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
