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]
[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] [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] [2]
--
Kind regards Nick
Links:
------
[1]
http://11.3.3.210/compilers_and_libraries_2016.33.210/linux/mkl/lib/intel64
[1]
[1]
[2] 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
