AMBER: Problems during compilation

From: Sébastien Kozlowskyj <>
Date: Wed, 18 Jul 2007 11:26:06 +0200



I've tried to build Amber9 to IBM POWER 4 machine with AIX 5.2 but I can not!

There are the errors we got during the compilation:

            Following the steps below:

./configure xlf90_aix
make serial

we get the error:


Target "mexit.o" is up to date.

        xlf90 -qfree=f90 -o ambmask ambmask.o findmask.o amopen.o ../lib/mexit.o ../lib/nxtsec.o -L/usr/lib -lmassv -L/usr/lib -lblas

        xlf90 -qfree=f90 -o sander.PIMD parms.o constants.o qmmm_module.PIMD.o qm_link_atoms.PIMD.o qm_nb_list.PIMD.o qm_mm.PIMD.o pimd_vars.PIMD.o pimd_init.PIMD.o pimd_force.PIMD.o dynlib.PIMD.o ew_force.PIMD.o force.PIMD.o mdread.PIMD.o nonbond_list.PIMD.o rdparm.PIMD.o runmd.PIMD.o sander.PIMD.o short_ene.PIMD.o ew_setup.PIMD.o trace.o lmod.o decomp.o icosasurf.o egb.PIMD.o findmask.o pb_force.o pb_exmol.o pb_mpfrc.o pb_direct.o pb_list.o np_force.o sa_driver.o relax_mat.o nmr.LES.o multisander.o trajene.o cshf.o nmrcal.o pearsn.o printe.o runmin.o locmem.LES.o getcor.o degcnt.LES.o decnvh.o fastwt.o parallel.PIMD.o shake.o ene.PIMD.o mdwrit.o minrit.o set.o mdfil.o nmlsrc.o ew_box.o ew_bspline.o ew_fft.o ew_recip.LES.o pcshift.o align.o stack.o rfree.o rgroup.o random.o amopen.o debug.o ew_recip_reg.o ew_handle_dips.o ew_dipole_recip.o mexit.o new_time.o extra_pts.LES.o thermo_int.o matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o veclib.o constantph.o prn_dipoles.o ips.o sglds.o qm_zero_charges.o qm_print_info.o qm_assign_atom_types.o qm_gb.o qm_ewald.o qm_extract_coords.o qm2_allocate_e_repul.o qm2_calc_charges.o qm2_calc_rij_and_eqns.o qm2_dihed.o qm2_energy.o qm2_fock.o qm2_get_qm_forces.o qm2_get_qmmm_forces.o qm2_h1elec.o qm2_hcore_qmqm.o qm2_hcore_qmmm.o qm2_identify_peptide_links.o qm2_load_params_and_allocate.o qm2_repp.o qm2_rotate_qmqm.o qm2_scf.o qm2_setup_orb_exp.o qm2_smallest_number.o qm2_dftb_module.o qm2_dftb_broyden.o qm2_dftb_dispersion_egr.o qm2_dftb_dispersion_params.o qm2_dftb_dispersionread.o qm2_dftb_eglcao.o qm2_dftb_energy.o qm2_dftb_ewevge.o qm2_dftb_externalchgrad.o qm2_dftb_externalshift.o qm2_dftb_fermi.o qm2_dftb_forces.o qm2_dftb_gamma.o qm2_dftb_gammamat.o qm2_dftb_get_qmmm_forces.o qm2_dftb_gettab.o qm2_dftb_load_params.o qm2_dftb_long_range.o qm2_dftb_main.o qm2_dftb_my_gradient.o qm2_dftb_my_mulliken.o qm2_dftb_repulsiv.o qm2_dftb_self.o qm2_dftb_shift.o qm2_dftb_short_range.o qm2_dftb_skpar.o qm2_dftb_slkode.o qm2_dftb_slktrafo.o is_init.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 spatial_recip.o spatial_fft.o evb_vars.o evb_input.o evb_init.o evb_alloc.o evb_dealloc.o check_input.o evb_io.o evb_keywrd.o exchange_CM.o evb_mcp.o evb_force.o diabatic.o evb_2stdebug.o egap_umb_2stdebug.o exchange_gauss.o exchange_warshel.o morsify.o morse_anal2num.o evb_matrix.PIMD.o evb_ntrfc.PIMD.o evb_pimd_init.PIMD.o out_evb.PIMD.o ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a -L/usr/lib -lmassv -L/usr/lib -lblas

        /bin/mv sander sander.LES ambmask sander.PIMD ../../exe

        cd ptraj; make install

        xlc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -DCLINK_PLAIN -o analyze.o analyze.c

"analyze.c", line 470.70: 1506-046 (S) Syntax error.

"analyze.c", line 471.25: 1506-282 (S) The type of the parameters must be specified in a prototype.

"analyze.c", line 471.22: 1506-343 (S) Redeclaration of safe_malloc differs from previous declaration on line 65 of "utility.h".

"analyze.c", line 471.22: 1506-050 (I) Return type "double*" in redeclaration is not compatible with the previous return type "void*".

"analyze.c", line 471.15: 1506-275 (S) Unexpected text 'double' encountered.

"analyze.c", line 474.26: 1506-046 (S) Syntax error.

"analyze.c", line 474.29: 1506-045 (S) Undeclared identifier get.

"analyze.c", line 479.26: 1506-046 (S) Syntax error.

"analyze.c", line 493.9: 1506-046 (S) Syntax error.

make: 1254-004 The error code from the last command is 1.




make: 1254-004 The error code from the last command is 2.





Thank you very much for your help,


Looking forward to hearing from you,


Sebastien Kozlowskyj



Sébastien Kozlowskyj
Administrateur Système
Service de Chimie des Matériaux Nouveaux
Centre de Recherche en Electronique et Photonique Moléculaires
Université de Mons-Hainaut
Place du Parc, 20
B-7000 Mons (Belgique)

Tel.: ++32-(0)65-373866
Fax: ++32-(0)65-373861


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Received on Sun Jul 22 2007 - 06:07:04 PDT
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