ex_03.py in sisl/examples could not finish normally. about sisl

[zerothi]

Yes.

Do you still see problems?
Could you please supply as much information as possible. I can't reproduce your errors.

[zerothi]

ok, you need to compile phtrans with netcdf-4 support.

Please read the tbtrans manual on compilation and assert you have netcdf-4 support.

[staniba]

I failed to create libncdf.a.

What I did so far after recieving your help:
(1) Downloaded five files:{ m4-latest, zlib-1.2.11, hdf5-1.8.18, netcdf-c-4.4.1.1, netcdf-fortran-4.4.4 }.
(2) Installed m4-latest.
(3) Moved four files { zlib, hdf5, netcdf-c, netcdf-fortran } to "siesta-4.1-b3/Doc".
(4) Carried out "install_netcdf4.bash".
(5) Obtained the following message in the tail:

Please add the following to the BOTTOM of your arch.make file

INCFLAGS += -I/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include
LDFLAGS += -L/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib
LDFLAGS += -L/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib
LDFLAGS += -L/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib
LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
COMP_LIBS += libncdf.a libfdict.a
FPPFLAGS += -DCDF -DNCDF -DNCDF_4

(6) Added those above to my arch.make, and moved to "siesta-4.1-b3/Util/TS/TBtrans" .
(7) Typed "make phtrans".
(8) Obtained Some error messages in the tails.

compilation aborted for netcdf_ncdf.f90 (code 1)
failed in the recipe of 'netcdf_ncdf.o'
failed in the recipe of 'libncdf.a'

satoru

[staniba]

Details of error message related to compilation of " netcdf_netcdf.f90 ":

mpif90 -c -o netcdf_ncdf.o -g -I/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include -I../ netcdf_ncdf.f90
netcdf_ncdf.f90(59): error #7013: This module file was not generated by any release of this compiler. [NETCDF]
use netcdf
------^
netcdf_ncdf.f90(95): error #8237: The character length in a component declaration shall either be a colon, be an initialization expression, or be a specification expression. [GRP]
character(len=NF90_MAX_NAME) :: grp = " "
-------------------------------------^
netcdf_ncdf.f90(95): error #6404: This name does not have a type, and must have an explicit type. [NF90_MAX_NAME]
character(len=NF90_MAX_NAME) :: grp = " "
-------------------^
netcdf_ncdf.f90(255): error #6404: This name does not have a type, and must have an explicit type. [NF90_MPIIO]
par = iand(NF90_MPIIO,this%mode) == NF90_MPIIO
---------------^
netcdf_ncdf.f90(255): warning #7319: This argument's data type is incompatible with this intrinsic procedure; procedure assumed EXTERNAL. [IAND]
par = iand(NF90_MPIIO,this%mode) == NF90_MPIIO
---------------^
netcdf_ncdf.f90(255): error #6363: The intrinsic data types of the arguments must be the same. [IAND]
par = iand(NF90_MPIIO,this%mode) == NF90_MPIIO
--------------------------^
netcdf_ncdf.f90(255): error #6404: This name does not have a type, and must have an explicit type. [IAND]
par = iand(NF90_MPIIO,this%mode) == NF90_MPIIO
----------^
netcdf_ncdf.f90(257): error #6404: This name does not have a type, and must have an explicit type. [NF90_MPIPOSIX]
par = iand(NF90_MPIPOSIX,this%mode) == NF90_MPIPOSIX
---------------^
netcdf_ncdf.f90(259): error #6404: This name does not have a type, and must have an explicit type. [NF90_PNETCDF]
par = iand(NF90_PNETCDF,this%mode) == NF90_PNETCDF
---------------^
netcdf_ncdf.f90(303): error #6404: This name does not have a type, and must have an explicit type. [NF90_64BIT_OFFSET]
this%mode = IOR(this%mode,NF90_64BIT_OFFSET)
---------------------------------^
netcdf_ncdf.f90(303): error #6363: The intrinsic data types of the arguments must be the same. [IOR]
this%mode = IOR(this%mode,NF90_64BIT_OFFSET)
---------------------------------^
netcdf_ncdf.f90(323): error #6404: This name does not have a type, and must have an explicit type. [NF90_SHARE]
this%mode = ior(this%mode, NF90_SHARE)
----------------------------------^
netcdf_ncdf.f90(323): error #6363: The intrinsic data types of the arguments must be the same. [IOR]
this%mode = ior(this%mode, NF90_SHARE)
----------------------------------^
netcdf_ncdf.f90(336): error #6404: This name does not have a type, and must have an explicit type. [NF90_NOCLOBBER]
this%mode = ior(this%mode, NF90_NOCLOBBER)
-------------------------------------^
netcdf_ncdf.f90(336): error #6363: The intrinsic data types of the arguments must be the same. [IOR]
this%mode = ior(this%mode, NF90_NOCLOBBER)
-------------------------------------^
netcdf_ncdf.f90(362): error #6404: This name does not have a type, and must have an explicit type. [NF90_NETCDF4]
if ( iand(NF90_NETCDF4,this%mode) == NF90_NETCDF4 ) then
--------------^
netcdf_ncdf.f90(362): warning #7319: This argument's data type is incompatible with this intrinsic procedure; procedure assumed EXTERNAL. [IAND]
if ( iand(NF90_NETCDF4,this%mode) == NF90_NETCDF4 ) then
--------------^
netcdf_ncdf.f90(362): error #6363: The intrinsic data types of the arguments must be the same. [IAND]
if ( iand(NF90_NETCDF4,this%mode) == NF90_NETCDF4 ) then
---------------------------^
netcdf_ncdf.f90(362): error #6404: This name does not have a type, and must have an explicit type. [IAND]
if ( iand(NF90_NETCDF4,this%mode) == NF90_NETCDF4 ) then
---------^
netcdf_ncdf.f90(373): error #6404: This name does not have a type, and must have an explicit type. [NF90_CREATE]
call ncdf_err(nf90_create(filename, this%mode , this%f_id), &
---------------------^
netcdf_ncdf.f90(398): warning #7319: This argument's data type is incompatible with this intrinsic procedure; procedure assumed EXTERNAL. [IAND]
if ( iand(NF90_NETCDF4,this%mode) == NF90_NETCDF4 ) then
--------------^
netcdf_ncdf.f90(398): error #6363: The intrinsic data types of the arguments must be the same. [IAND]
if ( iand(NF90_NETCDF4,this%mode) == NF90_NETCDF4 ) then
---------------------------^
netcdf_ncdf.f90(398): error #6404: This name does not have a type, and must have an explicit type. [IAND]
if ( iand(NF90_NETCDF4,this%mode) == NF90_NETCDF4 ) then
---------^
netcdf_ncdf.f90(411): error #6404: This name does not have a type, and must have an explicit type. [NF90_NOWRITE]
this%mode = IOR(this%mode,NF90_NOWRITE)
---------------------------------^
netcdf_ncdf.f90(411): error #6363: The intrinsic data types of the arguments must be the same. [IOR]
this%mode = IOR(this%mode,NF90_NOWRITE)
---------------------------------^
netcdf_ncdf.f90(416): error #6404: This name does not have a type, and must have an explicit type. [NF90_OPEN]
call ncdf_err(nf90_open(filename, this%mode , this%f_id), &
---------------------^
netcdf_ncdf.f90(426): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQ_GRP_FULL_NCID]
call ncdf_err(nf90_inq_grp_full_ncid(this%f_id, trim(this%grp), this%id))
---------------------^
netcdf_ncdf.f90(627): error #6404: This name does not have a type, and must have an explicit type. [NF90_CLOSE]
call ncdf_err(nf90_close(this%f_id),"Closing NetCDF file: "//this)
------------------^
netcdf_ncdf.f90(653): error #6632: Keyword arguments are invalid without an explicit interface. [FORMATNUM]
call ncdf_err(nf90_inquire(this%id,ldims,lvars,latts,formatNum=lformat), &
---------------------------------------------------------^
netcdf_ncdf.f90(653): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQUIRE]
call ncdf_err(nf90_inquire(this%id,ldims,lvars,latts,formatNum=lformat), &
------------------^
netcdf_ncdf.f90(663): error #6632: Keyword arguments are invalid without an explicit interface. [NAME]
call ncdf_err(nf90_inquire_dimension(this%id,i,name=key))
---------------------------------------------------------^
netcdf_ncdf.f90(663): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQUIRE_DIMENSION]
call ncdf_err(nf90_inquire_dimension(this%id,i,name=key))
------------------------^
netcdf_ncdf.f90(2995): catastrophic error: Too many errors, exiting
compilation aborted for netcdf_ncdf.f90 (code 1)

[zerothi]

Try and do LIBS += $(LDFLAGS) and make clean ; make

[staniba]

I added LIBS += $(LDFLAGS) to my arch.make .
I moved to siesta-4.1-b3/Util/TS/TBtrans.
I typed " make clean ", then " make phtrans ".
However, it did not improve.
In setup.make, " LIBS += $(LDFLAGS) to my arch.make " was reflected.
The contents of setup.make is below:

FC=mpif90
AR=ar
RANLIB=ranlib
FFLAGS=-g
FPPFLAGS = -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DCDF -DNCDF -DNCDF_4 -DTBTRANS -DTBT_PHONON
INCLUDES = -I/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include -I../
LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_lapack95_lp64 -lmkl_blas95_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz -L/opt/intel/mkl/lib/intel64 -L/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib -L/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib -L/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -lfdict

[zerothi]

Perhaps it should be in front:

LIBS := $(LDFLAGS) $(LIBS)

[staniba]

It did not improve.
I replaced " LIBS += $(LDFLAGS) " to " LIBS := $(LDFLAGS) $(LIBS) ".
And I typed " make clean ", then " make phtrans ".
The above change of LIBS was reflected in setup.make in " Util/TS/TBtrans/ncdf ".

LIBS = -L/opt/intel/mkl/lib/intel64 -L/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib -L/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib -L/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_lapack95_lp64 -lmkl_blas95_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz -lfdict

[staniba]

Current status:

In siesta-4.1-b3/Util/TS/TBtrans/fdict/,
libfdict.a is created.

In siesta-4.1-b3/Util/TS/TBtrans/ncdf/,
libncdf.a is NOT created.

siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib/,
libnetcdf.a and libnetcdff.a are created.

[zerothi]

Could you run: /home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/bin/nf-config --all

[staniba]

Now I have done it.
The result is like this:

This netCDF-Fortran 4.4.4 has been built with the following features:

--cc -> gcc
--cflags -> -I/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include -DgFortran -I/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/include -I/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/include -I/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include

--fc -> gfortran
--fflags -> -I/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include
--flibs -> -L/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -lnetcdff -lnetcdf -L/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib -L/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib -L/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -lnetcdf -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz
--has-f90 -> no
--has-f03 -> yes

--has-nc2 -> yes
--has-nc4 -> yes

--prefix -> /home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1
--includedir-> /home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include
--version -> netCDF-Fortran 4.4.4

See you tomorrow.

satoru

[zerothi]

Could you list the files in:
/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include

[zerothi]

Sorry, now I know what has gone wrong. The libraries you compiled with install_netcdf was done using the gfortran compiler.
However, you are using the intel compiler for phtrans. And thus the error will occur.

1. You have to use the same compiler for all libraries to make this work.
2. Recompile the zlib, hdf5 and netcdf libraries with the intel compiler.
3. Compile phtrans.

[staniba]

The files in " /home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include ":

netcdf.h
netcdf.inc
netcdf.mod
netcdf4_f03.mod
netcdf4_nc_interfaces.mod
netcdf4_nf_interfaces.mod
netcdf_f03.mod
netcdf_fortv2_c_interfaces.mod
netcdf_mem.h
netcdf_meta.h
netcdf_nc_data.mod
netcdf_nc_interfaces.mod
netcdf_nf_data.mod
netcdf_nf_interfaces.mod
typesizes.mod

Now I will recompile the zlib, hdf5 and netcdf libraries with the intel compiler.
See you later.

satoru

[staniba]

Thank you very much for your help.
I think I succeeded in runnning ex_03.py .
All of files created while running ex_03.py are bellow:

CLOCK
DEVICE_zz.nc
ELEC_zz.nc
INPUT_TMP.1806877018
NON_TRIMMED_KP_LIST
ZZ.PHT.AVDOS
ZZ.PHT.AVTRANS_Left-Right
ZZ.PHT.CC
ZZ.PHT.DOS
ZZ.PHT.KP
ZZ.PHT.TRANS_Left-Right
ZZ.PHT.nc
ZZ.fdf
ZZ.out
ex_03.py
fdf-77021.log
zz.gin
zz.gout

satoru

[staniba]

The last time I compiled the zlib, hdf5 and netcdf libraries, I just typed " ./install_netcdf4.bash ".

This time, I edited it slightly.
I just added { export CC=icc, export CXX=icpc, export FC=ifort, export F90=ifort } to the bash script,
and also deleted " -Dgfortran " from CPPFLAGS in " Install NetCDF-Fortran ".

/Docs/build/netcdf/4.4.1.1/bin/nf-config --all

  --cc        -> icc
  --cflags    ->  -I/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include -I/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/include    -I/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/include -I/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include

  --fc        -> ifort
  --fflags    -> -I/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include
  --flibs     -> -L/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -lnetcdff  -lnetcdf -L/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/zlib/1.2.11/lib         -L/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/hdf5/1.8.18/lib        -L/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib -Wl,-rpath=/home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/lib   -lnetcdf -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz
  --has-f90   -> no
  --has-f03   -> yes

  --has-nc2   -> yes
  --has-nc4   -> yes

  --prefix    -> /home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1
  --includedir-> /home/satoru/siesta-4.1-b3/Docs/build/netcdf/4.4.1.1/include
  --version   -> netCDF-Fortran 4.4.4

satoru