Michael,
This is (at least) a python version issue. Use 3.10.x and not 3.11.x.
Also, look in the AMBER mailing list as this issue has been asked/addressed
before -
Cheers,
Todd
On Wed, Feb 7, 2024 at 11:32 AM Michael Shokhen via AMBER <amber.ambermd.org>
wrote:
>
> Dear Amber experts,
>
> For several years, AMBER20 worked perfectly under RedHat Linux on my server
> located in the university computer center.
> Recently RedHat was changed to Rocky Linux 8 on my server.
> So I had to install AMBER 20 from scratch, starting with the command:
>
> ./run_cmake
>
> After a short run, the process aborted with the last message:
>
> -- Configuring incomplete, errors occurred!
>
> See below the full protocol.
>
> I need your advice on how to solve the problem.
>
> Thank you,
> Michael
>
> > ./run_cmake
> --
> **************************************************************************
> -- Starting configuration of Amber version 20.0.0...
> -- CMake Version: 3.26.5
> -- For how to use this build system, please read this wiki:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake
> -- For a list of important CMake variables, check here:
> -- http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
> --
> **************************************************************************
> -- Setting C compiler to gcc
> -- Setting CXX compiler to g++
> -- Setting Fortran compiler to gfortran
> -- Amber source found, building AmberTools and Amber
> -- The C compiler identification is GNU 8.5.0
> -- The CXX compiler identification is GNU 8.5.0
> -- The Fortran compiler identification is GNU 8.5.0
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Check for working C compiler: /usr/bin/gcc - 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: /usr/bin/g++ - skipped
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Detecting Fortran compiler ABI info
> -- Detecting Fortran compiler ABI info - done
> -- Check for working Fortran compiler: /usr/bin/gfortran - skipped
> -- Testing if stdlib.h can be included...
> -- Testing if stdlib.h can be included... yes
> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
> -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
> -- 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 CUDA: /usr/local/cuda (found version "12.3")
> -- Downloading Python 3 Miniconda
> -- Detected Linux OS. Downloading the Linux installer
> -- Using 64 bit miniconda
> Downloading
> http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh ->
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/download/Miniconda3-latest-Linux-x86_64.sh
> #####################################################################################################################
> 100.0%
> Installing Miniconda Python.
>
> PREFIX=/home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install
> Unpacking payload ...
>
> Installing base environment...
>
>
> Downloading and Extracting Packages: ...working... done
>
> Downloading and Extracting Packages: ...working... done
> Preparing transaction: ...working... done
> Executing transaction: ...working... done
> installation finished.
> -- Updating and installing required and optional packages...
> Channels:
> - defaults
> Platform: linux-64
> Collecting package metadata (repodata.json): ...working... done
> Solving environment: ...working... done
>
> ## Package Plan ##
>
> environment location:
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install
>
> added / updated specs:
> - conda
>
>
> The following packages will be downloaded:
>
> package | build
> ---------------------------|-----------------
> conda-24.1.0 | py311h06a4308_0 1.2 MB
> ------------------------------------------------------------
> Total: 1.2 MB
>
> The following packages will be UPDATED:
>
> conda 23.11.0-py311h06a4308_0 -->
> 24.1.0-py311h06a4308_0
>
>
>
> Downloading and Extracting Packages: ...working... done
> Preparing transaction: ...working... done
> Verifying transaction: ...working... done
> Executing transaction: ...working... done
> Requirement already satisfied: pip in
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages
> (23.3.1)
> Collecting pip
> Using cached pip-23.3.2-py3-none-any.whl.metadata (3.5 kB)
> Using cached pip-23.3.2-py3-none-any.whl (2.1 MB)
> Installing collected packages: pip
> Attempting uninstall: pip
> Found existing installation: pip 23.3.1
> Uninstalling pip-23.3.1:
> Successfully uninstalled pip-23.3.1
> Successfully installed pip-23.3.2
> Channels:
> - defaults
> Platform: linux-64
> Collecting package metadata (repodata.json): ...working... done
> Solving environment: ...working... done
>
> ## Package Plan ##
>
> environment location:
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install
>
> added / updated specs:
> - nomkl
>
>
> The following packages will be downloaded:
>
> package | build
> ---------------------------|-----------------
> blas-1.0 | openblas 46 KB
> nomkl-3.0 | 0 46 KB
> ------------------------------------------------------------
> Total: 91 KB
>
> The following NEW packages will be INSTALLED:
>
> blas pkgs/main/linux-64::blas-1.0-openblas
> nomkl pkgs/main/linux-64::nomkl-3.0-0
>
>
>
> Downloading and Extracting Packages: ...working... done
> Preparing transaction: ...working... done
> Verifying transaction: ...working... done
> Executing transaction: ...working... done
> Channels:
> - defaults
> Platform: linux-64
> Collecting package metadata (repodata.json): ...working... done
> Solving environment: ...working... done
>
> ## Package Plan ##
>
> environment location:
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install
>
> added / updated specs:
> - conda-build
> - cython=0.29
> - ipython
> - notebook
> - numpy
> - pytest
> - scipy
>
>
> The following packages will be downloaded:
>
> package | build
> ---------------------------|-----------------
> anyio-4.2.0 | py311h06a4308_0 237 KB
> argon2-cffi-21.3.0 | pyhd3eb1b0_0 15 KB
> argon2-cffi-bindings-21.2.0| py311h5eee18b_0 33 KB
> asttokens-2.0.5 | pyhd3eb1b0_0 20 KB
> async-lru-2.0.4 | py311h06a4308_0 20 KB
> attrs-23.1.0 | py311h06a4308_0 161 KB
> babel-2.11.0 | py311h06a4308_0 6.1 MB
> beautifulsoup4-4.12.2 | py311h06a4308_0 268 KB
> bleach-4.1.0 | pyhd3eb1b0_0 123 KB
> chardet-4.0.0 |py311h06a4308_1003 218 KB
> click-8.1.7 | py311h06a4308_0 221 KB
> comm-0.1.2 | py311h06a4308_0 14 KB
> conda-build-24.1.0 | py311h06a4308_0 825 KB
> conda-index-0.4.0 | pyhd3eb1b0_0 173 KB
> cython-0.29.36 | py311h5eee18b_0 2.6 MB
> debugpy-1.6.7 | py311h6a678d5_0 2.4 MB
> decorator-5.1.1 | pyhd3eb1b0_0 12 KB
> defusedxml-0.7.1 | pyhd3eb1b0_0 23 KB
> executing-0.8.3 | pyhd3eb1b0_0 18 KB
> filelock-3.13.1 | py311h06a4308_0 24 KB
> iniconfig-1.1.1 | pyhd3eb1b0_0 8 KB
> ipykernel-6.28.0 | py311h06a4308_0 245 KB
> ipython-8.20.0 | py311h06a4308_0 1.4 MB
> jedi-0.18.1 | py311h06a4308_1 1.1 MB
> jinja2-3.1.3 | py311h06a4308_0 353 KB
> json5-0.9.6 | pyhd3eb1b0_0 21 KB
> jsonschema-4.19.2 | py311h06a4308_0 190 KB
> jsonschema-specifications-2023.7.1| py311h06a4308_0 15 KB
> jupyter-lsp-2.2.0 | py311h06a4308_0 107 KB
> jupyter_client-8.6.0 | py311h06a4308_0 233 KB
> jupyter_core-5.5.0 | py311h06a4308_0 91 KB
> jupyter_events-0.8.0 | py311h06a4308_0 41 KB
> jupyter_server-2.10.0 | py311h06a4308_0 577 KB
> jupyter_server_terminals-0.4.4| py311h06a4308_1 27 KB
> jupyterlab-4.0.11 | py311h06a4308_0 4.5 MB
> jupyterlab_pygments-0.1.2 | py_0 8 KB
> jupyterlab_server-2.25.1 | py311h06a4308_0 113 KB
> libgfortran-ng-11.2.0 | h00389a5_1 20 KB
> libgfortran5-11.2.0 | h1234567_1 2.0 MB
> liblief-0.12.3 | h6a678d5_0 1.9 MB
> libopenblas-0.3.21 | h043d6bf_0 5.4 MB
> libsodium-1.0.18 | h7b6447c_0 244 KB
> markupsafe-2.1.3 | py311h5eee18b_0 25 KB
> matplotlib-inline-0.1.6 | py311h06a4308_0 18 KB
> mistune-2.0.4 | py311h06a4308_0 107 KB
> more-itertools-10.1.0 | py311h06a4308_0 103 KB
> nbclient-0.8.0 | py311h06a4308_0 120 KB
> nbconvert-7.10.0 | py311h06a4308_0 513 KB
> nbformat-5.9.2 | py311h06a4308_0 158 KB
> nest-asyncio-1.5.6 | py311h06a4308_0 17 KB
> notebook-7.0.6 | py311h06a4308_0 3.1 MB
> notebook-shim-0.2.3 | py311h06a4308_0 26 KB
> numpy-1.26.3 | py311h24aa872_0 10 KB
> numpy-base-1.26.3 | py311hbfb1bba_0 8.3 MB
> overrides-7.4.0 | py311h06a4308_0 36 KB
> pandocfilters-1.5.0 | pyhd3eb1b0_0 11 KB
> parso-0.8.3 | pyhd3eb1b0_0 70 KB
> patch-2.7.6 | h7b6447c_1001 119 KB
> patchelf-0.17.2 | h6a678d5_0 98 KB
> pexpect-4.8.0 | pyhd3eb1b0_3 53 KB
> pkginfo-1.9.6 | py311h06a4308_0 65 KB
> prometheus_client-0.14.1 | py311h06a4308_0 120 KB
> prompt-toolkit-3.0.43 | py311h06a4308_0 745 KB
> prompt_toolkit-3.0.43 | hd3eb1b0_0 5 KB
> psutil-5.9.0 | py311h5eee18b_0 463 KB
> ptyprocess-0.7.0 | pyhd3eb1b0_2 17 KB
> pure_eval-0.2.2 | pyhd3eb1b0_0 14 KB
> py-lief-0.12.3 | py311h6a678d5_0 1.3 MB
> pygments-2.15.1 | py311h06a4308_1 2.1 MB
> pytest-7.4.0 | py311h06a4308_0 711 KB
> python-dateutil-2.8.2 | pyhd3eb1b0_0 233 KB
> python-fastjsonschema-2.16.2| py311h06a4308_0 247 KB
> python-json-logger-2.0.7 | py311h06a4308_0 18 KB
> python-libarchive-c-2.9 | pyhd3eb1b0_1 47 KB
> pytz-2023.3.post1 | py311h06a4308_0 216 KB
> pyyaml-6.0.1 | py311h5eee18b_0 210 KB
> pyzmq-25.1.2 | py311h6a678d5_0 540 KB
> referencing-0.30.2 | py311h06a4308_0 77 KB
> rfc3339-validator-0.1.4 | py311h06a4308_0 10 KB
> rfc3986-validator-0.1.1 | py311h06a4308_0 10 KB
> rpds-py-0.10.6 | py311hb02cf49_0 1007 KB
> scipy-1.11.4 | py311h24aa872_0 21.9 MB
> send2trash-1.8.2 | py311h06a4308_0 32 KB
> six-1.16.0 | pyhd3eb1b0_1 18 KB
> sniffio-1.3.0 | py311h06a4308_0 17 KB
> soupsieve-2.5 | py311h06a4308_0 92 KB
> stack_data-0.2.0 | pyhd3eb1b0_0 22 KB
> terminado-0.17.1 | py311h06a4308_0 37 KB
> tinycss2-1.2.1 | py311h06a4308_0 46 KB
> tornado-6.3.3 | py311h5eee18b_0 852 KB
> traitlets-5.7.1 | py311h06a4308_0 259 KB
> typing-extensions-4.9.0 | py311h06a4308_1 9 KB
> typing_extensions-4.9.0 | py311h06a4308_1 72 KB
> wcwidth-0.2.5 | pyhd3eb1b0_0 26 KB
> webencodings-0.5.1 | py311h06a4308_1 25 KB
> websocket-client-0.58.0 | py311h06a4308_4 87 KB
> yaml-0.2.5 | h7b6447c_0 75 KB
> zeromq-4.3.5 | h6a678d5_0 366 KB
> ------------------------------------------------------------
> Total: 77.0 MB
>
> The following NEW packages will be INSTALLED:
>
> anyio pkgs/main/linux-64::anyio-4.2.0-py311h06a4308_0
> argon2-cffi pkgs/main/noarch::argon2-cffi-21.3.0-pyhd3eb1b0_0
> argon2-cffi-bindi~
> pkgs/main/linux-64::argon2-cffi-bindings-21.2.0-py311h5eee18b_0
> asttokens pkgs/main/noarch::asttokens-2.0.5-pyhd3eb1b0_0
> async-lru pkgs/main/linux-64::async-lru-2.0.4-py311h06a4308_0
> attrs pkgs/main/linux-64::attrs-23.1.0-py311h06a4308_0
> babel pkgs/main/linux-64::babel-2.11.0-py311h06a4308_0
> beautifulsoup4
> pkgs/main/linux-64::beautifulsoup4-4.12.2-py311h06a4308_0
> bleach pkgs/main/noarch::bleach-4.1.0-pyhd3eb1b0_0
> chardet pkgs/main/linux-64::chardet-4.0.0-py311h06a4308_1003
> click pkgs/main/linux-64::click-8.1.7-py311h06a4308_0
> comm pkgs/main/linux-64::comm-0.1.2-py311h06a4308_0
> conda-build pkgs/main/linux-64::conda-build-24.1.0-py311h06a4308_0
> conda-index pkgs/main/noarch::conda-index-0.4.0-pyhd3eb1b0_0
> cython pkgs/main/linux-64::cython-0.29.36-py311h5eee18b_0
> debugpy pkgs/main/linux-64::debugpy-1.6.7-py311h6a678d5_0
> decorator pkgs/main/noarch::decorator-5.1.1-pyhd3eb1b0_0
> defusedxml pkgs/main/noarch::defusedxml-0.7.1-pyhd3eb1b0_0
> executing pkgs/main/noarch::executing-0.8.3-pyhd3eb1b0_0
> filelock pkgs/main/linux-64::filelock-3.13.1-py311h06a4308_0
> iniconfig pkgs/main/noarch::iniconfig-1.1.1-pyhd3eb1b0_0
> ipykernel pkgs/main/linux-64::ipykernel-6.28.0-py311h06a4308_0
> ipython pkgs/main/linux-64::ipython-8.20.0-py311h06a4308_0
> jedi pkgs/main/linux-64::jedi-0.18.1-py311h06a4308_1
> jinja2 pkgs/main/linux-64::jinja2-3.1.3-py311h06a4308_0
> json5 pkgs/main/noarch::json5-0.9.6-pyhd3eb1b0_0
> jsonschema pkgs/main/linux-64::jsonschema-4.19.2-py311h06a4308_0
> jsonschema-specif~
> pkgs/main/linux-64::jsonschema-specifications-2023.7.1-py311h06a4308_0
> jupyter-lsp pkgs/main/linux-64::jupyter-lsp-2.2.0-py311h06a4308_0
> jupyter_client
> pkgs/main/linux-64::jupyter_client-8.6.0-py311h06a4308_0
> jupyter_core pkgs/main/linux-64::jupyter_core-5.5.0-py311h06a4308_0
> jupyter_events
> pkgs/main/linux-64::jupyter_events-0.8.0-py311h06a4308_0
> jupyter_server
> pkgs/main/linux-64::jupyter_server-2.10.0-py311h06a4308_0
> jupyter_server_te~
> pkgs/main/linux-64::jupyter_server_terminals-0.4.4-py311h06a4308_1
> jupyterlab pkgs/main/linux-64::jupyterlab-4.0.11-py311h06a4308_0
> jupyterlab_pygmen~ pkgs/main/noarch::jupyterlab_pygments-0.1.2-py_0
> jupyterlab_server
> pkgs/main/linux-64::jupyterlab_server-2.25.1-py311h06a4308_0
> libgfortran-ng pkgs/main/linux-64::libgfortran-ng-11.2.0-h00389a5_1
> libgfortran5 pkgs/main/linux-64::libgfortran5-11.2.0-h1234567_1
> liblief pkgs/main/linux-64::liblief-0.12.3-h6a678d5_0
> libopenblas pkgs/main/linux-64::libopenblas-0.3.21-h043d6bf_0
> libsodium pkgs/main/linux-64::libsodium-1.0.18-h7b6447c_0
> markupsafe pkgs/main/linux-64::markupsafe-2.1.3-py311h5eee18b_0
> matplotlib-inline
> pkgs/main/linux-64::matplotlib-inline-0.1.6-py311h06a4308_0
> mistune pkgs/main/linux-64::mistune-2.0.4-py311h06a4308_0
> more-itertools
> pkgs/main/linux-64::more-itertools-10.1.0-py311h06a4308_0
> nbclient pkgs/main/linux-64::nbclient-0.8.0-py311h06a4308_0
> nbconvert pkgs/main/linux-64::nbconvert-7.10.0-py311h06a4308_0
> nbformat pkgs/main/linux-64::nbformat-5.9.2-py311h06a4308_0
> nest-asyncio pkgs/main/linux-64::nest-asyncio-1.5.6-py311h06a4308_0
> notebook pkgs/main/linux-64::notebook-7.0.6-py311h06a4308_0
> notebook-shim
> pkgs/main/linux-64::notebook-shim-0.2.3-py311h06a4308_0
> numpy pkgs/main/linux-64::numpy-1.26.3-py311h24aa872_0
> numpy-base pkgs/main/linux-64::numpy-base-1.26.3-py311hbfb1bba_0
> overrides pkgs/main/linux-64::overrides-7.4.0-py311h06a4308_0
> pandocfilters pkgs/main/noarch::pandocfilters-1.5.0-pyhd3eb1b0_0
> parso pkgs/main/noarch::parso-0.8.3-pyhd3eb1b0_0
> patch pkgs/main/linux-64::patch-2.7.6-h7b6447c_1001
> patchelf pkgs/main/linux-64::patchelf-0.17.2-h6a678d5_0
> pexpect pkgs/main/noarch::pexpect-4.8.0-pyhd3eb1b0_3
> pkginfo pkgs/main/linux-64::pkginfo-1.9.6-py311h06a4308_0
> prometheus_client
> pkgs/main/linux-64::prometheus_client-0.14.1-py311h06a4308_0
> prompt-toolkit
> pkgs/main/linux-64::prompt-toolkit-3.0.43-py311h06a4308_0
> prompt_toolkit pkgs/main/noarch::prompt_toolkit-3.0.43-hd3eb1b0_0
> psutil pkgs/main/linux-64::psutil-5.9.0-py311h5eee18b_0
> ptyprocess pkgs/main/noarch::ptyprocess-0.7.0-pyhd3eb1b0_2
> pure_eval pkgs/main/noarch::pure_eval-0.2.2-pyhd3eb1b0_0
> py-lief pkgs/main/linux-64::py-lief-0.12.3-py311h6a678d5_0
> pygments pkgs/main/linux-64::pygments-2.15.1-py311h06a4308_1
> pytest pkgs/main/linux-64::pytest-7.4.0-py311h06a4308_0
> python-dateutil pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0
> python-fastjsonsc~
> pkgs/main/linux-64::python-fastjsonschema-2.16.2-py311h06a4308_0
> python-json-logger
> pkgs/main/linux-64::python-json-logger-2.0.7-py311h06a4308_0
> python-libarchive~ pkgs/main/noarch::python-libarchive-c-2.9-pyhd3eb1b0_1
> pytz pkgs/main/linux-64::pytz-2023.3.post1-py311h06a4308_0
> pyyaml pkgs/main/linux-64::pyyaml-6.0.1-py311h5eee18b_0
> pyzmq pkgs/main/linux-64::pyzmq-25.1.2-py311h6a678d5_0
> referencing pkgs/main/linux-64::referencing-0.30.2-py311h06a4308_0
> rfc3339-validator
> pkgs/main/linux-64::rfc3339-validator-0.1.4-py311h06a4308_0
> rfc3986-validator
> pkgs/main/linux-64::rfc3986-validator-0.1.1-py311h06a4308_0
> rpds-py pkgs/main/linux-64::rpds-py-0.10.6-py311hb02cf49_0
> scipy pkgs/main/linux-64::scipy-1.11.4-py311h24aa872_0
> send2trash pkgs/main/linux-64::send2trash-1.8.2-py311h06a4308_0
> six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
> sniffio pkgs/main/linux-64::sniffio-1.3.0-py311h06a4308_0
> soupsieve pkgs/main/linux-64::soupsieve-2.5-py311h06a4308_0
> stack_data pkgs/main/noarch::stack_data-0.2.0-pyhd3eb1b0_0
> terminado pkgs/main/linux-64::terminado-0.17.1-py311h06a4308_0
> tinycss2 pkgs/main/linux-64::tinycss2-1.2.1-py311h06a4308_0
> tornado pkgs/main/linux-64::tornado-6.3.3-py311h5eee18b_0
> traitlets pkgs/main/linux-64::traitlets-5.7.1-py311h06a4308_0
> typing-extensions
> pkgs/main/linux-64::typing-extensions-4.9.0-py311h06a4308_1
> typing_extensions
> pkgs/main/linux-64::typing_extensions-4.9.0-py311h06a4308_1
> wcwidth pkgs/main/noarch::wcwidth-0.2.5-pyhd3eb1b0_0
> webencodings pkgs/main/linux-64::webencodings-0.5.1-py311h06a4308_1
> websocket-client
> pkgs/main/linux-64::websocket-client-0.58.0-py311h06a4308_4
> yaml pkgs/main/linux-64::yaml-0.2.5-h7b6447c_0
> zeromq pkgs/main/linux-64::zeromq-4.3.5-h6a678d5_0
>
>
> Preparing transaction: ...working... done
> Verifying transaction: ...working... done
> Executing transaction: ...working... done
> Collecting matplotlib
> Downloading
> matplotlib-3.8.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
> (5.8 kB)
> Collecting contourpy>=1.0.1 (from matplotlib)
> Downloading
> contourpy-1.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
> (5.8 kB)
> Collecting cycler>=0.10 (from matplotlib)
> Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
> Collecting fonttools>=4.22.0 (from matplotlib)
> Downloading
> fonttools-4.47.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
> (157 kB)
> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 157.6/157.6 kB 828.8 kB/s
> eta 0:00:00
> Collecting kiwisolver>=1.3.1 (from matplotlib)
> Downloading
> kiwisolver-1.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
> (6.4 kB)
> Requirement already satisfied: numpy<2,>=1.21 in
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages
> (from matplotlib) (1.26.3)
> Requirement already satisfied: packaging>=20.0 in
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages
> (from matplotlib) (23.1)
> Collecting pillow>=8 (from matplotlib)
> Downloading pillow-10.2.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata
> (9.7 kB)
> Collecting pyparsing>=2.3.1 (from matplotlib)
> Downloading pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB)
> Requirement already satisfied: python-dateutil>=2.7 in
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages
> (from matplotlib) (2.8.2)
> Requirement already satisfied: six>=1.5 in
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install/lib/python3.11/site-packages
> (from python-dateutil>=2.7->matplotlib) (1.16.0)
> Downloading
> matplotlib-3.8.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> (11.6 MB)
> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 25.2 MB/s eta
> 0:00:00
> Downloading
> contourpy-1.2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> (313 kB)
> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 313.4/313.4 kB 5.3 MB/s eta
> 0:00:00
> Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB)
> Downloading
> fonttools-4.47.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> (4.9 MB)
> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 20.7 MB/s eta
> 0:00:00
> Downloading
> kiwisolver-1.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
> (1.4 MB)
> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.4/1.4 MB 17.5 MB/s eta
> 0:00:00
> Downloading pillow-10.2.0-cp311-cp311-manylinux_2_28_x86_64.whl (4.5 MB)
> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 23.4 MB/s eta
> 0:00:00
> Downloading pyparsing-3.1.1-py3-none-any.whl (103 kB)
> ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.1/103.1 kB 1.4 MB/s eta
> 0:00:00
> Installing collected packages: pyparsing, pillow, kiwisolver, fonttools,
> cycler, contourpy, matplotlib
> Successfully installed contourpy-1.2.0 cycler-0.12.1 fonttools-4.47.2
> kiwisolver-1.4.5 matplotlib-3.8.2 pillow-10.2.0 pyparsing-3.1.1
> Will remove 174 (182.3 MB) tarball(s).
> Will remove 1 index cache(s).
> Will remove 11 (19.2 MB) package(s).
> There are no tempfile(s) to remove.
> There are no logfile(s) to remove.
> -- Miniconda install successful!
> -- Found PythonLibs:
> /home/enz/shokhen/localdisk/amber20_src/build/CMakeFiles/miniconda/install/lib/
> libpython3.11.so (found version "3.11.5")
> -- Checking for Python package numpy -- found
> -- Checking for Python package scipy -- found
> -- Checking for Python package matplotlib -- found
> -- Checking for Python package setuptools -- found
> -- Checking for Python package tkinter -- found
> -- Checking for Python package distutils.sysconfig -- found
> CMake Error at cmake/PythonBuildConfig.cmake:129 (message):
> Failed to determine relative PYTHONPATH: python command failed with error
> Traceback (most recent call last):
>
> File "<string>", line 1, in <module>
>
> KeyError: 'unix_prefix'
>
> Call Stack (most recent call first):
> CMakeLists.txt:122 (include)
>
>
> -- Configuring incomplete, errors occurred!
>
> If the cmake build report looks OK, you should now do the following:
>
> make install
> source /home/enz/shokhen/localdisk/amber20/amber.sh
>
> Consider adding the last line to your login startup script, e.g. ~/.bashrc
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Feb 07 2024 - 10:00:02 PST
