>From the output of siesta, it is compiled in parallel, (it says PARALLEL).
It may be that you are not using the same mpirun as that shipped with mpifc?
Maybe you should be using mpiifort?

These are long shots... but...
Secondly, it may be a problem with the scheduler and the "~" in the path.
Could you try and move the executable to another folder?

If either of the above does not work, I think you should consult your local
HPC administrator, from the output you provide SIESTA is enabled in
parallel mode.

2016-10-18 14:41 GMT+02:00 T. Liu <tl...@cam.ac.uk>:

> Dear Nick,
>
> Thanks for your reply.
>
> it is
> mpirun -ppn $mpi_tasks_per_node -np $np $application $options
>
> translated as
> mpirun -ppn 16 -np 16 /home/tl439/~siesta-maint/siesta/trunk/Obj/siesta <
> h2o.relax.fdf > h2o.relax.out
>
> I also tried
> mpirun -np 16 /home/tl439/~siesta-maint/siesta/trunk/Obj/siesta <
> h2o.relax.fdf > h2o.relax.out
> it doesn't work neither.
>
> I used same execution command for siesta 4.0, it works.
>
> Regards,
> Tao
>
>
>
> On 2016-10-18 13:13, Nick Papior wrote:
>
>> Please show us your execution command line.
>>
>> 2016-10-18 14:08 GMT+02:00 T. Liu <tl...@cam.ac.uk>:
>>
>> 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
>>
>>> [1] -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 <tl...@cam.ac.uk>:
>>>
>>> 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 [2] [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 [2]
>>>
>>
>> --
>>
>> Kind regards Nick
>>
>> Links:
>> ------
>> [1] http://11.3.3.210/compilers_and_libraries_2016.33.210/linux/
>> mkl/lib/intel64
>> [2] http://www.gnu.org/copyleft/gpl.txt
>>
>


-- 
Kind regards Nick

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