Error in installation

[TrupeshKumarPatel]

I tried to follow the readme installation instructions and build a t-route in the system but got the following error.

OS Information

OS Name: Rocky Linux
OS Version: 9.2

Pre-installed Packages

dnf install tar git gcc-c++ gcc gcc-gfortran  make cmake bzip2 python3 python3-devel python3-pip udunits2-devel -y
dnf install libstdc++ libstdc++-devel glibc glibc-devel libgfortran openmpi openmpi-devel -y
dnf install lapack gdal-libs gdal gdal-devel -y
dnf install netcdf netcdf-devel netcdf-fortran netcdf-fortran-devel netcdf-openmpi netcdf-openmpi-devel netcdf-fortran-openmpi netcdf-fortran-openmpi-devel -y 
pip3 install wheel deprecated dask pyarrow geopandas pyproj fiona pandas xarray netcdf4 joblib toolz pyyaml Cython

Installation Steps

git clone --progress --single-branch --branch master http://github.com/NOAA-OWP/t-route.git
cd t-route
./compiler.sh

Compilation Log

using F90=gfortran
using CC=gcc
using NETCDFINC=/usr/include
rm -f *.o *.mod
gfortran -g -c -O2 -fPIC -lgfortran -lgcc -static-libgfortran -static-libgcc -nodefaultlibs varPrecision.f90
gfortran -g -c -O2 -fPIC -lgfortran -lgcc -static-libgfortran -static-libgcc -nodefaultlibs -o mc_single_seg.o MCsingleSegStime_f2py_NOLOOP.f90
gfortran -g -c -O2 -fPIC -lgfortran -lgcc -static-libgfortran -static-libgcc -nodefaultlibs -o pymc_single_seg.o pyMCsingleSegStime_NoLoop.f90
cp *.o ../../../src/troute-routing/troute/routing/fast_reach
rm -f *.o *.mod
gfortran -g -c -O2 -fPIC -fbounds-check -o diffusive.o diffusive.f90
diffusive.f90:1440:20:

 1440 |          pause !test
      |                    1
Warning: Deleted feature: PAUSE statement at (1)
gfortran -g -c -O2 -fPIC -fbounds-check -o pydiffusive.o pydiffusive.f90
cp *.o ../../../src/troute-routing/troute/routing/fast_reach
rm -f *.o
rm -f *.mod
rm -f *.a
rm -f reservoir_tests
rm -f test_main
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_reservoir.o module_reservoir.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_levelpool_properties.o ./Level_Pool/module_levelpool_properties.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_levelpool_state.o ./Level_Pool/module_levelpool_state.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_levelpool.o ./Level_Pool/module_levelpool.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o bind_lp.o bind_lp.f90
ar rc binding_lp.a module_reservoir.o module_levelpool_properties.o module_levelpool_state.o module_levelpool.o bind_lp.o
make: *** No rule to make target 'bind_hybrid.a', needed by 'all'.  Stop.
cp binding_lp.a ../../troute-network/libs;
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_hydro_stop.o module_hydro_stop.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_reservoir_utilities.o module_reservoir_utilities.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_rfc_forecasts_properties.o ./RFC_Forecasts/module_rfc_forecasts_properties.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_rfc_forecasts_state.o ./RFC_Forecasts/module_rfc_forecasts_state.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_reservoir_read_rfc_time_series_data.o module_reservoir_read_rfc_time_series_data.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o module_rfc_forecasts.o ./RFC_Forecasts/module_rfc_forecasts.F
gfortran -g -w -c -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -static-libgfortran -lgfortran -lgcc -static-libgcc  -I/usr/include -I/usr/include/openmpi-x86_64 -I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lnetcdff  -nodefaultlibs -fPIC -L/usr/lib64/openmpi/lib -lnetcdff -c -o bind_rfc.o bind_rfc.f90
ar rc bind_rfc.a module_reservoir.o module_hydro_stop.o module_reservoir_utilities.o module_rfc_forecasts_properties.o module_rfc_forecasts_state.o module_levelpool_properties.o module_levelpool_state.o module_levelpool.o module_reservoir_read_rfc_time_series_data.o module_rfc_forecasts.o bind_rfc.o
cp bind_rfc.a ../../troute-network/libs;
performance hint: troute/network/reservoirs/levelpool/levelpool.pyx:23:5: Exception check on 'run_lp_c' will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on the function to allow an error code to be returned.
performance hint: troute/network/reservoirs/levelpool/levelpool.pyx:26:5: Exception check on 'update_lp_c' will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on the function to allow an error code to be returned.
performance hint: troute/network/reservoirs/rfc/rfc.pyx:22:5: Exception check on 'run_rfc_c' will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on the function to allow an error code to be returned.
Fortran compiler type is: gnu95
Compiling troute/network/reach.pyx because it changed.
Compiling troute/network/reservoirs/levelpool/levelpool.pyx because it changed.
Compiling troute/network/reservoirs/rfc/rfc.pyx because it changed.
Compiling troute/network/musking/mc_reach.pyx because it changed.
[1/4] Cythonizing troute/network/musking/mc_reach.pyx
[2/4] Cythonizing troute/network/reach.pyx
[3/4] Cythonizing troute/network/reservoirs/levelpool/levelpool.pyx
[4/4] Cythonizing troute/network/reservoirs/rfc/rfc.pyx
running build_ext
building 'troute.network.reach' extension
creating build
creating build/temp.linux-x86_64-3.9
creating build/temp.linux-x86_64-3.9/troute
creating build/temp.linux-x86_64-3.9/troute/network
gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Itroute/network -I/usr/local/lib64/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c troute/network/reach.c -o build/temp.linux-x86_64-3.9/troute/network/reach.o -g -g
In file included from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from troute/network/reach.c:1209:
/usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g build/temp.linux-x86_64-3.9/troute/network/reach.o -L/usr/lib64 -lgfortran -o /tmp/t-route/src/troute-network/troute/network/reach.cpython-39-x86_64-linux-gnu.so
building 'troute.network.reservoirs.levelpool.levelpool' extension
creating build/temp.linux-x86_64-3.9/troute/network/reservoirs
creating build/temp.linux-x86_64-3.9/troute/network/reservoirs/levelpool
gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Itroute/network/reservoirs/levelpool -Itroute/network -I/usr/local/lib64/python3.9/site-packages/numpy/core/include -Itroute/network/ -I/usr/include/python3.9 -c troute/network/reservoirs/levelpool/levelpool.c -o build/temp.linux-x86_64-3.9/troute/network/reservoirs/levelpool/levelpool.o -g -g
In file included from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from troute/network/reservoirs/levelpool/levelpool.c:1219:
/usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
troute/network/reservoirs/levelpool/levelpool.c: In function ‘__pyx_f_6troute_7network_10reservoirs_9levelpool_9levelpool_12MC_Levelpool_run’:
troute/network/reservoirs/levelpool/levelpool.c:20111:10: warning: ‘result.f1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
20111 |   return __pyx_r;
      |          ^~~~~~~
troute/network/reservoirs/levelpool/levelpool.c:20111:10: warning: ‘result.f0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g build/temp.linux-x86_64-3.9/troute/network/reservoirs/levelpool/levelpool.o ./libs/binding_lp.a -L/usr/lib64 -lnetcdff -lnetcdf -lgfortran -o /tmp/t-route/src/troute-network/troute/network/reservoirs/levelpool/levelpool.cpython-39-x86_64-linux-gnu.so
building 'troute.network.reservoirs.rfc.rfc' extension
creating build/temp.linux-x86_64-3.9/troute/network/reservoirs/rfc
gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Itroute/network/reservoirs/rfc -Itroute/network -I/usr/local/lib64/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c troute/network/reservoirs/rfc/rfc.c -o build/temp.linux-x86_64-3.9/troute/network/reservoirs/rfc/rfc.o -g -g
In file included from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from troute/network/reservoirs/rfc/rfc.c:1218:
/usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
troute/network/reservoirs/rfc/rfc.c: In function ‘__pyx_f_6troute_7network_10reservoirs_3rfc_3rfc_6MC_RFC_run’:
troute/network/reservoirs/rfc/rfc.c:20385:10: warning: ‘result.f1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
20385 |   return __pyx_r;
      |          ^~~~~~~
troute/network/reservoirs/rfc/rfc.c:20385:10: warning: ‘result.f0’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g build/temp.linux-x86_64-3.9/troute/network/reservoirs/rfc/rfc.o ./libs/bind_rfc.a -L/usr/lib64 -lnetcdff -lnetcdf -lgfortran -o /tmp/t-route/src/troute-network/troute/network/reservoirs/rfc/rfc.cpython-39-x86_64-linux-gnu.so
building 'troute.network.musking.mc_reach' extension
creating build/temp.linux-x86_64-3.9/troute/network/musking
gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Itroute/network/musking -Itroute/network -I/usr/local/lib64/python3.9/site-packages/numpy/core/include -Itroute/network/ -I/usr/include/python3.9 -c troute/network/musking/mc_reach.c -o build/temp.linux-x86_64-3.9/troute/network/musking/mc_reach.o -g -g
In file included from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from troute/network/musking/mc_reach.c:1212:
/usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g build/temp.linux-x86_64-3.9/troute/network/musking/mc_reach.o -L/usr/lib64 -lgfortran -o /tmp/t-route/src/troute-network/troute/network/musking/mc_reach.cpython-39-x86_64-linux-gnu.so
Obtaining file:///tmp/t-route/src/troute-network
Installing collected packages: troute.network
  Running setup.py develop for troute.network
Successfully installed troute.network-0.0.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
warning: troute/routing/fast_reach/mc_reach.pyx:143:60: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
performance hint: troute/routing/fast_reach/mc_reach.pyx:69:5: Exception check on 'compute_reach_kernel' will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on the function to allow an error code to be returned.
performance hint: troute/routing/fast_reach/mc_reach.pyx:139:5: Exception check on 'fill_buffer_column' will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on the function to allow an error code to be returned.
performance hint: troute/routing/fast_reach/mc_reach.pyx:299:36: Index should be typed for more efficient access
performance hint: troute/routing/fast_reach/mc_reach.pyx:104:26: Exception check will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on the function to allow an error code to be returned.
warning: troute/routing/fast_reach/mc_reach.pyx:147:39: Use boundscheck(False) for faster access
warning: troute/routing/fast_reach/mc_reach.pyx:147:33: Use boundscheck(False) for faster access
warning: troute/routing/fast_reach/mc_reach.pyx:147:17: Use boundscheck(False) for faster access
warning: troute/routing/fast_reach/mc_reach.pyx:147:11: Use boundscheck(False) for faster access
performance hint: troute/routing/fast_reach/reach.pyx:7:5: Exception check on 'muskingcunge' will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on the function to allow an error code to be returned.
performance hint: troute/routing/fast_reach/reach.pyx:119:6: Exception check on 'compute_reach' will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.

performance hint: troute/routing/fast_reach/reach.pyx:183:20: Exception check will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
	2. Use an 'int' return type on the function to allow an error code to be returned.
performance hint: troute/routing/fast_reach/simple_da.pyx:21:5: Exception check on 'simple_da' will always require the GIL to be acquired. Possible solutions:
	1. Declare the function as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.

Fortran compiler type is: gnu95
Compiling troute/routing/fast_reach/reach.pyx because it changed.
Compiling troute/routing/fast_reach/mc_reach.pyx because it changed.
Compiling troute/routing/fast_reach/diffusive.pyx because it changed.
Compiling troute/routing/fast_reach/simple_da.pyx because it changed.
[1/4] Cythonizing troute/routing/fast_reach/diffusive.pyx
[2/4] Cythonizing troute/routing/fast_reach/mc_reach.pyx
[3/4] Cythonizing troute/routing/fast_reach/reach.pyx
[4/4] Cythonizing troute/routing/fast_reach/simple_da.pyx
/usr/lib64/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'ext_packages'
  warnings.warn(msg)
running build_ext
building 'troute.routing.fast_reach.reach' extension
creating build
creating build/temp.linux-x86_64-3.9
creating build/temp.linux-x86_64-3.9/troute
creating build/temp.linux-x86_64-3.9/troute/routing
creating build/temp.linux-x86_64-3.9/troute/routing/fast_reach
gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Itroute/routing/fast_reach -I/usr/include/python3.9 -c troute/routing/fast_reach/reach.c -o build/temp.linux-x86_64-3.9/troute/routing/fast_reach/reach.o -O2 -g -g
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g build/temp.linux-x86_64-3.9/troute/routing/fast_reach/reach.o troute/routing/fast_reach/mc_single_seg.o troute/routing/fast_reach/pymc_single_seg.o -L/usr/lib64 -lgfortran -o /tmp/t-route/src/troute-routing/troute/routing/fast_reach/reach.cpython-39-x86_64-linux-gnu.so
building 'troute.routing.fast_reach.mc_reach' extension
gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/tmp/t-route/src/troute-network/troute/network/musking -I/tmp/t-route/src/troute-network/troute/network -I/tmp/t-route/src/troute-network/troute/network/reservoirs/rfc -I/tmp/t-route/src/troute-network/troute/network/reservoirs/levelpool -I/usr/local/lib64/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c troute/routing/fast_reach/mc_reach.c -o build/temp.linux-x86_64-3.9/troute/routing/fast_reach/mc_reach.o -O2 -g -g
In file included from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from troute/routing/fast_reach/mc_reach.c:1216:
/usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
troute/routing/fast_reach/mc_reach.c:21417:13: warning: ‘__pyx_f_6troute_7routing_10fast_reach_8mc_reach_fill_buffer_column’ defined but not used [-Wunused-function]
21417 | static void __pyx_f_6troute_7routing_10fast_reach_8mc_reach_fill_buffer_column(__Pyx_memviewslice __pyx_v_srows, Py_ssize_t const __pyx_v_scol, __Pyx_memviewslice __pyx_v_drows, Py_ssize_t const __pyx_v_dcol, __Pyx_memviewslice __pyx_v_src, __Pyx_memviewslice __pyx_v_out) {
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g build/temp.linux-x86_64-3.9/troute/routing/fast_reach/mc_reach.o -L/usr/lib64 -lgfortran -o /tmp/t-route/src/troute-routing/troute/routing/fast_reach/mc_reach.cpython-39-x86_64-linux-gnu.so
building 'troute.routing.fast_reach.diffusive' extension
gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Itroute/routing/fast_reach -I/usr/local/lib64/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c troute/routing/fast_reach/diffusive.c -o build/temp.linux-x86_64-3.9/troute/routing/fast_reach/diffusive.o -O2 -g -g
In file included from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5,
                 from troute/routing/fast_reach/diffusive.c:1217:
/usr/local/lib64/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
   17 | #warning "Using deprecated NumPy API, disable it with " \
      |  ^~~~~~~
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g build/temp.linux-x86_64-3.9/troute/routing/fast_reach/diffusive.o troute/routing/fast_reach/diffusive.o troute/routing/fast_reach/pydiffusive.o -L/usr/lib64 -lgfortran -o /tmp/t-route/src/troute-routing/troute/routing/fast_reach/diffusive.cpython-39-x86_64-linux-gnu.so
building 'troute.routing.fast_reach.simple_da' extension
gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -march=x86-64-v2 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/local/lib64/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c troute/routing/fast_reach/simple_da.c -o build/temp.linux-x86_64-3.9/troute/routing/fast_reach/simple_da.o -O2 -g -g
gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g build/temp.linux-x86_64-3.9/troute/routing/fast_reach/simple_da.o -L/usr/lib64 -lgfortran -o /tmp/t-route/src/troute-routing/troute/routing/fast_reach/simple_da.cpython-39-x86_64-linux-gnu.so
Obtaining file:///tmp/t-route/src/troute-routing
Installing collected packages: troute.routing
  Running setup.py develop for troute.routing
Successfully installed troute.routing-0.0.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
ERROR: File "setup.py" or "setup.cfg" not found. Directory cannot be installed in editable mode: /tmp/t-route/src/troute-config
(A "pyproject.toml" file was found, but editable mode currently requires a setuptools-based build.)

[jameshalgren]

@TrupeshKumarPatel -- if this is going on the Pantarhei node, it might be from not having a non-root login yet. Or it could be related to a missing setuptools -- do you need to run pip install setuptools?

[TrupeshKumarPatel]

No, I am creating a Docker image using my local machine (MacBook). Also, I double-checked the setuptools; it is installed already. The problem may be because the t-route/src/troute-routing directory does not have a setup.py file.

[hellkite500]

You might try the patch in #643 which also allows you to disable the editable install with an arg to ./compiler.sh

[TrupeshKumarPatel]

The patch #643 worked fine for me. Wondering, why the pull request is not merged yet?

[TrupeshKumarPatel]

Update: The installation worked fine when I applied the patch by downloading files from #643 and replacing them. But now, since the pull request is merged, I tried installation without replacing them, and it shows the same error as before.

I checked the difference between compile.sh in #643 and complile.sh in master branch, and seems like following code is deleted in #643 but not in master.

build_config=true

...

if [[ "$build_config" == true ]]; then
  #updates troute package with the execution script
  cd $REPOROOT/src/troute-config
  pip install -e . || exit
fi

In short, I am getting errors in the installation during build_config=true, please guide me to resolve it.

[JoshCu]

I have a wip dockerfile for installing troute on rocky 9.2, created as part of the debugging of the ngen image segfault issue

Dockerfile.troute

It's rough for now while I'm looking into the segfault, but I can clean it up and make a PR if it's something that would be useful to have in this repo.
The dockerfile also has the issue running the LowerColorado test cases, I'll post an update to that issue if I figure it out.