Re: [AMBER] AMBER12 installation error

From: Peter Fojan <>
Date: Wed, 25 Apr 2012 12:45:32 +0000

Hi again,
sorry for being not precise.
I did install amber12 single processor version and gnu compiler without any problem or error message and tests did pass all of them.
Next step I did was installing mpich2 as in the manual and downloaded from this site
and unpacked and installed mpich2 in

i ran ./configure_mpich2 gnu
make install
it installed without error message.

I did run
 ./configure -mpi gnu
configure ran wiothout any comment

make install proceeded until:
mpif90 -DBINTRAJ -DMPI -ffree-form -I../../AmberTools/src/pbsa -I../../AmberTools/src/sqm -I../../AmberTools/src/rism -I../../include -I/usr/local/amber12/include -I/usr/local/amber12/include -o sander.MPI 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 evb_vars.o evb_mathf.o evb_init.o evb_bcast.o evb_dealloc.o check_input.o evb_io.o evb_keywrd.o exchange_gauss.o exchange_warshel.o react_flux_init.o react_path.o react_flux.o kappa_keck.o schlegel_dg.o schlegel_full.o schlegel_diis.o schlegel_gmres.o schlegel_gbasis.o schlegel_pgbasis.o bnd_strtch.o ang_bend.o dihed_tors.o torinternal.o evb_gfchk.o bmat_inv.o bmat_grad.o unitv.o crossv.o cart2internal.o wdc_bmat.o select_coord.o schlegel_uff.o schlegel_dihed.o schlegel_angle.o schlegel_poh_uff.o schlegel_poh_irc.o schlegel_hcn_cart.o schlegel_hcn_int_irc.o schlegel_hcn_cart_irc.o evb_outoptions.o evb_2stdebug.o egap_umb_2stdebug.o dg_debug.o evb_io_debug.o bmat_debug.o bmat_inv_debug.o evb_io_debug2.o morse_anal2num.o xwarshel_anal2num.o xgauss_anal2num.o vdw_anal2num.o rcdbonds_anal2num.o rcbond_anal2num.o dg_grad_anal2num.o evb_input.o evb_alloc.o evb_matrix.o morsify.o mod_vdw.o evb_ntrfc.o evb_f
orce.o out_evb.o dbonds_anal2num.o bond_anal2num.o evb_umb.o evb_umb_primitive.o force.o \
              -L/usr/local/amber12/lib -lsqm -lFpbsa \
              ../lib/nxtsec.o ../lib/sys.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-cv-PCA.o ncsu-read-pca.o ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o mt19937.o -L/usr/local/amber12/lib -lnetcdf \
               -larpack -llapack -lblas \
/usr/local/amber12/lib/ undefined reference to `MPL_trfree'
/usr/local/amber12/lib/ undefined reference to `MPL_env2str'
/usr/local/amber12/lib/ undefined reference to `MPL_trlevel'
/usr/local/amber12/lib/ undefined reference to `MPL_trvalid'
/usr/local/amber12/lib/ undefined reference to `MPL_trmalloc'
/usr/local/amber12/lib/ undefined reference to `MPL_trspace'
/usr/local/amber12/lib/ undefined reference to `MPL_env2range'
/usr/local/amber12/lib/ undefined reference to `MPL_trcalloc'
/usr/local/amber12/lib/ undefined reference to `MPL_env2int'
/usr/local/amber12/lib/ undefined reference to `MPL_trdump'
/usr/local/amber12/lib/ undefined reference to `MPL_env2bool'
/usr/local/amber12/lib/ undefined reference to `MPL_trstrdup'
/usr/local/amber12/lib/ undefined reference to `MPL_trrealloc'
/usr/local/amber12/lib/ undefined reference to `MPL_TrSetMaxMem'
/usr/local/amber12/lib/ undefined reference to `MPL_trinit'
/usr/local/amber12/lib/ undefined reference to `MPL_trDebugLevel'
/usr/local/amber12/lib/ undefined reference to `MPL_trid'
collect2: ld returned 1 exit status
make[2]: *** [sander.MPI] Error 1
make[2]: Leaving directory `/usr/local/amber12/src/sander'
make[1]: *** [parallel] Error 2
make[1]: Leaving directory `/usr/local/amber12/src'
make: *** [install] Error 2

I hope I did not miss out on anything.

which mpif90

gnu compilers gcc 4.4.5
gfortran 4.4.5

                              ( o o )
Peter Fojan, PhD Tel. 0045/9940 7491
Associate Professor email:
Molecular Engineering Group web:
<SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: 'Courier New'; mso-fareast-font-family: 'Times New Roman'; mso-fareast-theme-font: mi
Fra: David A Case []
Sendt: 25. april 2012 14:16
Til: AMBER Mailing List
Emne: Re: [AMBER] AMBER12 installation error

On Wed, Apr 25, 2012, Peter Fojan wrote:

> I just tried to install the mpi version of amber12 and just to be on the
> safe side also installed the suggested version of mpich2.
> but i do get the following error message and the installation stops.
> -larpack -llapack -lblas \
> /usr/local/amber12/lib/ undefined reference to `MPL_trfree'
> Anybody has any suggestions what to do?

Give more details? What compiler? What is the result of "which mpif90"?
Can you give the full command that failed, probably starting with "mpif90...."
Can you be more explicit when you say that you "installed the suggested
version of mpich2"? (That is, tell us what you actually did, not what you
intended to do or thought you did.)


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