Hi,
For the record I've tried the alternative approach of linking the gcc44 executables into a local directory as gcc, g++ and gfortran and adding that directory to the beginning of my PATH. And it works - no build errors and all tests pass!
Suggests to me that perhaps there is some pattern matching on the compiler name somewhere in the build process?
Kevin
> -----Original Message-----
> From: Kevin Parkes
> Sent: 31 May 2012 14:22
> To: AMBER Mailing List
> Subject: Re: [AMBER] Amber 12 on x86_64 CentOS 5
>
> Jason,
>
> Unfortunately that does not seem to be the case. I've tried
> re-configuring and re-building after 'make clean uninstall'
> and get the same error. The timestamp on ./lib/libnetcdf.a
> is compatible with the current build.
>
> Kevin
>
> > -----Original Message-----
> > From: Jason Swails [mailto:jason.swails.gmail.com]
> > Sent: 30 May 2012 16:02
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Amber 12 on x86_64 CentOS 5
> >
> > 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
> > > > >
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> > > > > _______________________________________________
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> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Candidate
> > > > 352-392-4032
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> > >
> > >
> >
> >
> > --
> > 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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Received on Fri Jun 01 2012 - 03:00:02 PDT
