With intel compilers you should probably not compile with so high
optimizations. First try and lower the optimization (-O2 for instance).

2016-10-18 15:28 GMT+02:00 T. Liu <tl...@cam.ac.uk>:

> Dear Nick,
> Thanks for your help.
>
> I compiled it again without "~", It works!
> Instead, I met an old error message which I have already posted before,
> but haven't got an answer. There is no DM file in the folder.
>
> the bottom of output file
>
> Setting up quadratic distribution...
> ExtMesh (bp) on 0 =   147 x   144 x   134 =     2836512
> PhiOnMesh: Number of (b)points on node 0 =                 3800
> PhiOnMesh: nlist on node 0 =               985489
>
> stepf: Fermi-Dirac step function
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:    8
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:   15
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:    1
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:    2
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:    3
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:    4
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:    5
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:    6
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:    7
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:    9
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:   10
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:   11
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:   12
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:   13
> Bad DM normalization: Qtot, Tr[D*S] =         64.00000000
> 9.15895573
> Stopping Program from Node:   14
> Stopping Program from Node:    0
>
>
> INPUT file is
>
> SystemName      H2O
> SystemLabel     H2O
>
> NumberOfSpecies 2
> NumberOfAtoms   24
>
> %block ChemicalSpeciesLabel
> 1    1 H
> 2    8 O
> %endblock ChemicalSpeciesLabel
>
> LatticeConstant 6.3612 Ang
>
> %block LatticeVectors
> 1.0 0.0 0.0
> 0.0 1.0 0.0
> 0.0 0.0 1.0
> %endblock LatticeVectors
> AtomicCoordinatesFormat  Fractional
> %block AtomicCoordinatesAndAtomicSpecies
> 0.29160 0.29160 0.30827 1
> 0.95832 0.95832 0.30827 1
> 0.04168 0.20840 0.05835 1
> 0.20840 0.04168 0.05835 1
> 0.54168 0.54168 0.22506 1
> 0.70839 0.70839 0.22506 1
> 0.79160 0.45831 0.97498 1
> 0.45830 0.79160 0.97498 1
> 0.45830 0.29160 0.47498 1
> 0.79160 0.95831 0.47498 1
> 0.70839 0.20839 0.72506 1
> 0.54170 0.04168 0.72506 1
> 0.20840 0.54168 0.55835 1
> 0.04168 0.70840 0.55835 1
> 0.95832 0.45832 0.80827 1
> 0.29160 0.79160 0.80827 1
> 0.12504 0.12504 0.14171 2
> 0.62504 0.62504 0.14171 2
> 0.62504 0.12504 0.64171 2
> 0.12504 0.62504 0.64171 2
> 0.37496 0.37496 0.39163 2
> 0.87496 0.87496 0.39163 2
> 0.87496 0.37496 0.89163 2
> 0.37496 0.87496 0.89163 2
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> MD.TypeOfRun    CG
> MD.NumCGsteps   200
>
> SCFMustConverge             T
>
> XC.Functional GGA
> XC.authors PBE
>
> %block PAO.Basis # DZPQ-8.5
> O 3
> n=2 0 2 E 50. 7.5
>     8.0 2.7
> n=2 1 2 E 10. 8.3
>     8.5 2.6
> n=3 2 1 E 40. 8.3 Q 6.8 0.22
>     8.5
> H 2
> n=1 0 2 E 50. 8.3
>     8.5 2.2
> n=2 1 1 E 20. 7.8 Q 6.5 0.9
>     8.0
> %endblock PAO.Basis
>
> DM.Tolerance       0.1000000000E-04
> MD.MaxForceTol 0.001 eV/Ang
> MD.MaxStressTol 0.01 GPa
>
> MD.VariableCell              T
>
> kgrid_cutoff          10.00 Ang
> MeshCutoff     400 Ry
>
> I don't think there is any error in the input file, because it works for
> siesta 4.0.
> So I guess it must be still something wrong with the compilation?
>
> Regards,
> Tao
>
>
>
>
> On 2016-10-18 13:48, Nick Papior wrote:
>
>> 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]
>>> [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] [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] [2]
>>>
>>> --
>>>
>>> Kind regards Nick
>>>
>>> Links:
>>> ------
>>> [1]
>>>
>>> http://11.3.3.210/compilers_and_libraries_2016.33.210/linux/
>> mkl/lib/intel64
>>
>>> [1]
>>> [2] 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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