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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> > Thank you for your cooperation.
> >
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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 - 06:30:04 PDT
