[JOSS] Install from source fails

[hgandhi2411]

• For conda install, the command should be conda install -c conda-forge thermofun instead of conda install thermofun in README.

• Installation from source fails with this message:

  
  >>> ./install-dependencies.sh
  Cloning into 'json'...
  remote: Enumerating objects: 35355, done.
  remote: Counting objects: 100% (1004/1004), done.
  remote: Compressing objects: 100% (385/385), done.
  remote: Total 35355 (delta 461), reused 874 (delta 375), pack-reused 34351
  Receiving objects: 100% (35355/35355), 178.64 MiB | 8.38 MiB/s, done.
  Resolving deltas: 100% (21772/21772), done.
  -- The CXX compiler identification is AppleClang 13.1.6.13160021
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
  -- Detecting CXX compile features
  -- Detecting CXX compile features - done
  -- Using the multi-header code from /Users/hetagandhi/code/json/include/
  -- Configuring done
  -- Generating done
  -- Build files have been written to: /Users/hetagandhi/code/json/build
  Install the project...
  -- Install configuration: ""
  -- Installing: /usr/local/include
  -- Installing: /usr/local/include/nlohmann
  -- Installing: /usr/local/include/nlohmann/ordered_map.hpp
  -- Installing: /usr/local/include/nlohmann/json.hpp
  -- Installing: /usr/local/include/nlohmann/adl_serializer.hpp
  -- Installing: /usr/local/include/nlohmann/byte_container_with_subtype.hpp
  -- Installing: /usr/local/include/nlohmann/detail
  -- Installing: /usr/local/include/nlohmann/detail/hash.hpp
  -- Installing: /usr/local/include/nlohmann/detail/string_escape.hpp
  -- Installing: /usr/local/include/nlohmann/detail/json_custom_base_class.hpp
  -- Installing: /usr/local/include/nlohmann/detail/json_ref.hpp
  -- Installing: /usr/local/include/nlohmann/detail/conversions
  -- Installing: /usr/local/include/nlohmann/detail/conversions/to_chars.hpp
  -- Installing: /usr/local/include/nlohmann/detail/conversions/from_json.hpp
  -- Installing: /usr/local/include/nlohmann/detail/conversions/to_json.hpp
  -- Installing: /usr/local/include/nlohmann/detail/value_t.hpp
  -- Installing: /usr/local/include/nlohmann/detail/input
  -- Installing: /usr/local/include/nlohmann/detail/input/position_t.hpp
  -- Installing: /usr/local/include/nlohmann/detail/input/parser.hpp
  -- Installing: /usr/local/include/nlohmann/detail/input/json_sax.hpp
  -- Installing: /usr/local/include/nlohmann/detail/input/binary_reader.hpp
  -- Installing: /usr/local/include/nlohmann/detail/input/input_adapters.hpp
  -- Installing: /usr/local/include/nlohmann/detail/input/lexer.hpp
  -- Installing: /usr/local/include/nlohmann/detail/string_concat.hpp
  -- Installing: /usr/local/include/nlohmann/detail/macro_scope.hpp
  -- Installing: /usr/local/include/nlohmann/detail/output
  -- Installing: /usr/local/include/nlohmann/detail/output/output_adapters.hpp
  -- Installing: /usr/local/include/nlohmann/detail/output/serializer.hpp
  -- Installing: /usr/local/include/nlohmann/detail/output/binary_writer.hpp
  -- Installing: /usr/local/include/nlohmann/detail/meta
  -- Installing: /usr/local/include/nlohmann/detail/meta/is_sax.hpp
  -- Installing: /usr/local/include/nlohmann/detail/meta/call_std
  -- Installing: /usr/local/include/nlohmann/detail/meta/call_std/end.hpp
  -- Installing: /usr/local/include/nlohmann/detail/meta/call_std/begin.hpp
  -- Installing: /usr/local/include/nlohmann/detail/meta/identity_tag.hpp
  -- Installing: /usr/local/include/nlohmann/detail/meta/type_traits.hpp
  -- Installing: /usr/local/include/nlohmann/detail/meta/cpp_future.hpp
  -- Installing: /usr/local/include/nlohmann/detail/meta/detected.hpp
  -- Installing: /usr/local/include/nlohmann/detail/meta/void_t.hpp
  -- Installing: /usr/local/include/nlohmann/detail/meta/std_fs.hpp
  -- Installing: /usr/local/include/nlohmann/detail/json_pointer.hpp
  -- Installing: /usr/local/include/nlohmann/detail/exceptions.hpp
  -- Installing: /usr/local/include/nlohmann/detail/abi_macros.hpp
  -- Installing: /usr/local/include/nlohmann/detail/macro_unscope.hpp
  -- Installing: /usr/local/include/nlohmann/detail/iterators
  -- Installing: /usr/local/include/nlohmann/detail/iterators/iter_impl.hpp
  -- Installing: /usr/local/include/nlohmann/detail/iterators/json_reverse_iterator.hpp
  -- Installing: /usr/local/include/nlohmann/detail/iterators/iteration_proxy.hpp
  -- Installing: /usr/local/include/nlohmann/detail/iterators/iterator_traits.hpp
  -- Installing: /usr/local/include/nlohmann/detail/iterators/internal_iterator.hpp
  -- Installing: /usr/local/include/nlohmann/detail/iterators/primitive_iterator.hpp
  -- Installing: /usr/local/include/nlohmann/thirdparty
  -- Installing: /usr/local/include/nlohmann/thirdparty/hedley
  -- Installing: /usr/local/include/nlohmann/thirdparty/hedley/hedley.hpp
  -- Installing: /usr/local/include/nlohmann/thirdparty/hedley/hedley_undef.hpp
  -- Installing: /usr/local/include/nlohmann/json_fwd.hpp
  -- Installing: /usr/local/share/cmake/nlohmann_json/nlohmann_jsonConfig.cmake
  -- Installing: /usr/local/share/cmake/nlohmann_json/nlohmann_jsonConfigVersion.cmake
  -- Installing: /usr/local/share/cmake/nlohmann_json/nlohmann_jsonTargets.cmake
  -- Installing: /usr/local/share/pkgconfig/nlohmann_json.pc
  ./install-dependencies.sh: line 41: wget: command not found
  tar: Error opening archive: Failed to open 'default.tar.bz2'
  CMake Warning:
  Ignoring extra path from command line:
  
  ".."

CMake Error: The source directory "/Users/hetagandhi/code/eigen-code" does not appear to contain CMakeLists.txt. Specify --help for usage, or press the help button on the CMake GUI. Cloning into 'pybind11'... remote: Enumerating objects: 24615, done. remote: Counting objects: 100% (170/170), done. remote: Compressing objects: 100% (101/101), done. remote: Total 24615 (delta 78), reused 126 (delta 59), pack-reused 24445 Receiving objects: 100% (24615/24615), 9.21 MiB | 6.78 MiB/s, done. Resolving deltas: 100% (17232/17232), done. -- The CXX compiler identification is AppleClang 13.1.6.13160021 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- pybind11 v2.11.0 dev1 -- CMake 3.24.1 -- Found PythonInterp: /Users/hetagandhi/opt/anaconda3/envs/thermofun/bin/python (found suitable version "3.7.13", minimum required is "3.6") -- Found PythonLibs: /Users/hetagandhi/opt/anaconda3/envs/thermofun/lib/libpython3.7m.dylib -- PYTHON 3.7.13 -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- pybind11::lto enabled -- Performing Test HAS_FLTO_THIN -- Performing Test HAS_FLTO_THIN - Success -- pybind11::thin_lto enabled -- Configuring done -- Generating done -- Build files have been written to: /Users/hetagandhi/code/pybind11/build Install the project... -- Install configuration: "" -- Installing: /usr/local/include/pybind11 -- Installing: /usr/local/include/pybind11/attr.h -- Installing: /usr/local/include/pybind11/embed.h -- Installing: /usr/local/include/pybind11/numpy.h -- Installing: /usr/local/include/pybind11/pybind11.h -- Installing: /usr/local/include/pybind11/operators.h -- Installing: /usr/local/include/pybind11/iostream.h -- Installing: /usr/local/include/pybind11/gil.h -- Installing: /usr/local/include/pybind11/chrono.h -- Installing: /usr/local/include/pybind11/stl_bind.h -- Installing: /usr/local/include/pybind11/buffer_info.h -- Installing: /usr/local/include/pybind11/options.h -- Installing: /usr/local/include/pybind11/stl -- Installing: /usr/local/include/pybind11/stl/filesystem.h -- Installing: /usr/local/include/pybind11/functional.h -- Installing: /usr/local/include/pybind11/stl.h -- Installing: /usr/local/include/pybind11/detail -- Installing: /usr/local/include/pybind11/detail/type_caster_base.h -- Installing: /usr/local/include/pybind11/detail/typeid.h -- Installing: /usr/local/include/pybind11/detail/descr.h -- Installing: /usr/local/include/pybind11/detail/internals.h -- Installing: /usr/local/include/pybind11/detail/common.h -- Installing: /usr/local/include/pybind11/detail/class.h -- Installing: /usr/local/include/pybind11/detail/init.h -- Installing: /usr/local/include/pybind11/common.h -- Installing: /usr/local/include/pybind11/eval.h -- Installing: /usr/local/include/pybind11/cast.h -- Installing: /usr/local/include/pybind11/eigen.h -- Installing: /usr/local/include/pybind11/pytypes.h -- Installing: /usr/local/include/pybind11/complex.h -- Installing: /usr/local/share/cmake/pybind11/pybind11Config.cmake -- Installing: /usr/local/share/cmake/pybind11/pybind11ConfigVersion.cmake -- Installing: /usr/local/share/cmake/pybind11/FindPythonLibsNew.cmake -- Installing: /usr/local/share/cmake/pybind11/pybind11Common.cmake -- Installing: /usr/local/share/cmake/pybind11/pybind11Tools.cmake -- Installing: /usr/local/share/cmake/pybind11/pybind11NewTools.cmake -- Installing: /usr/local/share/cmake/pybind11/pybind11Targets.cmake -- Installing: /usr/local/share/pkgconfig/pybind11.pc Cloning into 'chemicalfun'... remote: Enumerating objects: 1172, done. remote: Counting objects: 100% (1172/1172), done. remote: Compressing objects: 100% (946/946), done. remote: Total 1172 (delta 639), reused 406 (delta 169), pack-reused 0 Receiving objects: 100% (1172/1172), 1.13 MiB | 3.49 MiB/s, done. Resolving deltas: 100% (639/639), done. -- The CXX compiler identification is AppleClang 13.1.6.13160021 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- CondaAware: conda environment recognized! -- CondaAware: CONDA_PREFIX=/Users/hetagandhi/opt/anaconda3/envs/thermofun -- CondaAware: CONDA_AWARE_PREFIX=CONDA_PREFIX (/Users/hetagandhi/opt/anaconda3/envs/thermofun) -- CondaAware: CMAKE_INSTALL_PREFIX set to CONDA_AWARE_PREFIX -- CondaAware: appended CONDA_AWARE_PREFIX to CMAKE_PREFIX_PATH -- CondaAware: appended CONDA_AWARE_PREFIX/include to include directories -- CondaAware: appended CONDA_AWARE_PREFIX/lib to link directories -- Found PythonInterp: /Users/hetagandhi/opt/anaconda3/envs/thermofun/bin/python (found suitable version "3.7.13", minimum required is "3.6") -- Found PythonLibs: /Users/hetagandhi/opt/anaconda3/envs/thermofun/lib/libpython3.7m.dylib -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Performing Test HAS_FLTO_THIN -- Performing Test HAS_FLTO_THIN - Success -- Found pybind11: /usr/local/include (found version "2.11.0dev1") -- Found pybind11 v2.11.0: /usr/local/include;/Users/hetagandhi/opt/anaconda3/envs/thermofun/include/python3.7m -- Found pybind11 v2.11.0: /usr/local/include;/Users/hetagandhi/opt/anaconda3/envs/thermofun/include/python3.7m CMake Error at cmake/modules/ChemicalFunFindDeps.cmake:14 (find_package): By not providing "Findspdlog.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "spdlog", but CMake did not find one.

Could not find a package configuration file provided by "spdlog" with any of the following names:

spdlogConfig.cmake
spdlog-config.cmake

Add the installation prefix of "spdlog" to CMAKE_PREFIX_PATH or set "spdlog_DIR" to a directory containing one of the above files. If "spdlog" provides a separate development package or SDK, be sure it has been installed. Call Stack (most recent call first): CMakeLists.txt:115 (include)

-- Configuring incomplete, errors occurred! See also "/Users/hetagandhi/code/chemicalfun/build/CMakeFiles/CMakeOutput.log". See also "/Users/hetagandhi/code/chemicalfun/build/CMakeFiles/CMakeError.log". expr: syntax error

[allanleal]

Hi @hgandhi2411 You need to build & install spdlog first (https://github.com/gabime/spdlog).

@gdmiron In the README, the conda-forge channel must be added for the conda install thermofun to work:

conda config --add channels conda-forge

One needs to check if conda install -c conda-forge thermofun (alternatively, conda install conda-forge::thermofun) does not end up installing dependencies from other channels if the conda-forge channel is not the priority one (first in the list of channels in ~/.condarc).

[hgandhi2411]

I am using the install_dependencies.sh file, shouldn't that file install all required dependencies for me? If that is not the case, I would recommend creating a list of requirements and add steps that users should follow in order to get dependencies installed while building thermofun from source.

[gdmiron]

I am using the install_dependencies.sh file, shouldn't that file install all required dependencies for me? If that is not the case, I would recommend creating a list of requirements and add steps that users should follow in order to get dependencies installed while building thermofun from source.

Thanks for testing the build. I will make an update to the install dependencies file in the following days. Seems that spdlog is missing.

[defencedog]

@hgandhi2411 @gdmiron will there be any support forARM64architecture?

[gdmiron]

@defencedog I am totally for supporting different architectures. Do you have any experience with what one needs to adapt in the build and setup tools?

[defencedog]

@gdmiron sir thanks for response give me a day! I as a chemical engineer had already compiled a fair amount of libraries on a rather unorthodox platform. Yes on Android with termux + jupyter

I will reply back give me a day

[gdmiron]

@hgandhi2411 I made the requested updates to the install dependencies and readme, see #41

[defencedog]

@gdmiron on Android ARM64 the package successfully builds but doesn't run under python. Configure / Make log is here

n [1]: import thermofun as tf
----------------------------------------------------------------------
ImportError                          Traceback (most recent call last)
Input In [1], in <cell line: 1>()
----> 1 import thermofun as tf

File /data/data/com.termux/files/usr/lib/python3.9/site-packages/thermofun/__init__.py:1, in <module>
----> 1 from thermofun.PyThermoFun import *

ImportError: dlopen failed: cannot locate symbol "_ZN6spdlog7details7log_msgC1ENS_10source_locEN3fmt2v817basic_string_viewIcEENS_5level10level_enumES6_" referenced by "/data/data/com.termux/files/usr/lib/libThermoFun.so"...

In [2]: import chemicalfun as cf
----------------------------------------------------------------------
ImportError                          Traceback (most recent call last)
Input In [2], in <cell line: 1>()
----> 1 import chemicalfun as cf

File /data/data/com.termux/files/usr/lib/python3.9/site-packages/chemicalfun/__init__.py:1, in <module>
----> 1 from chemicalfun.PyChemicalFun import *

ImportError: dlopen failed: cannot locate symbol "_ZN6spdlog7details7log_msgC1ENS_10source_locEN3fmt2v817basic_string_viewIcEENS_5level10level_enumES6_" referenced by "/data/data/com.termux/files/usr/lib/libChemicalFun.so"...

The source of this problem is chemicalfun & the error is mentioned here Now chemicalfun is not on github so who will address this issue don't know

[gdmiron]

@defencedog when you build you should try without having fmt installed. The spdlog 1.10.0 should have an internal version of fmt that it uses. Maybe there is a conflict between fmt in spdlog and fmt installed. So try without having any fmt, but only splog v.1.10.0. In any case I can help with chemicalfun also. I maintain it on Bitbucket.

[hgandhi2411]

@gdmiron Thermofun build from source doesn't seem to work for Mac ARM64 processors. Seems like @defencedog was able to build the package fine on Android ARM64. So, I am going to proceed with testing on the conda install.

Pasting the error here in case you decide to provide support in the future

ld: symbol(s) not found for architecture arm64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [ThermoFun/libThermoFun.dylib] Error 1
make[1]: *** [ThermoFun/CMakeFiles/ThermoFun.dir/all] Error 2
make: *** [all] Error 2

[defencedog]

@hgandhi2411 No I couldn't run ...though I could build https://github.com/thermohub/thermofun/issues/39#issuecomment-1291063466

[hgandhi2411]

@gdmiron Please add a comment in the readme file that the "build from source" doesn't work for ARM processors, unless you plan to fix it.

[defencedog]

@hgandhi2411 Problem is resolved on ARM64 Android: https://github.com/thermohub/thermofun/issues/39#issuecomment-1320903633