AMBER: installation amber9

From: Geoff Wood <>
Date: Mon, 31 Mar 2008 13:02:01 +0200

Dear Amber community,

I am having a little trouble with the installation of amber 9.


uname -a
Linux master1.cluster 2.4.20-20.9smp #1 SMP Mon Aug 18 11:18:01 EDT
2003 i686 athlon i386 GNU/Linux

Linux version (Red Hat Linux 3.2.2-5))

I have installed new versions of mpich2 (version 1.0.6), gcc (version
4.03) and g95 (version 0.91) but I have a fairly old version of MKL
viz 6.0.

If I try:

./configure -mpich2 g95

then the configure file gives me:
AMBERHOME is set to /home/gpw501/amber9
Setting up Amber configuration file for architecture: g95
Using parallel communications library: mpich2
MPI_HOME is set to /home/gpw501/mpich2-install
MKL_HOME is set to /opt/intel/mkl60/
Using MKL libraries from /opt/intel/mkl60//lib/32

The configuration file, config.h, was successfully created.

When I start with make parallel I get warnings such as:

In file _evb_init.f:722

          call mpi_bcast ( xdat_dia(n)% q, ndim, MPI_DOUBLE_PRECISION,
0, commwo
Warning (155): Inconsistent types (CHARACTER(1)/REAL(8)) in actual
argument lists at (1) and (2)
In file _evb_init.f:736

          call mpi_bcast ( xdat_xch(n)% filename, 512, MPI_CHARACTER,
0, commwor
In file _evb_init.f:683

    call mpi_bcast ( natm3, 1, MPI_INTEGER, 0, commworld, ierr )


Warning (155): Inconsistent types (CHARACTER(1)/INTEGER(4)) in actual
argument lists at (1) and (2)
In file _evb_init.f:736


Finally the installation stops with the error:
make[2]: Leaving directory `/imports/home/gpw501/amber9/src/lmod'
cd ../lmod; cp lmodprmtop ../../exe; chmod 0755 ../../exe/lmodprmtop
g95 -ffree-form -o sander.MPI 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.o evb_ntrfc.o out_evb.o constants.o
stack.o qmmm_module.o trace.o lmod.o decomp.o icosasurf.o egb.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.o multisander.o sander.o
trajene.o cshf.o nmrcal.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 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.o thermo_int.o matinv.o assert.o mmtsb.o
mmtsb_client.o erfcfun.o veclib.o is_init.o constantph.o prn_dipoles.o
ips.o sglds.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 parms.o qm_mm.o qm_link_atoms.o
qm_nb_list.o qm_extract_coords.o qm_ewald.o qm_gb.o qm_zero_charges.o
qm_print_info.o qm_assign_atom_types.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 \
                    qm_div.o force.o \
        ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
        ../lib/nxtsec.o ../lib/sys.a -L/home/gpw501/mpich2-install//lib -
lmpichf90 -lmpichf90 -lmpich -lpthread -lrt -L/opt/intel/mkl60//lib/32
-lvml -lmkl_lapack -lmkl -lguide -lpthread
evb_init.o(.data+0x430): undefined reference to
evb_io.o(.data+0x42c): undefined reference to `mpi_conversion_fn_null_'
qmmm_module.o(.data+0x428): undefined reference to
egb.o(.data+0x42c): undefined reference to `mpi_conversion_fn_null_'
egb.o(.data+0x24c8): undefined reference to `mpi_conversion_fn_null_'
multisander.o(.data+0x42c): more undefined references to
`mpi_conversion_fn_null_' follow
/opt/intel/mkl60//lib/32/libmkl_lapack.a(ilaenv.o)(.text+0x52a): In
function `__MKL_SERV_ilaenv':
: undefined reference to `s_copy'
/opt/intel/mkl60//lib/32/libmkl_lapack.a(ilaenv.o)(.text+0x541): In
function `__MKL_SERV_ilaenv':
: undefined reference to `s_copy'
/opt/intel/mkl60//lib/32/libmkl_lapack.a(ilaenv.o)(.text+0x556): In
function `__MKL_SERV_ilaenv':
: undefined reference to `s_copy'
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/imports/home/gpw501/amber9/src/sander'
make: *** [parallel] Error 2

It has partially made lmodprmtop ptraj rdparm sander.LES.MPI
sander.MPI sander.PIMD.MPI

But some libraries are not linked for example:

ldd sander.MPI => /lib/ (0x40025000) => /lib/ (0x40028000) => /lib/tls/ (0x4002c000) => /lib/tls/ (0x4003b000) => not found => not found => /lib/tls/ (0x42000000)
        /lib/ => /lib/ (0x40000000)

Any help would be much appreciated.

Geoffrey Wood
Ecole Polytechnique Fédérale de Lausanne
BCH 4108
CH - 1015 Lausanne

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Received on Fri Apr 18 2008 - 21:15:32 PDT
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