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
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Received on Wed May 30 2012 - 06:00:05 PDT
