Dear AMBER user,
Can you please help me how to install AMBER9 on a
linux cluster? I am facing some problems during installation which is
unclear to me. I have istalled mpich2 and g95 on each node
individually. PATH and LD_LIBRARY_PATH are setted in .bashrc as
export MPI_HOME=/usr/local
export PATH=$PATH:$MPI_HOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MPI_HOME/lib
export AMBERHOME='/usr/local/amber9'
Then we have typed the commands which are given in user manual
patch -p0 -N -r patch-rejects < bugfix.all
cd src
make clean
make[1]: Entering directory `/usr/local/amber9/src/lib'
Makefile:25: ../config.h: No such file or directory
make[1]: *** No rule to make target `../config.h'. Stop.
make[1]: Leaving directory `/usr/local/amber9/src/lib'
make: *** [clean] Error 2
./configure -mpich2 g95
AMBERHOME is set to /usr/local/amber9
Setting up Amber configuration file for architecture: g95
Using parallel communications library: mpich2
MPI_HOME is set to /usr/local/
The MKL_HOME environment variable is not defined.
The configuration file, config.h, was successfully created.
make parallel
make[2]: Leaving directory `/usr/local/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/usr/local/lib -lmpichf90
-lmpichf90 -lmpich -lpthread -lrt
evb_init.o(.data+0x460): undefined reference to `mpi_conversion_fn_null_'
evb_io.o(.data+0x458): undefined reference to `mpi_conversion_fn_null_'
qmmm_module.o(.data+0x448): undefined reference to `mpi_conversion_fn_null_'
egb.o(.data+0x458): undefined reference to `mpi_conversion_fn_null_'
egb.o(.data+0x2550): undefined reference to `mpi_conversion_fn_null_'
multisander.o(.data+0x458): more undefined references to
`mpi_conversion_fn_null_' follow
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory `/usr/local/amber9/src/sander'
make: *** [parallel] Error 2
this is the last portion of the error
If anybody aware about this problem, please tell me.
Thanks and regards
sudipta
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Received on Sun May 04 2008 - 06:07:28 PDT
