Tyler sent out a patch that fixed my issues with sander.RISM.MPI that
caused issues that look very much like this as I recall. I've
attached the patch to this email.
All the best,
Jason
Tyler just beat me to it.
On Tue, Apr 6, 2010 at 7:06 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi All,
>
> Have others encountered this:
>
> Using the Mar 31st Release Candidate.
>
> wget http://ambermd.org/downloads/AmberTools.31mar10.tar.bz2
> wget http://ambermd.org/downloads/Amber11.31mar10.tar.bz2
> tar xvjf AmberTools.31mar10.tar.bz2
> tar xvjf Amber11.31mar10.tar.bz2
> cd amber11/AmberTools/src
> wget
> http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.1.tar.bz2
> tar xvjf openmpi-1.4.1.tar.bz2
> ./configure_openmpi gnu
> export AMBERHOME=/path_to_amber/amber11
> export PATH=$AMBERHOME/bin/
> ./configure -mpi gnu
> cd ../../src
> make parallel
>
> This dies with:
>
> mpif90 -o sander.RISM.MPI constants.o state.o memory_module.o stack.o
> nose_hoover.o nose_hoover_vars.o nose_hoover_init.o qmmm_module.o trace.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.RISM.o trajene.o cshf.o
> nmrcal.o mtmdcall.o pearsn.o printe.RISM.o runmin.o rdparm.o mdread.RISM.o
> locmem.o runmd.RISM.o getcor.o degcnt.o decnvh.o fastwt.o parallel.o shake.o
> ene.o mdwrit.o minrit.o set.o dynlib.RISM.o mdfil.RISM.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.RISM.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 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 softcore.o
> mbar.o molecule.o xref.o dssp.o charmm.o qm_mm.o qm_ewald.o
> qm2_variable_solvent.o qmmm_qmtheorymodule.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_force.o
> out_evb.o dbonds_anal2num.o bond_anal2num.o evb_umb.o evb_umb_primitive.o
> force.RISM.o \
> ../../AmberTools/src/rism/amber_rism_interface.o \
> ../lib/nxtsec.o
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/librism.a
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/libsqm.a \
>
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/libFpbsa.a
> ../lib/sys.a mt19937.o ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o
> ncsu-cftree.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o
> ncsu-colvar.o ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o
> ncsu-cv-HANDEDNESS.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-cv-LCOD.o ncsu-cv-COS_OF_DIHEDRAL.o ncsu-lexer.o ncsu-parser.o
> ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o
> ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o
> ../netcdf/lib/libnetcdf.a \
>
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/arpack.a
> -L/opt/intel/mkl/10.1.1.019//lib/em64t -Wl,--start-group
> /opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_intel_lp64.a
> /opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_sequential.a
> /opt/intel/mkl/10.1.1.019//lib/em64t/libmkl_core.a -Wl,--end-group -lpthread
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/librism.a(ris
> m3d_c.o)(.text+0x3303): In function `__rism3d_c__rism3d_destroy':
> : undefined reference to `rfftwnd_f77_mpi_destroy_plan_'
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/librism.a(ris
> m3d_c.o)(.text+0x4b87): In function `__rism3d_c__reallocbox':
> : undefined reference to `rfftwnd_f77_mpi_destroy_plan_'
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/librism.a(ris
> m3d_c.o)(.text+0x4b8f): In function `__rism3d_c__reallocbox':
> : undefined reference to `rfftwnd_f77_mpi_destroy_plan_'
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/librism.a(ris
> m3d_c.o)(.text+0x330c): In function `__rism3d_c__rism3d_destroy':
> : undefined reference to `rfftwnd_f77_mpi_destroy_plan_'
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/librism.a(ris
> m_fft.o)(.text+0x73): In function `__rism_fft__fftw_make_plans':
> : undefined reference to `rfftw3d_f77_mpi_create_plan_'
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/librism.a(ris
> m_fft.o)(.text+0x97): In function `__rism_fft__fftw_make_plans':
> : undefined reference to `rfftw3d_f77_mpi_create_plan_'
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/librism.a(ris
> m_fft.o)(.text+0x885): In function `__rism_fft__rlft3i':: undefined
> reference to `rfftwnd_f77_mpi_'
> /home/rcw/cvs_checkouts/amber11_release_candidates/amber11/lib/librism.a(ris
> m_fft.o)(.text+0xd8): In function `__rism_fft__fftw_make_plans':
> : undefined reference to `rfftwnd_f77_mpi_local_sizes_'
> collect2: ld returned 1 exit status
> make[1]: *** [sander.RISM.MPI] Error 1
> make[1]: Leaving directory
> `/server-home/rcw/cvs_checkouts/amber11_release_candidates/amber11/src/sande
> r'
> make: *** [parallel] Error 2
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Apr 06 2010 - 16:30:08 PDT
