format syntax error when reading .TEIG file
Hello everyone,
when running the tutorial case RUN.fdf from https://github.com/zerothi/ts-tbt-sisl-tutorial/tree/main/TB_05, I entered such error:
START OF OUTPUT
tbt: [memory] electrode: 81.797 kB
tbt: [memory] H, S and auxiliary matrices: 265.059 kB
tbt: [memory] sum of electrode and sparse: 346.855 kB
tbt: Initializing data file: siesta.TBT.nc
tbt: Estimated file size of siesta.TBT.nc: 102.381 MB
tbt: [memory] LHS inversion + padding: 2.613 MB
tbt: [memory] RHS inversion + padding: 2.626 MB
tbt: Initial ETA in 3.1 s
tbt: Calculated 6.67 %, ETA in 2.3 s
tbt: Calculated 13.33 %, ETA in 1.7 s
tbt: Calculated 20.00 %, ETA in 1.5 s
tbt: Calculated 27.50 %, ETA in 1.3 s
tbt: Calculated 34.17 %, ETA in 1.2 s
tbt: Calculated 40.83 %, ETA in 1.0 s
tbt: Calculated 48.33 %, ETA in 0.9 s
tbt: Calculated 55.00 %, ETA in 0.8 s
tbt: Calculated 61.67 %, ETA in 0.7 s
tbt: Calculated 69.17 %, ETA in 0.5 s
tbt: Calculated 75.83 %, ETA in 0.4 s
tbt: Calculated 82.50 %, ETA in 0.3 s
tbt: Calculated 90.00 %, ETA in 0.2 s
tbt: Calculated 96.67 %, ETA in 0.1 s
tbt: Calculated 103.33 %, ETA in -0.1 s
tbt: Completed in 1.795 s
Currents (ensure entire Fermi function window):
forrtl: info (58): format syntax error at or near e16.8)
forrtl: severe (62): syntax error in format, unit 13, file /public21/home/sc91436/Workspace/SIESTA/ts-tbt-sisl-tutorial-main/TB_05/siesta.TBT.TEIG_Left-Right
Image PC Routine Line Source
tbtrans 000000000085FDEB Unknown Unknown Unknown
tbtrans 00000000008AED59 Unknown Unknown Unknown
tbtrans 0000000000462A52 m_tbt_savestate_c 2185 m_tbt_save.F90
tbtrans 000000000045EE46 m_tbt_save_mp_sta 1929 m_tbt_save.F90
tbtrans 000000000048C441 m_tbt_trik_mp_tbt 1664 m_tbt_trik.F90
tbtrans 000000000049043F m_tbtrans_mp_tbt_ 329 m_tbtrans.F90
tbtrans 00000000004969F4 MAIN__ 37 tbtrans.F90
tbtrans 00000000004124D2 Unknown Unknown Unknown
libc-2.17.so 00002B3CCFB2E555 __libc_start_main Unknown Unknown
tbtrans 00000000004123E9 Unknown Unknown Unknown
END OF OUTPUT
This error seems to be related with the NetCDF support? here siesta-5.0.0-beta1 was built with netcdf as below:
\# libcurl
export CURLDIR=/public21/home/sc91436/Software/
CC=icc ./configure --without-ssl --prefix=${CURLDIR}
siesta-test-20240406/install
make -j28
make -j28 test
make install
\# zlib
export ZDIR=/public21/home/sc91436/Software/siesta-test-20240406/install
CC=icc ./configure --prefix=${ZDIR}
make check
make install
\# hdf5
export H5DIR=/public21/home/sc91436/Software/siesta-test-20240406/install
CC=mpiicc ./configure --with-zlib=${ZDIR} --prefix=${H5DIR} --enable-hl --enable-parallel
make -j28 check
make install
\# netcdf-c
export NCDIR=/public21/home/sc91436/Software/siesta-test-20240406/install
CC=mpiicc CPPFLAGS="-I${H5DIR}/include -I${ZDIR}/include" LDFLAGS="-L${H5DIR}/lib -L${ZDIR}/lib" ./configure --enable-parallel-tests --prefix=${NCDIR}
make -j28 check
make install
\# netcdf-fortran (supporting SYSTEMLABEL.nc file)
export NFDIR=/public21/home/sc91436/Software/siesta-test-20240406/install
export LD_LIBRARY_PATH=${NCDIR}/lib:${LD_LIBRARY_PATH}
CC=mpiicc FC=mpiifort CPPFLAGS=-I${NCDIR}/include LDFLAGS=-L${NCDIR}/lib LIBS="-L/public21/home/sc91436/Software/siesta-test-20240406/install/lib -L/public21/home/sc91436/Software/siesta-test-20240406/install/lib -L/public21/home/sc91436/Software/siesta-test-20240406/install/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lbz2 -lxml2 -lcurl" ./configure --prefix=${NFDIR}
make -j28 check
make install
\# siesta
FC=ifort CC=icc \
cmake -S. -B_build -DCMAKE_INSTALL_PREFIX='/public21/home/sc91436/Software/siesta-test-20240406/install' \
-DSIESTA_TOOLCHAIN=none -DFortran_FLAGS='-g -traceback -O2 -prec-div -prec-sqrt -fp-model source' \
-DSCALAPACK_LIBRARY_DIR="${MKLROOT}/lib/intel64" \
-DSCALAPACK_LIBRARY="-lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64" \
-DBLAS_LIBRARY_DIR="${MKLROOT}/lib/intel64" \
-DLAPACK_LIBRARY_DIR="${MKLROOT}/lib/intel64" \
-DWITH_MPI=ON \
-DWITH_OPENMP=ON \
-DNetCDF_ROOT=/public21/home/sc91436/Software/siesta-test-20240406/install \
-DWITH_NCDF=ON \
-DWITH_NCDF_PARALLEL=ON \
-DCMAKE_INSTALL_PREFIX='/public21/home/sc91436/Software/siesta-test-20240406/siesta/_stage_root'
cmake --build _build -j 28
cmake --install _build
After siesta configuring, netcdf seems to be detected correctly:
+ \---- NetCDF is ON --------------------------------------------------------------
+ | Feature is turned ON and controlled by 'WITH_NETCDF'
+ | Variables used to enable feature:
+ | - NetCDF_ROOT=/public21/home/sc91436/Software/siesta-test-20240406/install
+ | - NetCDF_INCLUDE_DIRS=/public21/home/sc91436/Software/siesta-test-20240406/install/include
+ | - NetCDF_LIBRARIES=/public21/home/sc91436/Software/siesta-test-20240406/install/lib/libnetcdf.so;/public21/home/sc91436/Software/siesta-test-20240406/install/lib/libnetcdff.so
+ | - NetCDF_PARALLEL=TRUE
+ | - NetCDF_Fortran_LIBRARIES=-L/public21/home/sc91436/Software/siesta-test-20240406/install/lib -lnetcdff -L/public21/home/sc91436/Software/siesta-test-20240406/install/lib -lnetcdf -lm -L/public21/home/sc91436/Software/siesta-test-20240406/install/lib -L/public21/home/sc91436/Software/siesta-test-20240406/install/lib -L/public21/home/sc91436/Software/siesta-test-20240406/install/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lbz2 -lxml2 -lcurl
+ | - NetCDF_Fortran_INCLUDE_DIR=/public21/home/sc91436/Software/siesta-test-20240406/install/include
+ | - NetCDF_Fortran_INCLUDE_DIRS=/public21/home/sc91436/Software/siesta-test-20240406/install/include
+ | Empty or undefined variables (only useful for developers!):
+ | - NetCDF_PATH
+ | - NetCDF_INCLUDE_DIR
+
+
may i have the benefit of your thoughts on this issue?
Edited by Nick R. Papior