If that is the exact installation you've been using, then I perhaps see the problem.

You need to put Fortran in your installation request line.

CC=icc CXX=icpc Fortran=ifort cmake -DSKYNET_MATRIX_SOLVER=mkl -DCMAKE_INSTALL_PREFIX=~/skynet/install ..

Hope that helps :-)

Collette Curry

thank you.

i replace Fortan by Fortran, but it still does not work.

i have also try

CC=gcc CXX=g++ Fortran=gfortran cmake -DENABLE_MOVIE=no -DSKYNET_MATRIX_SOLVER=pardiso -DCMAKE_INSTALL_PREFIX=~/skynet/install ..

not work, too.

Have you installed all dependency files?

These need to be in place before running successfully.

If they are all in place.

Try changing /skynet/install to /skynet_install

Also, Skynet is not supported on Windows, what are you using it on?

Full compilation script is normally as follows

git clone [email protected]:jlippuner/skynet.git cd skynet mkdir build && cd build cmake -DSKYNET_MATRIX_SOLVER=pardiso -DCMAKE_INSTALL_PREFIX=$HOME/skynet_install .. make -j install make test

Collette Curry

good..thank you..

after cmake command:

[jcpei@ln3%tianhe build]$ CC=gcc CXX=g++ Fortan=gfortran cmake -DENABLE_MOVIE=no -DSKYNET_MATRIX_SOLVER=pardiso -DCMAKE_INSTALL_PREFIX=~/skynet/install ..

-- The CXX compiler identification is GNU 7.5.0

-- The C compiler identification is GNU 7.5.0

-- The Fortran compiler identification is GNU 7.5.0

-- Check for working CXX compiler: /vol6/software/gcc-7.5.0/bin/g++

-- Check for working CXX compiler: /vol6/software/gcc-7.5.0/bin/g++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Check for working C compiler: /vol6/software/gcc-7.5.0/bin/gcc

-- Check for working C compiler: /vol6/software/gcc-7.5.0/bin/gcc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Detecting C compile features

-- Detecting C compile features - done

-- Check for working Fortran compiler: /vol6/software/gcc-7.5.0/bin/gfortran

-- Check for working Fortran compiler: /vol6/software/gcc-7.5.0/bin/gfortran -- works

-- Detecting Fortran compiler ABI info

-- Detecting Fortran compiler ABI info - done

-- Checking whether /vol6/software/gcc-7.5.0/bin/gfortran supports Fortran 90

-- Checking whether /vol6/software/gcc-7.5.0/bin/gfortran supports Fortran 90 -- yes

-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration

-- Found HDF5: /vol6/software/io_tools/hdf5/serial/1.10.4-gcc49/lib/libhdf5_cpp.so;/vol6/software/io_tools/hdf5/serial/1.10.4-gcc49/lib/libhdf5.so;/usr/lib64/librt.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.4") found components: CXX

-- Found GSL: /vol6/software/gsl-1.16/lib/libgsl.so;/vol6/software/gsl-1.16/lib/libgslcblas.so

-- Boost version: 1.61.0

-- Found the following Boost libraries:

-- system

-- filesystem

-- serialization

-- Could NOT find SWIG: Found unsuitable version "1.3.40", but required is at least "3" (found /usr/bin/swig)

-- Found PythonLibs: /usr/lib64/libpython2.6.so (found suitable version "2.6.6", minimum required is "2.6")

-- Found Pardiso : /vol6/home/jcpei/usr/lib/libpardiso600-GNU720-X86-64.so;/vol6/home/jcpei/usr/lib/libpardiso600-GNU720-X86-64.so

-- Looking for Fortran sgemm

-- Looking for Fortran sgemm - found

-- Looking for pthread.h

-- Looking for pthread.h - found

-- Looking for pthread_create

-- Looking for pthread_create - not found

-- Looking for pthread_create in pthreads

-- Looking for pthread_create in pthreads - not found

-- Looking for pthread_create in pthread

-- Looking for pthread_create in pthread - found

-- Found Threads: TRUE

-- A library with BLAS API found.

-- Looking for Fortran cheev

-- Looking for Fortran cheev - found

-- A library with LAPACK API found.

-- A library with BLAS API found.

-- Try OpenMP C flag = [-fopenmp]

-- Performing Test OpenMP_FLAG_DETECTED

-- Performing Test OpenMP_FLAG_DETECTED - Success

-- Try OpenMP CXX flag = [-fopenmp]

-- Performing Test OpenMP_FLAG_DETECTED

-- Performing Test OpenMP_FLAG_DETECTED - Success

-- Try OpenMP Fortran flag = [-fopenmp]

-- Performing Test OpenMP_FLAG_DETECTED

-- Performing Test OpenMP_FLAG_DETECTED - Success

-- Found OpenMP: -fopenmp

--

--

-- Configuration options:

--

-- CMAKE_CXX_FLAGS: -Wall -Wextra -std=c++11 -g -fPIC -DSKYNET_USE_PARDISO

-- CMAKE_CXX_LINK_FLAGS:

-- CMAKE_CXX_FLAGS_DEBUG: -g -DDEBUG

-- CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG

-- CMAKE_Fortran_FLAGS: -g -fPIC

-- CMAKE_Fortran_LINK_FLAGS:

-- CMAKE_Fortran_FLAGS_DEBUG: -g

-- CMAKE_Fortran_FLAGS_RELEASE: -O3 -DNDEBUG -O3

--

--

-- Matrix solver: pardiso (sparse)

-- SWIG: disabled

-- making movies: disabled

--

--

-- Configuring done

-- Generating done

-- Build files have been written to: /vol6/home/jcpei/chaiqz/Skynet/build

It seems to be installed all dependency files...

But the follows,

-- Looking for pthread_create

-- Looking for pthread_create - not found

-- Looking for pthread_create in pthreads

-- Looking for pthread_create in pthreads - not found

may be the fault?

the "make -j install"

it goes to 86%

/vol6/home/jcpei/usr/lib/libpardiso600-GNU720-X86-64.so: undefined reference to `memcpy@GLIBC_2.14'

collect2: error: ld returned 1 exit status

make[2]: *** [tests/HelmholtzEOS/HelmholtzEOSTest] Error 1

make[1]: *** [tests/HelmholtzEOS/CMakeFiles/HelmholtzEOSTest.dir/all] Error 2

/vol6/home/jcpei/usr/lib/libpardiso600-GNU720-X86-64.so: undefined reference to `memcpy@GLIBC_2.14'

collect2: error: ld returned 1 exit status

make[2]: *** [tests/MatrixSolver/MatrixSolverTest] Error 1

make[1]: *** [tests/MatrixSolver/CMakeFiles/MatrixSolverTest.dir/all] Error 2

I add a flag "-lpthread" after CXX in , it still do not work...

please...

What version of cmake are you running? These errors can be reported in some versions of it. The latest stable version is 3.18.2

Also -- Could NOT find SWIG: Found unsuitable version "1.3.40", but required is at least "3" (found /usr/bin/swig)

update SWIG so it is enabled. Available here http://www.swig.org

SWIG is needed to run the C/C++ code

Possibly update Boost too https://www.boost.org/users/history/version_1_74_0.html

Hopefully that will sort the problem for you

I am inspired by this discussion for the following considerations. Well, what was the inspiration for giving this application the name Skynet? I am asking because that was the name of the main, centralized, integrated Internet system integrating all devices connected to the Internet in one cloud computing network, including all Internet of Things devices in the context of the plot of the saga of science fiction movies entitled "Terminator". Is there an analogy on this?

Best regards,

Dariusz Prokopowicz

Dariusz Prokopowicz

haha...

SkyNet is a general-purpose nuclear reaction network for nuclear astrophysics applications.

SkyNet is available at https://bitbucket.org/jlippuner/skynet

i think this name is based on its application.

it could calculate the nucleosynthesis process, which deals with thousands of nuclear species and tens of thousands reactions.

i agree with this name fully.

Collette Curry

Thank you very much....

i tried cmake 3.18, 3.16, 3.14, then i found only cmake 3.12 could work...

Under your suggestion:

cqz@tns:~/Downloads/skynet/build$ CC=gcc CXX=g++ Fortan=gfortran cmake -DSKYNET_MATRIX_SOLVER=pardiso -DPYTHON_INCLUDE_DIR=/lib/python/include/python3.7m -DPYTHON_LIBRARY=/lib/python/lib/libpython3.7m.a -DCMAKE_INSTALL_PREFIX=~/skynet/install ..

-- The CXX compiler identification is GNU 9.3.0

-- The C compiler identification is GNU 9.3.0

-- The Fortran compiler identification is GNU 9.3.0

-- Check for working CXX compiler: /usr/bin/g++

-- Check for working CXX compiler: /usr/bin/g++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Check for working C compiler: /usr/bin/gcc

-- Check for working C compiler: /usr/bin/gcc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Detecting C compile features

-- Detecting C compile features - done

-- Check for working Fortran compiler: /usr/bin/gfortran

-- Check for working Fortran compiler: /usr/bin/gfortran -- works

-- Detecting Fortran compiler ABI info

-- Detecting Fortran compiler ABI info - done

-- Checking whether /usr/bin/gfortran supports Fortran 90

-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes

-- Found HDF5: hdf5::hdf5_cpp-shared (found version "1.10.6") found components: CXX

-- Found GSL: /home/cqz/lib/gsl/lib/libgsl.so;/home/cqz/lib/gsl/lib/libgslcblas.so

-- Boost found.

-- Found Boost components:

system;filesystem;serialization

-- Found SWIG: /home/cqz/lib/swig/bin/swig (found suitable version "4.0.2", minimum required is "3")

-- Found PythonLibs: /lib/python/lib/libpython3.7m.a (found suitable version "3.7.9", minimum required is "2.6")

-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")

-- Checking for module 'freetype2'

-- Found freetype2, version 23.1.17

-- Found Freetype : /usr/lib/x86_64-linux-gnu/libfreetype.so

-- Checking for module 'cairo'

-- Found cairo, version 1.16.0

-- Found Cairo : /usr/lib/x86_64-linux-gnu/libcairo.so;/usr/lib/x86_64-linux-gnu/libfreetype.so

-- Checking for module 'sigc++-2.0'

-- Found sigc++-2.0, version 2.10.2

-- Found SigC++ : /usr/lib/x86_64-linux-gnu/libsigc-2.0.so

-- Checking for module 'cairomm-1.0'

-- Found cairomm-1.0, version 1.12.2

-- Found Cairomm : /usr/lib/x86_64-linux-gnu/libcairomm-1.0.so;/usr/lib/x86_64-linux-gnu/libcairo.so;/usr/lib/x86_64-linux-gnu/libfreetype.so

-- Found Pardiso : /home/cqz/lib/libpardiso600-GNU720-X86-64.so;/home/cqz/lib/libpardiso600-GNU720-X86-64.so

-- Looking for Fortran sgemm

-- Looking for Fortran sgemm - found

-- Looking for pthread.h

-- Looking for pthread.h - found

-- Looking for pthread_create

-- Looking for pthread_create - not found

-- Looking for pthread_create in pthreads

-- Looking for pthread_create in pthreads - not found

-- Looking for pthread_create in pthread

-- Looking for pthread_create in pthread - found

-- Found Threads: TRUE

-- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so

-- Looking for Fortran cheev

-- Looking for Fortran cheev - found

-- A library with LAPACK API found.

-- Found OpenMP_C: -fopenmp (found version "4.5")

-- Found OpenMP_CXX: -fopenmp (found version "4.5")

-- Found OpenMP_Fortran: -fopenmp (found version "4.5")

-- Found OpenMP: TRUE (found version "4.5")

--

--

-- Configuration options:

--

-- CMAKE_CXX_FLAGS: -Wall -Wextra -std=c++11 -g -fPIC -DSKYNET_USE_MOVIE -DSKYNET_USE_PARDISO

-- CMAKE_CXX_LINK_FLAGS:

-- CMAKE_CXX_FLAGS_DEBUG: -g -DDEBUG

-- CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG

-- CMAKE_Fortran_FLAGS: -g -fPIC

-- CMAKE_Fortran_LINK_FLAGS:

-- CMAKE_Fortran_FLAGS_DEBUG: -g

-- CMAKE_Fortran_FLAGS_RELEASE: -O3 -DNDEBUG -O3

--

--

-- Matrix solver: pardiso (sparse)

-- SWIG: enabled

-- making movies: enabled

--

--

-- Configuring done

-- Generating done

-- Build files have been written to: /home/cqz/Downloads/skynet/build

Then

vi CMakeFiles/CMakeError.log

make[1]: Entering directory '/home/cqz/Downloads/skynet/build/CMakeFiles/CMakeTmp'

Building C object CMakeFiles/cmTC_f16d8.dir/CheckSymbolExists.c.o

/usr/bin/gcc -o CMakeFiles/cmTC_f16d8.dir/CheckSymbolExists.c.o -c /home/cqz/Downloads/skynet/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c

Linking C executable cmTC_f16d8

/home/cqz/Downloads/cmake-3.12.0-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_f16d8.dir/link.txt --verbose=1

/usr/bin/gcc -rdynamic CMakeFiles/cmTC_f16d8.dir/CheckSymbolExists.c.o -o cmTC_f16d8

/usr/bin/ld: CMakeFiles/cmTC_f16d8.dir/CheckSymbolExists.c.o: in function `main':

CheckSymbolExists.c:(.text+0x1f): undefined reference to `pthread_create'

collect2: error: ld returned 1 exit status

make[1]: *** [CMakeFiles/cmTC_f16d8.dir/build.make:87: cmTC_f16d8] Error 1

make[1]: Leaving directory '/home/cqz/Downloads/skynet/build/CMakeFiles/CMakeTmp'

make: *** [Makefile:121: cmTC_f16d8/fast] Error 2

File /home/cqz/Downloads/skynet/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:

/* */

#include

int main(int argc, char** argv)

{

(void)argv;

#ifndef pthread_create

return ((int*)(&pthread_create))[argc];

#else

(void)argc;

return 0;

#endif

}

Determining if the function pthread_create exists in the pthreads failed with the following output:

Change Dir: /home/cqz/Downloads/skynet/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_92f68/fast"

/usr/bin/make -f CMakeFiles/cmTC_92f68.dir/build.make CMakeFiles/cmTC_92f68.dir/build

make[1]: Entering directory '/home/cqz/Downloads/skynet/build/CMakeFiles/CMakeTmp'

Building C object CMakeFiles/cmTC_92f68.dir/CheckFunctionExists.c.o

/usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_92f68.dir/CheckFunctionExists.c.o -c /home/cqz/Downloads/cmake-3.12.0-Linux-x86_64/share/cmake-3.12/Modules/CheckFunctionExists.c

Linking C executable cmTC_92f68

/home/cqz/Downloads/cmake-3.12.0-Linux-x86_64/bin/cmake -E cmake_link_script CMakeFiles/cmTC_92f68.dir/link.txt --verbose=1

/usr/bin/gcc -DCHECK_FUNCTION_EXISTS=pthread_create -rdynamic CMakeFiles/cmTC_92f68.dir/CheckFunctionExists.c.o -o cmTC_92f68 -lpthreads

/usr/bin/ld: cannot find -lpthreads

collect2: error: ld returned 1 exit status

make[1]: *** [CMakeFiles/cmTC_92f68.dir/build.make:87: cmTC_92f68] Error 1

make[1]: Leaving directory '/home/cqz/Downloads/skynet/build/CMakeFiles/CMakeTmp'

make: *** [Makefile:121: cmTC_92f68/fast] Error 2

when make -j install,

cqz@tns:~/Downloads/skynet/build$ make -j install

Scanning dependencies of target MakeBuildInfo

Scanning dependencies of target CheckResults

Scanning dependencies of target SkyNet_swig_compilation

[ 1%] Building CXX object tests/FortranOperatorSplitting/CMakeFiles/CheckResults.dir/CheckResults.cpp.o

[ 1%] Built target MakeBuildInfo

Scanning dependencies of target src

[ 2%] Swig source

[ 3%] Building CXX object src/CMakeFiles/src.dir/BuildInfo.cpp.o

[ 3%] Built target src

Scanning dependencies of target tinyxml2

Scanning dependencies of target DensityProfiles

Scanning dependencies of target EquationsOfState

Scanning dependencies of target HelmholtzEOS

[ 3%] Building CXX object src/DensityProfiles/CMakeFiles/DensityProfiles.dir/ConstantFunction.cpp.o

[ 4%] Building CXX object src/tinyxml2/CMakeFiles/tinyxml2.dir/tinyxml2.cpp.o

Scanning dependencies of target FortranInterface

Scanning dependencies of target MovieMaker

[ 5%] Building CXX object src/DensityProfiles/CMakeFiles/DensityProfiles.dir/ExpTMinus3.cpp.o

[ 5%] Building Fortran object src/EquationsOfState/Helmholtz/CMakeFiles/HelmholtzEOS.dir/helmholtz.f90.o

Scanning dependencies of target MatrixSolver

[ 6%] Building Fortran object src/EquationsOfState/Helmholtz/CMakeFiles/HelmholtzEOS.dir/helmholtz_addition.f90.o

[ 6%] Building CXX object src/EquationsOfState/CMakeFiles/EquationsOfState.dir/HelmholtzEOS.cpp.o

[ 7%] Building CXX object src/DensityProfiles/CMakeFiles/DensityProfiles.dir/PowerLawContinuation.cpp.o

Scanning dependencies of target Network

[ 12%] Building Fortran object src/FortranInterface/CMakeFiles/FortranInterface.dir/SkyNet.f90.o

Scanning dependencies of target NuclearData

[ 8%] Building CXX object src/EquationsOfState/CMakeFiles/EquationsOfState.dir/NeutrinoDistributionFermiDirac.cpp.o

[ 9%] Building CXX object src/DensityProfiles/CMakeFiles/DensityProfiles.dir/Homologous.cpp.o

[ 10%] Building CXX object src/EquationsOfState/CMakeFiles/EquationsOfState.dir/NeutrinoHistoryBlackBody.cpp.o

[ 11%] Building CXX object src/EquationsOfState/CMakeFiles/EquationsOfState.dir/NeutrinoHistoryFermiDirac.cpp.o

Scanning dependencies of target Reactions

[ 13%] Building CXX object src/EquationsOfState/CMakeFiles/EquationsOfState.dir/SkyNetScreening.cpp.o

Scanning dependencies of target Utilities

Scanning dependencies of target Utilities_Interpolators

[ 14%] Building CXX object src/MovieMaker/CMakeFiles/MovieMaker.dir/ColorScale.cpp.o

[ 14%] Building CXX object src/MovieMaker/CMakeFiles/MovieMaker.dir/Scale.cpp.o

[ 14%] Building CXX object src/FortranInterface/CMakeFiles/FortranInterface.dir/FortranInterface.cpp.o

[ 15%] Building CXX object src/Utilities/CMakeFiles/Utilities.dir/BisectionMethod.cpp.o

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[ 17%] Building CXX object src/NuclearData/CMakeFiles/NuclearData.dir/Nuclide.cpp.o

[ 17%] Building CXX object src/Utilities/CMakeFiles/Utilities.dir/CodeError.cpp.o

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[ 35%] Building CXX object src/Reactions/CMakeFiles/Reactions.dir/REACLIB.cpp.o

[ 35%] Building CXX object src/MatrixSolver/CMakeFiles/MatrixSolver.dir/MatrixSolver_mkl.cpp.o

[ 37%] Building CXX object src/Network/CMakeFiles/Network.dir/NetworkOptions.cpp.o

[ 38%] Building CXX object src/MatrixSolver/CMakeFiles/MatrixSolver.dir/MatrixSolver_trilinos.cpp.o

[ 39%] Building CXX object src/Reactions/CMakeFiles/Reactions.dir/REACLIBEntry.cpp.o

[ 40%] Building CXX object src/Network/CMakeFiles/Network.dir/NetworkOutputDataset.cpp.o

[ 41%] Building CXX object src/Network/CMakeFiles/Network.dir/NetworkOutput.cpp.o

[ 42%] Building CXX object src/Reactions/CMakeFiles/Reactions.dir/REACLIBReactionLibrary.cpp.o

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[ 43%] Building CXX object src/Utilities/CMakeFiles/Utilities.dir/Profiler.cpp.o

[ 43%] Building CXX object src/Network/CMakeFiles/Network.dir/NSE.cpp.o

[ 44%] Building CXX object src/Utilities/CMakeFiles/Utilities.dir/OutputMuter.cpp.o

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[ 52%] Building CXX object src/Reactions/CMakeFiles/Reactions.dir/ReactionPostProcess.cpp.o

/home/cqz/Downloads/skynet/src/Utilities/OutputMuter.cpp: In static member function ‘static void OutputMuter::Mute()’:

/home/cqz/Downloads/skynet/src/Utilities/OutputMuter.cpp:20:12: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]

20 | freopen("/dev/null", "w", stdout);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/EquationsOfState/Screening.hpp:15,

from /home/cqz/Downloads/skynet/src/EquationsOfState/SkyNetScreening.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/SkyNetScreening.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/SkyNetScreening.cpp:37:57: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

[ 52%] Built target DensityProfiles

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp: In instantiation of ‘void NetworkOutputDataset::InitForWriting(H5::H5File*, hsize_t, hsize_t, bool) [with T = double; hsize_t = long long unsigned int]’:

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:287:16: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:101:14: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy]

101 | mH5Dataset = pH5File->createDataSet(mName, mDataType, dataSpace, props);

| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5Cpp.h:45,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.hpp:16,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:9:

/home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’

100 | DataSet(const DataSet& original);

| ^~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Utilities/Profiler.hpp:14,

from /home/cqz/Downloads/skynet/src/Utilities/Profiler.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/Utilities/Profiler.cpp:52:39: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp: In instantiation of ‘void NetworkOutputDataset::ReadFromFile(const H5::H5File&) [with T = double]’:

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:287:16: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:175:14: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy]

175 | mH5Dataset = H5File.openDataSet(mName);

| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5Cpp.h:45,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.hpp:16,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:9:

/home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’

100 | DataSet(const DataSet& original);

| ^~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp: In instantiation of ‘void NetworkOutputDataset::InitForWriting(H5::H5File*, hsize_t, hsize_t, bool) [with T = int; hsize_t = long long unsigned int]’:

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:288:16: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:101:14: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy]

101 | mH5Dataset = pH5File->createDataSet(mName, mDataType, dataSpace, props);

| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5Cpp.h:45,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.hpp:16,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:9:

/home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’

100 | DataSet(const DataSet& original);

| ^~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp: In instantiation of ‘void NetworkOutputDataset::ReadFromFile(const H5::H5File&) [with T = int]’:

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:288:16: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:175:14: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy]

175 | mH5Dataset = H5File.openDataSet(mName);

| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5Cpp.h:45,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.hpp:16,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:9:

/home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’

100 | DataSet(const DataSet& original);

| ^~~~~~~

In file included from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:15,

from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistoryFermiDirac.hpp:14,

from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistoryFermiDirac.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp: In instantiation of ‘void NetworkOutputDataset::InitForWriting(H5::H5File*, hsize_t, hsize_t, bool) [with T = std::vector; hsize_t = long long unsigned int]’:

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:289:16: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:101:14: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy]

101 | mH5Dataset = pH5File->createDataSet(mName, mDataType, dataSpace, props);

| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5Cpp.h:45,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.hpp:16,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:9:

/home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’

100 | DataSet(const DataSet& original);

| ^~~~~~~

In file included from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:15,

from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistoryBlackBody.hpp:14,

from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistoryBlackBody.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp: In instantiation of ‘void NetworkOutputDataset::ReadFromFile(const H5::H5File&) [with T = std::vector]’:

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:289:16: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:175:14: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy]

175 | mH5Dataset = H5File.openDataSet(mName);

| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5Cpp.h:45,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.hpp:16,

from /home/cqz/Downloads/skynet/src/Network/NetworkOutputDataset.cpp:9:

/home/cqz/Downloads/CMake-hdf5-1.10.6/HDF5-1.10.6-Linux/HDF_Group/HDF5/1.10.6/include/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’

100 | DataSet(const DataSet& original);

| ^~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.cpp:54:63: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOutput.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.cpp:332:33: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/NuclearData/NuclideLibrary.cpp:15:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/NuclearData/NuclideLibrary.cpp:196:37: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/FortranOperatorSplitting/CheckResults.cpp:17:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/MatrixSolver/Jacobian.hpp:17,

from /home/cqz/Downloads/skynet/src/Reactions/ReactionLibraryBase.hpp:20,

from /home/cqz/Downloads/skynet/src/Reactions/ReactionLibraryBase.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/Reactions/ReactionLibraryBase.cpp:315:21: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:15,

from /home/cqz/Downloads/skynet/src/MovieMaker/MovieData.hpp:18,

from /home/cqz/Downloads/skynet/src/MovieMaker/MovieData.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

[ 52%] Built target HelmholtzEOS

In file included from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:15,

from /home/cqz/Downloads/skynet/src/Reactions/ReactionPostProcess.hpp:15,

from /home/cqz/Downloads/skynet/src/Reactions/ReactionPostProcess.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:15,

from /home/cqz/Downloads/skynet/src/MovieMaker/MovieData.hpp:18,

from /home/cqz/Downloads/skynet/src/MovieMaker/NucleiChart.hpp:23,

from /home/cqz/Downloads/skynet/src/MovieMaker/NucleiChart.cpp:9:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:15,

from /home/cqz/Downloads/skynet/src/Network/ReactionNetwork.hpp:17,

from /home/cqz/Downloads/skynet/src/Network/ReactionNetwork_ConstructorsEvolveOverloads.cpp:9,

from /home/cqz/Downloads/skynet/src/Network/ReactionNetwork.cpp:11:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

[ 52%] Built target Utilities

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/src/FortranInterface/FortranInterface.cpp:13:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

[ 52%] Built target tinyxml2

[ 52%] Built target MatrixSolver

[ 52%] Built target EquationsOfState

[ 52%] Built target Utilities_Interpolators

[ 52%] Built target SkyNet_swig_compilation

[ 52%] Built target NuclearData

[ 52%] Built target MovieMaker

[ 52%] Built target Network

[ 53%] Linking CXX static library libCheckResults.a

[ 53%] Built target CheckResults

[ 53%] Built target FortranInterface

[ 53%] Built target Reactions

Scanning dependencies of target SkyNet

Scanning dependencies of target SkyNet_static

[ 54%] Linking CXX static library libSkyNet_static.a

[ 54%] Linking CXX shared library libSkyNet.so

[ 54%] Built target SkyNet

[ 54%] Built target SkyNet_static

Scanning dependencies of target MatrixSolverTest

Scanning dependencies of target StopWatch

Scanning dependencies of target FunctionIntegrator_test

Scanning dependencies of target _SkyNet

Scanning dependencies of target ReadFissionReactions

Scanning dependencies of target ReadReaclib

Scanning dependencies of target ReadWinv

Scanning dependencies of target ReadWebnucleo

Scanning dependencies of target ReadFFN

Scanning dependencies of target NetworkOutput

[ 55%] Building CXX object tests/FunctionIntegrator/CMakeFiles/FunctionIntegrator_test.dir/FunctionIntegrator_test.cpp.o

[ 55%] Building CXX object tests/StopWatch/CMakeFiles/StopWatch.dir/StopWatch.cpp.o

[ 57%] Building CXX object tests/ReadWinv/CMakeFiles/ReadWinv.dir/ReadWinv.cpp.o

[ 57%] Building CXX object tests/ReadFFN/CMakeFiles/ReadFFN.dir/ReadFFN.cpp.o

[ 58%] Building CXX object tests/ReadWebnucleo/CMakeFiles/ReadWebnucleo.dir/ReadWebnucleo.cpp.o

[ 59%] Building CXX object tests/MatrixSolver/CMakeFiles/MatrixSolverTest.dir/MatrixSolver.cpp.o

Scanning dependencies of target HelmholtzEOSTest

[ 60%] Building CXX object tests/NetworkOutput/CMakeFiles/NetworkOutput.dir/NetworkOutput.cpp.o

[ 61%] Building CXX object tests/ReadReaclib/CMakeFiles/ReadReaclib.dir/ReadReaclib.cpp.o

[ 62%] Generating NSE_test_input_files

[ 62%] Building CXX object tests/ReadFissionReactions/CMakeFiles/ReadFissionReactions.dir/ReadFissionReactions.cpp.o

Scanning dependencies of target TrivialNetworks

Scanning dependencies of target SmallNetworks

Scanning dependencies of target NSE_screening

Scanning dependencies of target NeutrinoNetwork

Scanning dependencies of target AlphaNetwork

[ 63%] Generating FortranOperatorSplitting_test_input_files

[ 64%] Building CXX object tests/HelmholtzEOS/CMakeFiles/HelmholtzEOSTest.dir/HelmholtzEOS.cpp.o

Scanning dependencies of target InverseRates

[ 65%] Generating XRayBurst_test_input_files

[ 66%] Building CXX object tests/TrivialNetworks/CMakeFiles/TrivialNetworks.dir/TrivialNetworks.cpp.o

[ 67%] Building CXX object tests/NSE_screening/CMakeFiles/NSE_screening.dir/NSE_screening.cpp.o

[ 68%] Building CXX object tests/SmallNetworks/CMakeFiles/SmallNetworks.dir/SmallNetworks.cpp.o

[ 69%] Building CXX object CMakeFiles/_SkyNet.dir/CMakeFiles/_SkyNet.dir/SkyNetPYTHON_wrap.cxx.o

[ 69%] Building CXX object tests/AlphaNetwork/CMakeFiles/AlphaNetwork.dir/AlphaNetwork.cpp.o

[ 70%] Building CXX object tests/NeutrinoNetwork/CMakeFiles/NeutrinoNetwork.dir/NeutrinoNetwork.cpp.o

[ 71%] Generating ReactionTurnOff_test_input_files

Scanning dependencies of target NSE

Scanning dependencies of target FortranOperatorSplitting

[ 72%] Building CXX object tests/InverseRates/CMakeFiles/InverseRates.dir/InverseRates.cpp.o

[ 72%] Generating r-process_test_input_files

Scanning dependencies of target InternalEnergyConservation

[ 73%] Generating NSEEvolution_test_input_files

Scanning dependencies of target movie

[ 73%] Building Fortran object tests/FortranOperatorSplitting/CMakeFiles/FortranOperatorSplitting.dir/__/__/src/FortranInterface/SkyNet.f90.o

Scanning dependencies of target r-process

Scanning dependencies of target XRayBurst

[ 74%] Building CXX object tests/NSE/CMakeFiles/NSE.dir/NSE.cpp.o

Scanning dependencies of target ReactionTurnOff

[ 75%] Building CXX object tests/InternalEnergyConservation/CMakeFiles/InternalEnergyConservation.dir/InternalEnergyConservation.cpp.o

[ 75%] Building CXX object examples/movie/CMakeFiles/movie.dir/movie.cpp.o

Scanning dependencies of target r-process_test

Scanning dependencies of target NSEEvolution

[ 76%] Building CXX object tests/ReactionTurnOff/CMakeFiles/ReactionTurnOff.dir/ReactionTurnOff.cpp.o

[ 77%] Building CXX object examples/r-process/CMakeFiles/r-process.dir/r-process.cpp.o

[ 77%] Building CXX object tests/XRayBurst/CMakeFiles/XRayBurst.dir/XRayBurst.cpp.o

[ 78%] Building Fortran object tests/FortranOperatorSplitting/CMakeFiles/FortranOperatorSplitting.dir/FortranOperatorSplitting.f90.o

[ 79%] Building CXX object tests/r-process/CMakeFiles/r-process_test.dir/r-process.cpp.o

[ 80%] Building CXX object tests/NSEEvolution/CMakeFiles/NSEEvolution.dir/NSEEvolution.cpp.o

[ 81%] Linking Fortran executable FortranOperatorSplitting

[ 82%] Linking CXX executable StopWatch

[ 83%] Linking CXX executable FunctionIntegrator_test

[ 83%] Built target StopWatch

[ 84%] Linking CXX executable ReadWinv

[ 84%] Built target FunctionIntegrator_test

[ 84%] Built target ReadWinv

[ 84%] Built target FortranOperatorSplitting

[ 84%] Linking CXX executable ReadWebnucleo

[ 84%] Built target ReadWebnucleo

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/NeutrinoNetwork/NeutrinoNetwork.cpp:13:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

[ 85%] Linking CXX executable MatrixSolverTest

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/TrivialNetworks/TrivialNetworks.cpp:14:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:15,

from /home/cqz/Downloads/skynet/src/MovieMaker/MovieData.hpp:18,

from /home/cqz/Downloads/skynet/src/MovieMaker/NucleiChart.hpp:23,

from /home/cqz/Downloads/skynet/examples/movie/movie.cpp:12:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

[ 86%] Linking CXX executable HelmholtzEOSTest

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/SmallNetworks/SmallNetworks.cpp:13:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/ReactionTurnOff/ReactionTurnOff.cpp:16:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

[ 86%] Built target MatrixSolverTest

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/examples/r-process/r-process.cpp:10:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/AlphaNetwork/AlphaNetwork.cpp:15:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/XRayBurst/XRayBurst.cpp:16:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/InternalEnergyConservation/InternalEnergyConservation.cpp:19:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/r-process/r-process.cpp:18:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

In file included from /home/cqz/Downloads/skynet/src/Network/NetworkOptions.hpp:12,

from /home/cqz/Downloads/skynet/src/EquationsOfState/HelmholtzEOS.hpp:15,

from /home/cqz/Downloads/skynet/tests/NSEEvolution/NSEEvolution.cpp:19:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

[ 86%] Built target HelmholtzEOSTest

[ 87%] Linking CXX executable ReadReaclib

[ 87%] Linking CXX executable NetworkOutput

[ 88%] Linking CXX executable ReadFFN

[ 88%] Built target ReadReaclib

[ 88%] Built target NetworkOutput

[ 88%] Built target ReadFFN

[ 89%] Linking CXX executable movie

/usr/bin/ld: /lib/x86_64-linux-gnu/libpng16.so.16: undefined reference to `inflateReset2@ZLIB_1.2.3.4'

/usr/bin/ld: /lib/x86_64-linux-gnu/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'

collect2: error: ld returned 1 exit status

make[2]: *** [examples/movie/CMakeFiles/movie.dir/build.make:106: examples/movie/movie] Error 1

make[1]: *** [CMakeFiles/Makefile2:2511: examples/movie/CMakeFiles/movie.dir/all] Error 2

make[1]: *** Waiting for unfinished jobs....

In file included from /home/cqz/Downloads/skynet/src/MatrixSolver/Jacobian.hpp:17,

from /home/cqz/Downloads/skynet/src/Reactions/ReactionLibraryBase.hpp:20,

from /home/cqz/Downloads/skynet/build/CMakeFiles/_SkyNet.dir/SkyNetPYTHON_wrap.cxx:3572:

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp: In instantiation of ‘void NetworkOutput::Log(const char*, Args ...) [with Args = {}]’:

/home/cqz/Downloads/skynet/src/EquationsOfState/NeutrinoHistory.hpp:77:67: required from here

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:243:10: warning: format not a string literal and no format arguments [-Wformat-security]

243 | fprintf(mLogFile, format, args...);

| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~

/home/cqz/Downloads/skynet/src/Network/NetworkOutput.hpp:247:11: warning: format not a string literal and no format arguments [-Wformat-security]

247 | printf(format, args...);

| ~~~~~~^~~~~~~~~~~~~~~~~

[ 90%] Linking CXX executable SmallNetworks

[ 91%] Linking CXX executable TrivialNetworks

[ 92%] Linking CXX executable NeutrinoNetwork

[ 92%] Built target SmallNetworks

[ 92%] Built target TrivialNetworks

[ 92%] Built target NeutrinoNetwork

[ 93%] Linking CXX executable ReadFissionReactions

[ 93%] Linking CXX executable NSE_screening

[ 94%] Linking CXX executable r-process

[ 94%] Linking CXX executable NSE

[ 95%] Linking CXX executable InverseRates

[ 95%] Linking CXX executable ReactionTurnOff

[ 96%] Linking CXX executable AlphaNetwork

[ 97%] Linking CXX executable NSEEvolution

[ 98%] Linking CXX executable r-process_test

[ 98%] Linking CXX executable InternalEnergyConservation

[ 99%] Linking CXX executable XRayBurst

[ 99%] Built target ReadFissionReactions

[ 99%] Built target NSE

[ 99%] Built target NSE_screening

[ 99%] Built target InverseRates

[ 99%] Built target AlphaNetwork

[ 99%] Built target NSEEvolution

[ 99%] Built target ReactionTurnOff

[ 99%] Built target r-process

[ 99%] Built target r-process_test

[ 99%] Built target InternalEnergyConservation

[ 99%] Built target XRayBurst

[100%] Linking CXX shared module _SkyNet.so

/usr/bin/ld: /lib/python/lib/libpython3.7m.a(abstract.o): relocation R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC

/usr/bin/ld: final link failed: bad value

collect2: error: ld returned 1 exit status

make[2]: *** [CMakeFiles/_SkyNet.dir/build.make:108: _SkyNet.so] Error 1

make[1]: *** [CMakeFiles/Makefile2:106: CMakeFiles/_SkyNet.dir/all] Error 2

many errors, ...could you help me?

I'd reinstall all dependencies, as Threads isn't fully installed. It is required by Pardiso.

You could just try a different linear solver instead of Pardiso. Try Armadillo available at http://arma.sourceforge.net or as a Linux package usually under the name libarmadillo-dev

Try installing Python 2.7 as that's recommended with SkyNet.

In make movies you'll need FreeType. Cairomm, SigC++, Cairo, FFmpeg.

sudo apt-get install build-essential cmake libhdf5-dev swig3.0 libpython-dev \

git libgsl-dev libboost-dev libfreetype6-dev libcairo2-dev \

libcairomm-1.0-dev libsigc++-2.0-dev ffmpeg

_______________________________________________________

To install:

mkdir

cd

cmake -DSKYNET_MATRIX_SOLVER=\

-DCMAKE_INSTALL_PREFIX=

_______________________________________________________

Skynet must not be installed inside the root directory.

_________________________________________________________

can be sparse solver (for medium to large networks), Pardiso, trilinos_klu, trilinos_umpack, mkl, trilinos_superlu

or dense solver (for small networks), armadillo, LAPACK, trilinos_lapack.

_____________________________

compile and install SKyNet

make -j4 install

make test

Collette Curry

Many thanks....

I do not know why i can't install SkyNet on my computer [Ubuntu 18.04.5 Desktop (64-bit))]...

After the reinstallation of the system Ubuntu (server for United States), i input the commands as follows,

sudo apt-get update

sudo apt-get install build-essential cmake libhdf5-dev swig3.0 libpython-dev git libgsl-dev libboost-dev libfreetype6-dev libcairo2-dev libcairomm-1.0-dev libsigc++-2.0-dev ffmpeg

sudo apt-get install gfortran

Then i unzip and install boost_1_63_0.tar.gz

copy libpardiso600-GNU720-X86-64.so to file /lib/

sudo apt-get install liblapack-dev

sudo apt-get install libblas-dev

sudo apt-get install python2.7

Now, I think the preparation is over.

CC=gcc CXX=g++ Fortan=gfortran cmake -DENABLE_MOVIE=no -DSKYNET_MATRIX_SOLVER=pardiso -DCMAKE_INSTALL_PREFIX=~/skynet/install ..

However, "make -j install" shows a lot of warnings..

"make test" , only 52% test passed. 11 tests failed out of 23,

It frustrates me a lot these days....

Hi,

can you paste the log file of test failures?

Thanks

Collette Curry

Thanks again, you're so nice...

In attachment, "maketest.log" is obtained by "make test > maketest.log", which is

cqz@tns:~/Documents/skynet/build$ make test

Running tests...

Test project /home/cqz/Documents/skynet/build

Start 1: StopWatch

1/23 Test #1: StopWatch ........................ Passed 1.00 sec

Start 2: MatrixSolver

2/23 Test #2: MatrixSolver .....................***Exception: Child aborted 0.11 sec

Start 3: FunctionIntegrator

3/23 Test #3: FunctionIntegrator ............... Passed 0.21 sec

Start 4: ReadReaclib

4/23 Test #4: ReadReaclib ...................... Passed 0.36 sec

Start 5: ReadFFN

5/23 Test #5: ReadFFN .......................... Passed 0.67 sec

Start 6: ReadWebnucleo

6/23 Test #6: ReadWebnucleo .................... Passed 0.44 sec

Start 7: ReadWinv

7/23 Test #7: ReadWinv ......................... Passed 0.05 sec

Start 8: ReadFissionReactions

8/23 Test #8: ReadFissionReactions ............. Passed 0.64 sec

Start 9: NetworkOutput

9/23 Test #9: NetworkOutput .................... Passed 3.46 sec

Start 10: NSE

10/23 Test #10: NSE .............................. Passed 12.89 sec

Start 11: NSE_screening

11/23 Test #11: NSE_screening .................... Passed 10.27 sec

Start 12: HelmholtzEOS

12/23 Test #12: HelmholtzEOS ..................... Passed 0.78 sec

Start 13: TrivialNetworks

13/23 Test #13: TrivialNetworks ..................***Exception: Child aborted 0.41 sec

Start 14: SmallNetworks

14/23 Test #14: SmallNetworks ....................***Exception: Child aborted 0.41 sec

Start 15: AlphaNetwork

15/23 Test #15: AlphaNetwork .....................***Exception: Child aborted 1.23 sec

Start 16: NeutrinoNetwork

16/23 Test #16: NeutrinoNetwork ..................***Exception: Child aborted 0.42 sec

Start 17: FortranOperatorSplitting

17/23 Test #17: FortranOperatorSplitting .........***Exception: Child aborted 1.77 sec

Start 18: InverseRates

18/23 Test #18: InverseRates ..................... Passed 1.64 sec

Start 19: XRayBurst

19/23 Test #19: XRayBurst ........................***Exception: SegFault 1.66 sec

Start 20: ReactionTurnOff

20/23 Test #20: ReactionTurnOff ..................***Exception: SegFault 2.29 sec

Start 21: r-process

21/23 Test #21: r-process ........................***Exception: SegFault 2.29 sec

Start 22: NSEEvolution

22/23 Test #22: NSEEvolution .....................***Exception: SegFault 2.27 sec

Start 23: InternalEnergyConservation

23/23 Test #23: InternalEnergyConservation .......***Exception: SegFault 0.42 sec

52% tests passed, 11 tests failed out of 23

Total Test time (real) = 45.75 sec

The following tests FAILED:

2 - MatrixSolver (Child aborted)

13 - TrivialNetworks (Child aborted)

14 - SmallNetworks (Child aborted)

15 - AlphaNetwork (Child aborted)

16 - NeutrinoNetwork (Child aborted)

17 - FortranOperatorSplitting (Child aborted)

19 - XRayBurst (SEGFAULT)

20 - ReactionTurnOff (SEGFAULT)

21 - r-process (SEGFAULT)

22 - NSEEvolution (SEGFAULT)

23 - InternalEnergyConservation (SEGFAULT)

Errors while running CTest

Makefile:118: recipe for target 'test' failed

make: *** [test] Error 8

Thanks.

I’ll take a closer look and get back to you asap.

You appear to have a few parts missing. I'd try installing the following if you haven't already.

• Teuchos available here: https://github.com/trilinos/Trilinos/tree/master/packages/teuchos
• Epetra available here: https://github.com/trilinos/Trilinos/tree/master/packages/epetra
• Amesos available here: https://github.com/trilinos/Trilinos/tree/master/packages/amesos
• Intel Maths Kernel Library (MKL) available here: https://software.intel.com/content/www/us/en/develop/tools/math-kernel-library/choose-download/linux.html

Try using the trilinos sparse solver instead of pardiso if all else fails.

- trilinos_kly or - trilinos_umfpack

or try the other sparse solver - mkl

In theory all the other dependencies will be installed by using the following code, however I think you already tried that.

sudo apt-get install build-essential cmake libhdf5-dev swig3.0 libpython-dev \

git libgsl-dev libboost-dev libfreetype6-dev libcairo2-dev \

libcairomm-1.0-dev libsigc++-2.0-dev ffmpeg

after make install

if run test (which is optional) still shows errors

try just calling SkyNet in Python without run test.

It may run even with some network errors.

The system will report any missing dependencies as it runs.

"from SkyNet import *"

$ echo "export PYTHONPATH=/lib:\$PYTHONPATH" >> ~/.bashrc

If I think of anything else, I'll let you know.

Hope you get it working soon.

@Collette Curry

okay, many thanks again...

I will try your advisements🤗best wishes to you...

Good luck with it 🙂