Please show us your execution command line. 2016-10-18 14:08 GMT+02:00 T. Liu <[email protected]>:
> Dear Nick, > > I followed your suggestion, and there is no error for the compilation. > But I only can run a serial mode on a parallel version. > > here is a piece of the top of output file > > > > *********************** > > *********************** > * WELCOME TO SIESTA * > *********************** > > *********************** > * WELCOME TO SIESTA * > *********************** > > *********************** > * WELCOME TO SIESTA * > *********************** > * WELCOME TO SIESTA * > *********************** > > reinit: Reading from standard input > > reinit: Reading from standard input > > > ... > > ... > > > * Running in serial mode > Siesta Version: trunk-572 > Architecture : x86_64-unknown-linux-gnu--unknown > Compiler flags: mpifc -g -O3 > PP flags : -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT > Libraries : -L/usr/local/Cluster-Apps/intel/mkl/11.3.3.210/compilers_ > and_libraries_2016.33.210/linux/mkl/lib/intel64 -lmkl_scalapack_lp64 > -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_lp64 > -lpthread -lm > PARALLEL version > > Could you suggest what to do please? > > Regards, > Tao > > > > > > > On 2016-10-14 12:18, T. Liu wrote: > >> Dera Nick, >> >> Thanks for your help. It works by adding .c and using latest SCALAPCK. >> >> Regards, >> Tao >> >> >> >> On 2016-10-14 11:40, Nick Papior wrote: >> >>> Try add .c to the SUFFIXES list. >>> >>> 2016-10-14 12:32 GMT+02:00 T. Liu <[email protected]>: >>> >>> Dear all, >>>> >>>> I can compile 4.0 with the following arch.make >>>> >>>> arch.make >>>> ---------------------------- >>>> # >>>> # Copyright (C) 1996-2016 The SIESTA group >>>> # This file is distributed under the terms of the >>>> # GNU General Public License: see COPYING in the top directory >>>> # or http://www.gnu.org/copyleft/gpl.txt [1]. >>>> # See Docs/Contributors.txt for a list of contributors. >>>> # >>>> .SUFFIXES: >>>> .SUFFIXES: .f .F .o .a .f90 .F90 >>>> >>>> SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown >>>> >>>> FPP= >>>> FPP_OUTPUT= >>>> FC=mpifc >>>> RANLIB=ranlib >>>> >>>> SYS=nag >>>> >>>> SP_KIND=4 >>>> DP_KIND=8 >>>> KINDS=$(SP_KIND) $(DP_KIND) >>>> >>>> FFLAGS=-g -O2 >>>> FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DMPI >>>> LDFLAGS= >>>> >>>> ARFLAGS_EXTRA= >>>> >>>> FCFLAGS_fixed_f= >>>> FCFLAGS_free_f90= >>>> FPPFLAGS_fixed_F= >>>> FPPFLAGS_free_F90= >>>> >>>> BLAS_LIBS=-lblas >>>> LAPACK_LIBS=-llapack >>>> BLACS_LIBS= >>>> SCALAPACK_LIBS= >>>> >>>> #DUMMY_FOX=--enable-dummy >>>> >>>> NETCDF_LIBS= >>>> NETCDF_INTERFACE= >>>> >>>> COMP_LIBS=dc_lapack.a >>>> >>>> #LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) >>>> $(NETCDF_LIBS) >>>> >>>> LIBS=-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 >>>> -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_lp64 -lpthread -lm >>>> >>>> #SIESTA needs an F90 interface to MPI >>>> #This will give you SIESTA's own implementation >>>> #If your compiler vendor offers an alternative, you may change >>>> #to it here. >>>> MPI_INTERFACE=libmpi_f90.a >>>> MPI_INCLUDE= . >>>> >>>> #Dependency rules are created by autoconf according to whether >>>> #discrete preprocessing is necessary or not. >>>> .F.o: >>>> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) >>>> $(FPPFLAGS_fixed_F) $< >>>> .F90.o: >>>> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) >>>> $(FPPFLAGS_free_F90) $< >>>> .f.o: >>>> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $< >>>> .f90.o: >>>> $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $< >>>> >>>> -------------------------------------- >>>> >>>> Then I just changed COMP_LIBS=dc_lapack.a to COMP_LIBS += >>>> libsiestaLAPACK.a to compile the Siesta trunk 572. It seems it >>>> almost finished but an error shows up at the bottom (error message >>>> shown below,"gfortran: sockets.o: No such file or directory"). Could >>>> you please suggest what happen and how to fix that? Thanks. >>>> >>>> ... >>>> ... >>>> mpifc -c -g -O2 `FoX/FoX-config --fcflags` -DFC_HAVE_FLUSH >>>> -DFC_HAVE_ABORT -DMPI >>>> /home/tl439/~siesta-maint/siesta/trunk/Src/m_monitor.F90 >>>> mpifc -c -g -O2 `FoX/FoX-config --fcflags` >>>> /home/tl439/~siesta-maint/siesta/trunk/Src/nag.f >>>> mpifc -c -g -O2 `FoX/FoX-config --fcflags` -DFC_HAVE_FLUSH >>>> -DFC_HAVE_ABORT -DMPI >>>> /home/tl439/~siesta-maint/siesta/trunk/Src/pxf.F90 >>>> mpifc -c -g -O2 `FoX/FoX-config --fcflags` -DFC_HAVE_FLUSH >>>> -DFC_HAVE_ABORT -DMPI >>>> /home/tl439/~siesta-maint/siesta/trunk/Src/siesta.F >>>> mpifc -o siesta >>>> automatic_cell.o atom_options.o arw.o atomlwf.o >>>> bands.o basis_enthalpy.o bessph.o bonds.o born_charge.o cellxc_mod.o >>>> cgwf.o chkdim.o chkgmx.o chempot.o coceri.o coxmol.o cross.o >>>> compute_norm.o denmat.o denmatlomem.o detover.o dfscf.o >>>> m_diagon_opt.o diagon.o digcel.o fft.o dhscf.o constr.o diagk_file.o >>>> diagg.o diagk.o diagkp.o diag2g.o diag2k.o diag3g.o diag3k.o >>>> diagpol.o diagsprl.o dipole.o dismin.o dnaefs.o doping_uniform.o >>>> dot.o m_efield.o egandd.o ener3.o ener3lomem.o errorf.o extrapolon.o >>>> m_fixed.o interpolation.o gradient.o gradientlomem.o grdsam.o >>>> hsparse.o idiag.o initatom.o inver.o iodm_netcdf.o iodmhs_netcdf.o >>>> iogrid_netcdf.o iolwf.o iozm.o ipack.o iopipes.o iosockets.o >>>> iowfs_netcdf.o kgrid.o kgridinit.o kinefsm.o ksv.o ksvinit.o >>>> linpack.o local_DOS.o madelung.o mesh.o meshphi.o meshdscf.o >>>> memory.o meshsubs.o metaforce.o m_supercell.o mulliken.o minvec.o >>>> naefs.o m_new_dm.o normalize_dm.o ordern.o outcell.o outcoor.o >>>> m_fft_gpfa.o paste.o pdos.o pdosg.o pdosk.o pdoskp.o phirphi.o >>>> pixmol.o plcharge.o projected_DOS.o propor.o m_partial_charges.o >>>> randomg.o reclat.o redcel.o reinit.o reord.o reordpsi.o rhoofd.o >>>> rhoofdsp.o rhooda.o savepsi.o shaper.o timer_tree.o timer.o vmb.o >>>> vmat.o vmatsp.o volcel.o cdiag.o rdiag.o cgvc.o cgvc_zmatrix.o >>>> m_convergence.o iocg.o ioeig.o iofa.o iokp.o iomd.o kpoint_pdos.o >>>> typecell.o ofc.o poison.o readsp.o radfft.o write_md_record.o >>>> kpoint_grid.o find_kgrid.o proximity_check.o state_init.o >>>> siesta_move.o setup_hamiltonian.o compute_dm.o mixer.o >>>> scfconvergence_test.o post_scf_work.o state_analysis.o write_subs.o >>>> siesta_init.o struct_init.o siesta_options.o read_options.o >>>> siesta_geom.o siesta_analysis.o siesta_end.o siesta_forces.o io.o >>>> sparse_matrices.o coor.o atm_transfer.o broadcast_basis.o eggbox.o >>>> dsyevds.o zheevds.o optical.o phirphi_opt.o reoptical.o >>>> transition_rate.o initparallel.o show_distribution.o setspatial.o >>>> setatomnodes.o uncell.o cart2frac.o obc.o precision.o sys.o m_cell.o >>>> files.o spatial.o parallel.o parallelsubs.o parsing.o chemical.o >>>> atom.o atmparams.o m_mpi_utils.o fdf_extra.o m_iorho.o atmfuncs.o >>>> listsc.o memoryinfo.o m_memory.o sorting.o atomlist.o atm_types.o >>>> old_atmfuncs.o radial.o alloc.o spher_harm.o periodic_table.o >>>> version.o timestamp.o basis_types.o xml.o pseudopotential.o >>>> basis_specs.o basis_io.o ldau.o ldau_specs.o onmod.o densematrix.o >>>> writewave.o on_subs.o fermid.o m_broyddj.o electrostatic.o mneighb.o >>>> globalise.o siesta_cmlsubs.o siesta_cml.o units.o zmatrix.o >>>> m_broyden_mixing.o forhar.o m_walltime.o m_wallclock.o m_iostruct.o >>>> nlefsm.o overfsm.o overlap.o conjgr.o conjgr_old.o m_energies.o >>>> m_steps.o m_broyddj_nocomm.o broyden_optim.o ioxv.o dynamics.o >>>> md_out.o molecularmechanics.o zm_broyden_optim.o >>>> cell_broyden_optim.o remove_intramol_pressure.o m_ntm.o m_dipol.o >>>> m_kinetic.o m_rmaxh.o m_forces.o m_stress.o m_eo.o m_spin.o >>>> m_gamma.o m_hsx.o m_fire.o setup_H0.o get_kpoints_scale.o >>>> get_target_stress.o fire_optim.o zm_fire_optim.o cell_fire_optim.o >>>> m_fire_para.o m_fire_mixing.o write_raw_efs.o pdos2g.o pdos2k.o >>>> pdos3g.o pdos3k.o spinorbit.o moments.o fsiesta_mpi.o >>>> final_H_f_stress.o debugmpi.o qsort.o save_density_matrix.o >>>> m_dscfcomm.o schecomm.o moremeshsubs.o domain_decom.o printmatrix.o >>>> mmio.o pspltm1.o lenstr.o setup_ordern_indexes.o m_iodm.o >>>> m_iodm_old.o m_filter.o m_io.o m_timer.o extrae_module.o >>>> extrae_eventllist.o moreParallelSubs.o read_xc_info.o >>>> siesta_master.o bsc_xcmod.o bsc_cellxc.o xc.o vacuum_level.o >>>> write_orb_indx.o rdiag_elpa.o elpa1.o elpa2.o elpa2_kernels.o >>>> rdiag_mrrr.o die.o m_pexsi.o m_pexsi_driver.o m_pexsi_dos.o >>>> m_pexsi_local_dos.o m_redist_spmatrix.o class_Distribution.o >>>> m_dminim.o m_zminim.o m_getopts.o f2kcli.o m_svd.o m_matio.o >>>> rusage.o memory_snapshot.o compute_ebs_shift.o memory_all.o >>>> matel_registry.o register_rfs.o new_matel.o kpoint_convert.o >>>> m_target_stress.o compute_max_diff.o m_initwf.o wavefunctions.o >>>> m_evolve.o evolk.o evolg.o changebasis.o m_iotddft.o m_matdiag.o >>>> m_matswinvers.o m_mixing.o m_mixing_scf.o m_trialorbitalclass.o >>>> siesta2wannier90.o m_planewavematrixvar.o delk.o m_planewavematrix.o >>>> m_digest_nnkp.o broadcast_projections.o compute_pw_matrix.o >>>> m_writedelk.o mmn.o m_noccbands.o amn.o m_overkkneig.o >>>> write_inp_wannier.o diagonalizeHk.o m_orderbands.o >>>> class_OrbitalDistribution.o class_Sparsity.o class_Data1D.o >>>> class_Data2D.o class_SpData1D.o class_SpData2D.o restructSpData2D.o >>>> extrapolateSpData2D.o class_Geometry.o class_Fstack_Data1D.o >>>> class_Pair_Data1D.o class_Fstack_Pair_Data1D.o >>>> class_Pair_Geometry_SpData2D.o class_Fstack_Pair_Geometry_SpData2D.o >>>> class_Pair_SpData1D.o class_Fstack_Pair_SpData1D.o class_TriMat.o >>>> m_trimat_invert.o m_uuid.o object_debug.o m_rhog.o rhofft.o m_diis.o >>>> compute_energies.o m_char.o m_os.o intrinsic_missing.o geom_helper.o >>>> m_sparse.o m_handle_sparse.o m_mesh_node.o create_Sparsity_SC.o >>>> create_Sparsity_Union.o m_gauss_quad.o m_gauss_fermi_inf.o >>>> m_gauss_fermi_30.o m_gauss_fermi_28.o m_gauss_fermi_26.o >>>> m_gauss_fermi_24.o m_gauss_fermi_22.o m_gauss_fermi_20.o >>>> m_gauss_fermi_19.o m_gauss_fermi_18.o m_gauss_fermi_17.o >>>> m_integrate.o m_interpolate.o m_mat_invert.o m_monitor.o >>>> m_iterator.o m_pivot_array.o m_pivot.o m_pivot_methods.o >>>> atom_graph.o m_geom_aux.o m_geom_objects.o m_geom_box.o >>>> m_geom_coord.o m_geom_square.o m_geom_plane.o m_charge_add.o >>>> m_hartree_add.o m_io_s.o m_region.o m_sparsity_handling.o >>>> m_ncdf_siesta.o m_ncdf_io.o m_exp_coord.o flook_siesta.o >>>> siesta_dicts.o m_cite.o m_ts_io.o nag.o pxf.o sockets.o fsockets.o >>>> siesta.o libfdf.a MatrixSwitch.a libxmlparser.a >>>> libSiestaXC.a libmpi_f90.a >>>> libsiestaLAPACK.a `FoX/FoX-config --libs --wcml` >>>> >>>> -L/usr/local/Cluster-Apps/intel/mkl/10.3.10.319/composer_xe_ >>> 2011_sp1.10.319/mkl/lib/intel64 >>> >>>> -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential >>>> -lmkl_blacs_intelmpi_lp64 -lpthread -lm >>>> gfortran: sockets.o: No such file or directory >>>> make: *** [siesta] Error 1 >>>> >>>> Regards, >>>> Tao >>>> >>> >>> -- >>> >>> Kind regards Nick >>> >>> Links: >>> ------ >>> [1] http://www.gnu.org/copyleft/gpl.txt >>> >> -- Kind regards Nick
