Cc-ing directly to Sishi, in case she is not reading amber-developers: Sishi--is ncsu_*_pca from you? What compilers did you test on? Thx...dac
On Jun 20, 2011, at 9:19 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Jun 20, 2011 at 5:59 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>>>> /home/rcw/amber11_patch/amber/lib/libFpbsa.a
>>>> /home/rcw/amber11_patch/amber/lib/arpack.a -Wl,--start-group
>>>> /opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_intel_lp64.a
>>>> /opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_sequential.a
>>>> /opt/intel/Compiler/11.1/069/mkl/lib/em64t/libmkl_core.a -Wl,--end-
>>> group
>>>>
>>>
>>> How did these pop up if you're using gnu?
>>
>> Nothing wrong with linking to Intel MKL while using the GNU compilers...
>>
>
> True enough. I forgot the MKL is in the Compiler/ directories nowadays...
> With the gnu 4.4 compilers on Mac, I got the errors:
>
> gfortran -c -O0 -ffree-form -I../../AmberTools/src/pbsa
> -I../../AmberTools/src/sqm -I../../AmberTools/src/rism -I../../include -o
> ncsu-colvar-utils.o _ncsu-colvar-utils.f
> _ncsu-colvar-utils.f:481.34:
>
> write (unit = lun, fmt = '(a,a,i)') ' NCSU : ', ' solute part total
> atom
> 1
> Error: Nonnegative width required in format string at (1)
> _ncsu-colvar-utils.f:482.34:
>
> write (unit = lun, fmt = '(a,a,i)') ' NCSU : ', ' ref part total
> atom
> 1
> Error: Nonnegative width required in format string at (1)
> _ncsu-colvar-utils.f:483.34:
>
> write (unit = lun, fmt = '(a,a,i)') ' NCSU : ', ' pca part total
> atom
> 1
> Error: Nonnegative width required in format string at (1)
> make[1]: *** [ncsu-colvar-utils.o] Error 1
> make: *** [serial] Error 2
>
>
> When I changed those (a,a,i) to (a,a,i1), I got:
>
> gfortran -ffree-form -I../../AmberTools/src/pbsa -I../../AmberTools/src/sqm
> -I../../AmberTools/src/rism -I../../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 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
> 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 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
> qmmm_adaptive_module.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 /Users/swails/amber/lib/libsqm.a \
> 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-smd-hooks.o ncsu-umbrella.o
> ncsu-utils.o ncsu-value.o mt19937.o \
> /Users/swails/amber/lib/libFpbsa.a
> /Users/swails/amber/lib/arpack.a -framework Accelerate
> ../../AmberTools/src/lib/nxtsec.o \
> ../../AmberTools/src/lib/sys.a /Users/swails/amber/lib/libnetcdf.a
> Undefined symbols:
> "___ncsu_read_pca_MOD_read_avgcrd", referenced from:
> ___ncsu_colvar_MOD_colvar_mdread in ncsu-colvar.o
> "___ncsu_cv_pca_MOD_colvar_value", referenced from:
> ___ncsu_colvar_MOD_colvar_value in ncsu-colvar.o
> "___ncsu_cv_pca_MOD_print_details", referenced from:
> ___ncsu_colvar_MOD_colvar_print in ncsu-colvar.o
> "___ncsu_read_pca_MOD_read_evec", referenced from:
> ___ncsu_colvar_MOD_colvar_mdread in ncsu-colvar.o
> "___ncsu_cv_pca_MOD_colvar_bootstrap", referenced from:
> ___ncsu_colvar_MOD_colvar_bootstrap in ncsu-colvar.o
> "___ncsu_read_pca_MOD_read_index", referenced from:
> ___ncsu_colvar_MOD_colvar_mdread in ncsu-colvar.o
> "___ncsu_cv_pca_MOD_colvar_force", referenced from:
> ___ncsu_colvar_MOD_colvar_force in ncsu-colvar.o
> "___ncsu_cv_pca_MOD_colvar_cleanup", referenced from:
> ___ncsu_colvar_MOD_colvar_cleanup in ncsu-colvar.o
> "___ncsu_read_pca_MOD_read_refcrd", referenced from:
> ___ncsu_colvar_MOD_colvar_mdread in ncsu-colvar.o
> ld: symbol(s) not found
> collect2: ld returned 1 exit status
> make[1]: *** [sander] Error 1
> make: *** [serial] Error 2
>
>
> So I can reproduce your errors. It seems that the recent NCSU changes broke
> stuff for multiple compilers...
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon Jun 20 2011 - 19:30:04 PDT
