local/medivir/amber/amber12/lib/libnetcdf.a(netcdf.o): In
> > > function
> > > `__netcdf_MOD_nf90_create':
> > > netcdf.f90:(.text+0xe6): undefined reference to `nf__create_'
> > > netcdf.f90:(.text+0x10b): undefined reference to `nf_create_'
> > > netcdf.f90:(.text+0x12e): undefined reference to `nf__create_'
> > >
> > > On the same workstation compilation without fftw3 (configured with
> > > -nofftw3) works ad the resulting executables pass all the
> > tests, and
> > > compilation of AmberTools12 without Amber12 works with gcc 4.4.6.
> > >
> > > Any suggestions on how to solve this problem would be welcome.
> > >
> > > Many thanks
> > >
> > > Kevin Parkes
> > >
> > > Dr K E B Parkes
> > > Director Computational Chemistry & Structural Biology Medivir AB
> > >
> > > Suite 10, The Mansion
> > > Chesterford Research Park
> > > Little Chesterford
> > > Essex CB10 1XL UK
> > >
> > > Tel +44 (0)1799 532102
> > > Mob +44 (0)7920 053412
> > > Fax +44 (0)1799 532101
> > > Registered Office: Stockholm, Reg.No. 556238-4361 www.medivir.com
> > >
> > > This transmission is intended for the person to whom or the
> > entity to
> > > which it is addressed and may contain information that is
> > privileged,
> > > confidential and exempt from disclosure under applicable
> > law. If you
> > > are not the intended recipient, please be notified that any
> > > dissemination, distribution or copying is strictly
> > prohibited. If you
> > > have received this transmission in error, please notify us
> > immediately.
> > > Thank you for your cooperation.
> > >
> > > _______________________________________________
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> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
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> 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 Wed May 30 2012 - 08:30:03 PDT
