I don't know if this will work, but no one else has replied so I might as
well make a suggestion!
perhaps if you put in an explicit path to the libraries included in the
amber distribution, and then compiled them yourself using the same compiler
as you intend to use for the rest of the installation.
A second option which would probably work as a bit of a sneaky workaround
would be to copy the relevant source code into the sander directory and let
the compiler link it in all on it's own.
Hope that helps,
Martin.
----- Original Message -----
From: "Hayden Eastwood" <s0237717.sms.ed.ac.uk>
To: <amber.scripps.edu>
Sent: Wednesday, September 19, 2007 3:24 PM
Subject: AMBER: problem compiling amber9 on IBM 64 bit machine with
xlf90_suse compiler
> Dear Amber guys
>
> I am having problems compiling sander (amber9, both serial and parallel)
> on
> a 64 bit IBM cluster with the xlf90_suse compiler. Typically, compillation
> begins without problem, but crashes out with references such as those
> below:
>
>
>
> ****************************************************************************
> ***********
> .
> .
> .
> a - ../obj/commandqmmm.o
> a - ../obj/initmem2.o
> a - ../obj/allocateMxAtomVarsqmmm.o
> /bin/true libdivcon.a
> mv libdivcon.a ../src/qmmm/
> make[2]: Leaving directory `/home/b23/barran/bin/amber9/src/dcqtp/mod'
> make[1]: Leaving directory `/home/b23/barran/bin/amber9/src/dcqtp'
> xlf90 -qfree=f90 -o sander 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 diabati
> c.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 amo
> pen.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 amoe
> ba_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 q
> m2_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_dispersion
> read.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_df
> tb_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 ../dcqtp/src/qmmm/libdivcon.a \
> ../lapack/lapack.a ../blas/blas.a \
> ../lib/nxtsec.o ../lib/sys.a
> evb_force.o(.text+0x560): In function `evb_force':
> : undefined reference to `dsyev'
> lmod.o(.text+0x848): In function `__lmod_driver_NMOD_run_xmin':
> : undefined reference to `xmin'
> lmod.o(.text+0x23f4): In function `__lmod_driver_NMOD_run_lmod':
> : undefined reference to `lmod'
> relax_mat.o(.text+0xfec): In function `__relax_mat_NMOD_remarc':
> : undefined reference to `dspev'
> sander.o(.text+0x1e14): In function `sander':
> : undefined reference to `amflsh'
> sander.o(.text+0x2f08): In function `sander':
> : undefined reference to `amflsh'
> sander.o(.text+0x39e8): In function `sander':
>
> Etc etc etc (there are a lot more)
>
> ****************************************************************************
> **************************
>
> My questions are these:
>
> 1. It looks like the libraries aren't loading for this. I tried
> implementing
> the idea suggested by DAC in an earlier post(see: "AMBER: Problem
> compiling
> AMBER 9 on ppc64" - sept 4th). However, my blas library does not appear to
> be in /usr/lib location. Indeed, I've used the "find" command within linux
> and not found any library by that name (I did of course find the "blas"
> folder within the amber9 directory). DACs suggestion of entering the
> USE_BLASLIB=$(SOURCE_COMPILED) line into the config file didn't work. Is
> it
> possible that the library doesn't exist?
>
> 2. With regards to the parallel compilation: I notice that the config.h
> file
> tries to implement mpif90. However, the mpich2 distribution on this
> machine
> does not have an mpif90 executable in the bin directory. There is however
> an
> mpixlf90 executable and an mpif77, can I use either of these instead?
>
> I attach with this e-mail config.h for both parallel and serial compiles.
>
> Many thanks for any advice on the matter.
>
> Best
>
> Hayden
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Sep 23 2007 - 06:07:12 PDT
