Siesta

tbtrans output IV information

Asked by Jianjun Mao

Dear Experts,

These days, I installed siesta4.1-b4 and tried to calculated the IV curve. However, after the calculation, I could not find IV information in the output of tbtrans. I tried several examples.
Here is the end output of tbtrans:

tbtrans: Electrode memory: 6.633 MB
tbtrans: Sparse Hamiltonian and overlap memory: 7.017 MB
tbtrans: Sum of electrode and sparse memory: 13.650 MB

tbtrans: LHS Green function size / memory: 1259712 / 19.22 MB
tbtrans: RHS Green function size / memory: 209952 / 3.20 MB
tbt: Initial ETA in 138.109 s
tbt: Calculated 5.000 %, ETA in 138.109 s
tbt: Calculated 10.000 %, ETA in 131.578 s
tbt: Calculated 15.000 %, ETA in 124.642 s
tbt: Calculated 20.000 %, ETA in 117.630 s
tbt: Calculated 25.000 %, ETA in 110.425 s
tbt: Calculated 30.000 %, ETA in 103.183 s
tbt: Calculated 35.000 %, ETA in 95.833 s
tbt: Calculated 40.000 %, ETA in 86.942 s
tbt: Calculated 45.000 %, ETA in 73.828 s
tbt: Calculated 50.000 %, ETA in 62.827 s
tbt: Calculated 55.000 %, ETA in 53.389 s
tbt: Calculated 60.000 %, ETA in 45.384 s
tbt: Calculated 65.000 %, ETA in 40.370 s
tbt: Calculated 70.000 %, ETA in 35.389 s
tbt: Calculated 75.000 %, ETA in 30.077 s
tbt: Calculated 80.000 %, ETA in 24.463 s
tbt: Calculated 85.000 %, ETA in 18.626 s
tbt: Calculated 90.000 %, ETA in 12.624 s
tbt: Calculated 95.000 %, ETA in 6.406 s
tbt: Completed in 129.849 s

             Section Calls Walltime %
 global_section 1 130.860 100.00
  tbtrans 1 130.860 100.00
   tri-init 1 0.036 0.03
    tri-init-elec 1 0.015 0.01
     TS-rgn2tri 1 0.001 0.00
    TS-rgn2tri 1 0.001 0.00
   TBT 1 130.254 99.54
    read-GS 20 118.735 90.73
    SE-dwn 20 1.892 1.45
     ts_expand 40 0.018 0.01
    Gf-prep 20 1.023 0.78
     V_TM_Pinv 20 0.981 0.75
    DOS-Gf-A-T 20 3.371 2.58
>> End of run: 21-FEB-2019 22:40:35

What should I do? Many thanks!

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Solved by:
Nick Papior
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Revision history for this message
Jianjun Mao (jjmao) said : 		#1

same problem in "TBTrans output and current vs voltage calculation".......I just see this.

Revision history for this message
Jianjun Mao (jjmao) said : 		#2

.SUFFIXES:
.SUFFIXES: .f .F .o .c .a .f90 .F90

SIESTA_ARCH = Intel2018@HPC2015

CC = icc
FPP = $(FC) -E -P
FC = mpiifort
MPI_INTERFACE = libmpi_f90.a
MPI_INCLUDE = /share1/intel/ics2018/impi/2018.4.274/include64
FC_SERIAL = ifort

FFLAGS = -O2 -fPIC -fp-model source

AR = ar
RANLIB = ranlib

SYS = nag

SP_KIND = 4
DP_KIND = 8
KINDS = $(SP_KIND) $(DP_KIND)

LDFLAGS =

COMP_LIBS = libsiestaLAPACK.a libsiestaBLAS.a

FPPFLAGS = $(DEFS_PREFIX)-DFC_HAVE_ABORT -DMPI

BLAS_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_intel_lp64
LAPACK_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_lapack95_lp64 -lmkl_sequential -lmkl_core
BLACS_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_blacs_intelmpi_lp64
SCALAPACK_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_scalapack_lp64
LIBS = $(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)

# Dependency rules ---------

FFLAGS_DEBUG = -g -O1 -fp-model source # your appropriate flags here...

# The atom.f code is very vulnerable. Particularly the Intel compiler
# will make an erroneous compilation of atom.f with high optimization
# levels.
atom.o: atom.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
state_analysis.o: state_analysis.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<

.c.o:
        $(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
.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) $<

Revision history for this message
Jianjun Mao (jjmao) said : 		#3

Dear Nick,

I have modified the arch.make just as following, but it is still installed with error

:
mpiifort -c -O2 -fPIC -fp-model source -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/netcdf/4.6.1/include -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/flook/0.7.0/include -DCDF -DNCDF -DNCDF_4 -DSIESTA__FLOOK -DFC_HAVE_ABORT -DMPI -DSIESTA__DIAG_2STAGE /home/jjmao/soft/siesta-4.1-b4/Src/find_kgrid.F
mpiifort -c -O2 -fPIC -fp-model source -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/netcdf/4.6.1/include -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/flook/0.7.0/include -DCDF -DNCDF -DNCDF_4 -DSIESTA__FLOOK -DFC_HAVE_ABORT -DMPI -DSIESTA__DIAG_2STAGE /home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90
/home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90(11): error #7013: This module file was not generated by any release of this compiler. [FLOOK]
  use flook, only : luaState
------^
/home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90(230): error #6406: Conflicting attributes or multiple declaration of name. [LUASTATE]
  type(luaState) :: LUA
-------^
/home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90(11): error #6580: Name in only-list does not exist or is not accessible. [LUASTATE]
  use flook, only : luaState
--------------------^
compilation aborted for /home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90 (code 1)

###########################
.SUFFIXES:
.SUFFIXES: .f .F .o .c .a .f90 .F90

SIESTA_ARCH = Intel2018@HPC2015

CC = icc
FPP = $(FC) -E -P
FC = mpiifort
MPI_INTERFACE = libmpi_f90.a
MPI_INCLUDE = /share1/intel/ics2018/impi/2018.4.274/include64
FC_SERIAL = ifort

FFLAGS = -O2 -fPIC -fp-model source

AR = ar
RANLIB = ranlib

SYS = nag

SP_KIND = 4
DP_KIND = 8
KINDS = $(SP_KIND) $(DP_KIND)

COMP_LIBS = libsiestaLAPACK.a libsiestaBLAS.a

INCFLAGS += -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/netcdf/4.6.1/include
LDFLAGS += -L/home/jjmao/soft/siesta-4.1-b4/Docs/build/zlib/1.2.11/lib -Wl,-rpath=/home/jjmao/soft/siesta-4.1-b4/Docs/build/zlib/1.2.11/lib
LDFLAGS += -L/home/jjmao/soft/siesta-4.1-b4/Docs/build/hdf5/1.8.21/lib -Wl,-rpath=/home/jjmao/soft/siesta-4.1-b4/Docs/build/hdf5/1.8.21/lib
LDFLAGS += -L/home/jjmao/soft/siesta-4.1-b4/Docs/build/netcdf/4.6.1/lib -Wl,-rpath=/home/jjmao/soft/siesta-4.1-b4/Docs/build/netcdf/4.6.1/lib
LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
COMP_LIBS += libncdf.a libfdict.a
FPPFLAGS += -DCDF -DNCDF -DNCDF_4

NCFLAGS += -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/flook/0.7.0/include
LDFLAGS += -L/home/jjmao/soft/siesta-4.1-b4/Docs/build/flook/0.7.0/lib -Wl,-rpath=/home/jjmao/soft/siesta-4.1-b4/Docs/build/flook/0.7.0/lib
LIBS += -lflookall -ldl
COMP_LIBS += libfdict.a
FPPFLAGS += -DSIESTA__FLOOK

FPPFLAGS += $(DEFS_PREFIX)-DFC_HAVE_ABORT -DMPI

BLAS_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_intel_lp64
LAPACK_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_lapack95_lp64 -lmkl_sequential -lmkl_core
BLACS_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_blacs_intelmpi_lp64
SCALAPACK_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_scalapack_lp64

LIBS += $(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)

# Dependency rules ---------

FFLAGS_DEBUG = -g -O1 -fp-model source # your appropriate flags here...

# The atom.f code is very vulnerable. Particularly the Intel compiler
# will make an erroneous compilation of atom.f with high optimization
# levels.
atom.o: atom.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
state_analysis.o: state_analysis.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<

.c.o:
        $(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
.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) $<

Revision history for this message
Nick Papior (nickpapior) said : 		#4

In https://answers.launchpad.net/siesta/+question/667589 it is clearly stated what is wrong!

You need NetCDF-4 support. Please correct your FPPFLAGS (and linker line) to add NetCDF-4 support.

Secondly, do NOT mix COMP_LIBS = libsiestaLAPACK.a libsiestaBLAS.a and MKL libraries.

Revision history for this message
Jianjun Mao (jjmao) said : 		#5

Many thanks Nick, and I have modified the arch.make. I found that I can install it successfully if I don't include the part of flook. Of course, the output of Tbtrans have IV information. But if I include the flook part, there is also this error:

......................................
......................................
(only show the end output)
 e -DCDF -DNCDF -DNCDF_4 -DSIESTA__FLOOK -DFC_HAVE_ABORT -DMPI /home/jjmao/soft/siesta-4.1-b4/Src/find_kgrid.F
mpiifort -c -O2 -fPIC -fp-model source -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/netcdf/4.6.1/include -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/flook/0.7.0/include -DCDF -DNCDF -DNCDF_4 -DSIESTA__FLOOK -DFC_HAVE_ABORT -DMPI /home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90
/home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90(11): error #7013: This module file was not generated by any release of this compiler. [FLOOK]
  use flook, only : luaState
------^
/home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90(230): error #6406: Conflicting attributes or multiple declaration of name. [LUASTATE]
  type(luaState) :: LUA
-------^
/home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90(11): error #6580: Name in only-list does not exist or is not accessible. [LUASTATE]
  use flook, only : luaState
--------------------^
compilation aborted for /home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90 (code 1)
make: *** [siesta_options.o] Error 1

#######################

.SUFFIXES:
.SUFFIXES: .f .F .o .c .a .f90 .F90

SIESTA_ARCH = Intel2018@HPC2015

CC = icc
FPP = $(FC) -E -P
FC = mpiifort
MPI_INTERFACE = libmpi_f90.a
MPI_INCLUDE = /share1/intel/ics2018/impi/2018.4.274/include64
FC_SERIAL = ifort

FFLAGS = -O2 -fPIC -fp-model source

AR = ar
RANLIB = ranlib

SYS = nag

SP_KIND = 4
DP_KIND = 8
KINDS = $(SP_KIND) $(DP_KIND)

INCFLAGS += -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/netcdf/4.6.1/include
LDFLAGS += -L/home/jjmao/soft/siesta-4.1-b4/Docs/build/zlib/1.2.11/lib -Wl,-rpath=/home/jjmao/soft/siesta-4.1-b4/Docs/build/zlib/1.2.11/lib
LDFLAGS += -L/home/jjmao/soft/siesta-4.1-b4/Docs/build/hdf5/1.8.21/lib -Wl,-rpath=/home/jjmao/soft/siesta-4.1-b4/Docs/build/hdf5/1.8.21/lib
LDFLAGS += -L/home/jjmao/soft/siesta-4.1-b4/Docs/build/netcdf/4.6.1/lib -Wl,-rpath=/home/jjmao/soft/siesta-4.1-b4/Docs/build/netcdf/4.6.1/lib
LIBS += -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
COMP_LIBS += libncdf.a libfdict.a
FPPFLAGS += -DCDF -DNCDF -DNCDF_4

INCFLAGS += -I/home/jjmao/soft/siesta-4.1-b4/Docs/build/flook/0.7.0/include
LDFLAGS += -L/home/jjmao/soft/siesta-4.1-b4/Docs/build/flook/0.7.0/lib -Wl,-rpath=/home/jjmao/soft/siesta-4.1-b4/Docs/build/flook/0.7.0/lib
LIBS += -lflookall -ldl
COMP_LIBS += libfdict.a
FPPFLAGS += -DSIESTA__FLOOK

FPPFLAGS += $(DEFS_PREFIX)-DFC_HAVE_ABORT -DMPI

#BLAS_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_blas95_lp64 -lmkl_intel_lp64
#LAPACK_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_lapack95_lp64 -lmkl_sequential -lmkl_core
#BLACS_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_blacs_intelmpi_lp64
#SCALAPACK_LIBS=-L/share1/intel/ics2018/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64 -lmkl_scalapack_lp64

#COMP_LIBS += libsiestaLAPACK.a libsiestaBLAS.a

#LIBS += $(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS)

# Dependency rules ---------

FFLAGS_DEBUG = -g -O1 -fp-model source # your appropriate flags here...

# The atom.f code is very vulnerable. Particularly the Intel compiler
# will make an erroneous compilation of atom.f with high optimization
# levels.
atom.o: atom.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
state_analysis.o: state_analysis.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<

.c.o:
        $(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
.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) $<

Why is it failed? Any help will be greatly appreciated, thank you very much. Nick.

Revision history for this message
Best Nick Papior (nickpapior) said : 		#6

/home/jjmao/soft/siesta-4.1-b4/Src/siesta_options.F90(11): error #7013: This module file was not generated by any release of this compiler. [FLOOK]

You haven't used the same compiler for flook.

Revision history for this message
Jianjun Mao (jjmao) said : 		#7

Thanks Nick Papior, that solved my question.