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GT-NucleicAcids / pnab

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compiling pnab on opensuse Tumbleweed with gnu 13.2 compiler #7

Open vcojocaru opened 6 months ago

vcojocaru commented 6 months ago

Dear all, I am trying to compile pnab on a Linux workstation with opensuse tumbleweed (gnu 13.2 compiler). I went through the steps of setting up the conda environment (by modifying the install.sh script) but unfortunately the cmake step fails for me with the following error. Any advice on how to fix this, highly appreciated

cmake -Bbuild -DCMAKE_BUILD_TYPE=Release -DBUILD_DOCS=ON -DPYTHON_EXECUTABLE="$CONDA_PREFIX/envs/pnab/bin/python" -DOPENBABEL_DIR="$CONDA_PREFIX/envs/pnab" -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /apps/anaconda/2024-01-29/envs/pnab/bin/x86_64-conda-linux-gnu-cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /apps/anaconda/2024-01-29/envs/pnab/bin/x86_64-conda-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Open Babel library at /apps/anaconda/2024-01-29/envs/pnab/lib/libopenbabel.so -- Found Eigen3: /apps/anaconda/2024-01-29/envs/pnab/include/eigen3 (Required is at least version "2.91.0") -- Found Doxygen: /usr/bin/doxygen (found version "1.9.6") found components: doxygen dot CMake Warning (dev) at /apps/anaconda/2024-01-29/envs/pnab/share/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first): /apps/anaconda/2024-01-29/envs/pnab/share/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /apps/anaconda/2024-01-29/envs/pnab/share/cmake/pybind11/pybind11Common.cmake:206 (include) /apps/anaconda/2024-01-29/envs/pnab/share/cmake/pybind11/pybind11Config.cmake:250 (include) CMakeLists.txt:36 (find_package) This warning is for project developers. Use -Wno-dev to suppress it.

-- Found PythonInterp: /apps/anaconda/2024-01-29/envs/pnab/envs/pnab/bin/python CMake Error at /apps/anaconda/2024-01-29/envs/pnab/share/cmake/pybind11/FindPythonLibsNew.cmake:146 (message): Python config failure:

Call Stack (most recent call first): /apps/anaconda/2024-01-29/envs/pnab/share/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /apps/anaconda/2024-01-29/envs/pnab/share/cmake/pybind11/pybind11Common.cmake:206 (include) /apps/anaconda/2024-01-29/envs/pnab/share/cmake/pybind11/pybind11Config.cmake:250 (include) CMakeLists.txt:36 (find_package)

-- Configuring incomplete, errors occurred!

alenaizan commented 6 months ago

Can you provide the output of conda list and the version of cmake? Maybe you can also compare the versions of your dependencies with the versions shown here. I do not know what is causing this issue, but the discussion here seems relevant.

vcojocaru commented 6 months ago

Thanks for answering. CMAKE is 3.29.2, conda list output is below. I will take a look at the discussion you suggested

packages in environment at /apps/anaconda/2024-01-29/envs/pnab:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge aiosqlite 0.19.0 pyhd8ed1ab_0 conda-forge anyio 4.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge atk-1.0 2.38.0 h04ea711_2 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge binutils_impl_linux-64 2.40 ha885e6a_0 conda-forge binutils_linux-64 2.40 hdade7a5_3 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.28.1 hd590300_0 conda-forge ca-certificates 2024.3.11 h06a4308_0
cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge certifi 2024.2.2 py310h06a4308_0
cffi 1.16.0 py310h2fee648_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge cmake 3.29.2 hcfe8598_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.2.2 pyhd8ed1ab_0 conda-forge debugpy 1.8.1 py310hc6cd4ac_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge eigen 3.4.0 h00ab1b0_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_1 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge gcc_impl_linux-64 13.2.0 h1d3d475_6 conda-forge gcc_linux-64 13.2.0 h1ed452b_3 conda-forge gdk-pixbuf 2.42.11 hb9ae30d_0 conda-forge giflib 5.2.2 hd590300_0 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge graphviz 9.0.0 h78e8752_1 conda-forge gtk2 2.24.33 h280cfa0_4 conda-forge gts 0.7.6 h977cf35_4 conda-forge gxx_impl_linux-64 13.2.0 h1d3d475_6 conda-forge gxx_linux-64 13.2.0 he8deefe_3 conda-forge harfbuzz 8.4.0 h3d44ed6_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge importlib-metadata 7.1.0 pyha770c72_0 conda-forge importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge ipykernel 6.29.3 pyhd33586a_0 conda-forge ipython 8.21.0 pyh707e725_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.8.0 pyhd8ed1ab_0 conda-forge isoduration 20.11.0 pyhd8ed1ab_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.3 pyhd8ed1ab_0 conda-forge json5 0.9.25 pyhd8ed1ab_0 conda-forge jsonpointer 2.4 py310hff52083_3 conda-forge jsonschema 4.21.1 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.21.1 pyhd8ed1ab_0 conda-forge jupyter_client 8.6.1 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py310hff52083_0 conda-forge jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge jupyter_server 2.14.0 pyhd8ed1ab_0 conda-forge jupyter_server_fileid 0.9.1 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge jupyter_server_ydoc 0.8.0 pyhd8ed1ab_0 conda-forge jupyter_ydoc 0.2.4 pyhd8ed1ab_0 conda-forge jupyterlab 3.6.7 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.3.0 pyhd8ed1ab_0 conda-forge jupyterlab_server 2.27.1 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 1.1.7 pyhd8ed1ab_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_17 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.21.2 h659d440_0 conda-forge ld_impl_linux-64 2.40 h55db66e_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libcurl 8.7.1 hca28451_0 conda-forge libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 13.2.0 h95c4c6d_106 conda-forge libgcc-ng 13.2.0 hc881cc4_6 conda-forge libgd 2.3.3 h119a65a_9 conda-forge libgfortran-ng 13.2.0 h69a702a_6 conda-forge libgfortran5 13.2.0 h43f5ff8_6 conda-forge libglib 2.80.0 hf2295e7_6 conda-forge libgomp 13.2.0 hc881cc4_6 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 22_linux64_openblas conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge libpng 1.6.43 h2797004_0 conda-forge librsvg 2.58.0 hadf69e7_1 conda-forge libsanitizer 13.2.0 h95c4c6d_6 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.45.3 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-devel_linux-64 13.2.0 h95c4c6d_106 conda-forge libstdcxx-ng 13.2.0 h95c4c6d_6 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libuv 1.48.0 hd590300_0 conda-forge libwebp 1.3.2 h658648e_1 conda-forge libwebp-base 1.3.2 hd590300_1 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxml2 2.12.6 h232c23b_2 conda-forge libzlib 1.2.13 hd590300_5 conda-forge markupsafe 2.1.5 py310h2372a71_0 conda-forge matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mistune 3.0.2 pyhd8ed1ab_0 conda-forge nbclassic 1.0.0 pyhb4ecaf3_1 conda-forge nbclient 0.10.0 pyhd8ed1ab_0 conda-forge nbconvert 7.16.3 hd8ed1ab_1 conda-forge nbconvert-core 7.16.3 pyhd8ed1ab_1 conda-forge nbconvert-pandoc 7.16.3 hd8ed1ab_1 conda-forge nbformat 5.10.4 pyhd8ed1ab_0 conda-forge ncurses 6.4.20240210 h59595ed_0 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge nglview 2.7.8 pyh59e0f4d_0 conda-forge nglview-js-widgets 2.7.7 pypi_0 pypi notebook 6.5.4 pyha770c72_0 conda-forge notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge numpy 1.26.4 py310hb13e2d6_0 conda-forge openbabel 3.1.1 py310hbff9852_9 conda-forge openssl 3.2.1 hd590300_1 conda-forge overrides 7.7.0 pyhd8ed1ab_0 conda-forge packaging 24.0 pyhd8ed1ab_0 conda-forge pandoc 3.1.13 ha770c72_0 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge pango 1.52.2 ha41ecd1_0 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge pcre2 10.43 hcad00b1_0 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pixman 0.43.2 h59595ed_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge platformdirs 4.2.1 pyhd8ed1ab_0 conda-forge pluggy 1.5.0 pyhd8ed1ab_0 conda-forge prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.42 pyha770c72_0 conda-forge psutil 5.9.8 py310h2372a71_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge pybind11 2.9.2 py310hbf28c38_1 conda-forge pybind11-global 2.9.2 py310hbf28c38_1 conda-forge pycparser 2.22 pyhd8ed1ab_0 conda-forge pygments 2.17.2 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 8.1.1 pyhd8ed1ab_0 conda-forge python 3.10.14 hd12c33a_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.19.1 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python_abi 3.10 4_cp310 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.1 py310h2372a71_1 conda-forge pyzmq 26.0.2 py310h6883aea_0 conda-forge readline 8.2 h8228510_1 conda-forge referencing 0.34.0 pyhd8ed1ab_0 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge rhash 1.4.4 hd590300_0 conda-forge rpds-py 0.18.0 py310hcb5633a_0 conda-forge send2trash 1.8.3 pyh0d859eb_0 conda-forge setuptools 69.5.1 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sniffio 1.3.1 pyhd8ed1ab_0 conda-forge soupsieve 2.5 pyhd8ed1ab_1 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge sysroot_linux-64 2.12 he073ed8_17 conda-forge terminado 0.18.1 pyh0d859eb_0 conda-forge tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.4 py310h2372a71_0 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge typing-extensions 4.11.0 hd8ed1ab_0 conda-forge typing_extensions 4.11.0 pyha770c72_0 conda-forge typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge uri-template 1.3.0 pyhd8ed1ab_0 conda-forge urllib3 2.2.1 pyhd8ed1ab_0 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge webcolors 1.13 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pyhd8ed1ab_2 conda-forge websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge wheel 0.43.0 pyhd8ed1ab_1 conda-forge widgetsnbextension 3.6.6 pyhd8ed1ab_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge y-py 0.5.9 py310h4426083_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge ypy-websocket 0.8.2 pyhd8ed1ab_0 conda-forge zeromq 4.3.5 h59595ed_1 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge

alenaizan commented 6 months ago

I used your exact dependencies and I was able to compile the package. I also got the same warning message:

CMake Warning (dev) at /apps/anaconda/2024-01-29/envs/pnab/share/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.

so the link I posted earlier does not seem relevant.

Maybe you should check your PATH and PYTHONPATH variables if you did not do that already. I can't reproduce your errors in my ubuntu machine.

In the meantime, you can use this link to run the package on the cloud.

vcojocaru commented 6 months ago

I am not sure. I have no PYTHONPATH set and nothing unusual in the PATH. Everything seems okay with my conda environment. The error seems to point out that there is something wrong with the python bindings. I have gnu 13.2 compiler on my machine. Is that the same for you ? I will try the cloud version

alenaizan commented 6 months ago

Yes, I used the same compiler that comes through conda.