Dear Martin
Thankyou for getting back to me.
Please forgive my ignorance but I'm not sure I follow what you're saying,
perhaps you could elaborate a bit?
> 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.
Are you refering to the files in the blas folder? I don't understand what
the blas files are, I presume they are just libraries required for
performing various operations. However, how do I go about compiling them?
Would I need to modify the config.h file or what? Why do I need to specify a
path to search for the blas library if these files are already known to be
located in amber9/blas ? Are there a mixture of blas files that come with
AMBER and blas files that are expected to be found on the local machine?
> 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.
Again please excuse my ignorance, what exactly would the "relevant source
code" be?
Many thanks
Hayden
> 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
>
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Received on Sun Sep 23 2007 - 06:07:13 PDT
