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
>
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--
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 - 06:30:02 PDT
