(base) lcmvar@lcmvar-System-Version:~/SOFT/amber22_src/build$ ./run_cmake -- ************************************************************************** -- Starting configuration of Amber version 22.0.0... -- CMake Version: 3.27.4 -- 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 10.5.0 -- The CXX compiler identification is GNU 10.5.0 -- The Fortran compiler identification is GNU 10.5.0 -- 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 CMake Warning (dev) at cmake/CudaConfig.cmake:11 (find_package): Policy CMP0146 is not set: The FindCUDA module is removed. Run "cmake --help-policy CMP0146" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:119 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found CUDA: /usr (found version "12.0") -- 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/lcmvar/SOFT/amber22_src/build/CMakeFiles/miniconda/download/Miniconda3-latest-Linux-x86_64.sh #################################################################################### 100.0% Installing Miniconda Python. PREFIX=/home/lcmvar/SOFT/amber22_src/build/CMakeFiles/miniconda/install Unpacking payload ... 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environment... Downloading and Extracting Packages: ...working... done Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Executing transaction: ...working... done installation finished. WARNING: You currently have a PYTHONPATH environment variable set. This may cause unexpected behavior when running the Python interpreter in Miniconda3. For best results, please verify that your PYTHONPATH only points to directories of packages that are compatible with the Python interpreter in Miniconda3: /home/lcmvar/SOFT/amber22_src/build/CMakeFiles/miniconda/install -- 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/lcmvar/SOFT/amber22_src/build/CMakeFiles/miniconda/install added / updated specs: - conda The following packages will be downloaded: package | build ---------------------------|----------------- archspec-0.2.3 | pyhd3eb1b0_0 47 KB ca-certificates-2024.3.11 | h06a4308_0 127 KB conda-24.3.0 | py312h06a4308_0 1.2 MB ------------------------------------------------------------ Total: 1.4 MB The following packages will be UPDATED: archspec 0.2.1-pyhd3eb1b0_0 --> 0.2.3-pyhd3eb1b0_0 ca-certificates 2023.12.12-h06a4308_0 --> 2024.3.11-h06a4308_0 conda 24.1.2-py312h06a4308_0 --> 24.3.0-py312h06a4308_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Requirement already satisfied: pip in ./CMakeFiles/miniconda/install/lib/python3.12/site-packages (23.3.1) Collecting pip Downloading pip-24.0-py3-none-any.whl.metadata (3.6 kB) Downloading pip-24.0-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 1.5 MB/s eta 0:00:00 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-24.0 Channels: - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/lcmvar/SOFT/amber22_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: - conda-forge - defaults Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/lcmvar/SOFT/amber22_src/build/CMakeFiles/miniconda/install added / updated specs: - f90nml The following packages will be downloaded: package | build ---------------------------|----------------- _libgcc_mutex-0.1 | conda_forge 3 KB conda-forge _openmp_mutex-4.5 | 2_gnu 23 KB conda-forge certifi-2024.2.2 | pyhd8ed1ab_0 157 KB conda-forge f90nml-1.4.4 | pyhd8ed1ab_0 33 KB conda-forge libgcc-ng-13.2.0 | h807b86a_5 752 KB conda-forge libgomp-13.2.0 | h807b86a_5 410 KB conda-forge openssl-3.2.1 | hd590300_1 2.7 MB conda-forge ------------------------------------------------------------ Total: 4.1 MB The following NEW packages will be INSTALLED: f90nml conda-forge/noarch::f90nml-1.4.4-pyhd8ed1ab_0 The following packages will be UPDATED: libgcc-ng pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-13.2.0-h807b86a_5 libgomp pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-13.2.0-h807b86a_5 openssl pkgs/main::openssl-3.0.13-h7f8727e_0 --> conda-forge::openssl-3.2.1-hd590300_1 The following packages will be SUPERSEDED by a higher-priority channel: _libgcc_mutex pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge _openmp_mutex pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_gnu certifi pkgs/main/linux-64::certifi-2024.2.2-~ --> conda-forge/noarch::certifi-2024.2.2-pyhd8ed1ab_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - defaults - conda-forge Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/lcmvar/SOFT/amber22_src/build/CMakeFiles/miniconda/install added / updated specs: - pandas The following packages will be downloaded: package | build ---------------------------|----------------- bottleneck-1.3.7 | py312ha883a20_0 140 KB libgfortran-ng-11.2.0 | h00389a5_1 20 KB libgfortran5-11.2.0 | h1234567_1 2.0 MB libopenblas-0.3.21 | h043d6bf_0 5.4 MB numexpr-2.8.7 | py312he7dcb8a_0 149 KB numpy-1.26.4 | py312h2809609_0 10 KB numpy-base-1.26.4 | py312he1a6c75_0 7.7 MB pandas-2.2.1 | py312h526ad5a_0 15.4 MB python-dateutil-2.8.2 | pyhd3eb1b0_0 233 KB python-tzdata-2023.3 | pyhd3eb1b0_0 140 KB pytz-2023.3.post1 | py312h06a4308_0 197 KB six-1.16.0 | pyhd3eb1b0_1 18 KB ------------------------------------------------------------ Total: 31.4 MB The following NEW packages will be INSTALLED: bottleneck pkgs/main/linux-64::bottleneck-1.3.7-py312ha883a20_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 libopenblas pkgs/main/linux-64::libopenblas-0.3.21-h043d6bf_0 numexpr pkgs/main/linux-64::numexpr-2.8.7-py312he7dcb8a_0 numpy pkgs/main/linux-64::numpy-1.26.4-py312h2809609_0 numpy-base pkgs/main/linux-64::numpy-base-1.26.4-py312he1a6c75_0 pandas pkgs/main/linux-64::pandas-2.2.1-py312h526ad5a_0 python-dateutil pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0 python-tzdata pkgs/main/noarch::python-tzdata-2023.3-pyhd3eb1b0_0 pytz pkgs/main/linux-64::pytz-2023.3.post1-py312h06a4308_0 six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1 The following packages will be SUPERSEDED by a higher-priority channel: certifi conda-forge/noarch::certifi-2024.2.2-~ --> pkgs/main/linux-64::certifi-2024.2.2-py312h06a4308_0 Downloading and Extracting Packages: ...working... done Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Channels: - defaults - conda-forge Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/lcmvar/SOFT/amber22_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 | py312h06a4308_0 238 KB argon2-cffi-21.3.0 | pyhd3eb1b0_0 15 KB argon2-cffi-bindings-21.2.0| py312h5eee18b_0 33 KB asttokens-2.0.5 | pyhd3eb1b0_0 20 KB async-lru-2.0.4 | py312h06a4308_0 20 KB attrs-23.1.0 | py312h06a4308_0 153 KB babel-2.11.0 | py312h06a4308_0 6.1 MB beautifulsoup4-4.12.2 | py312h06a4308_0 251 KB bleach-4.1.0 | pyhd3eb1b0_0 123 KB chardet-4.0.0 |py312h06a4308_1003 217 KB click-8.1.7 | py312h06a4308_0 203 KB comm-0.2.1 | py312h06a4308_0 16 KB conda-build-24.3.0 | py312h06a4308_0 758 KB conda-index-0.4.0 | pyhd3eb1b0_0 173 KB cython-0.29.36 | py312h5eee18b_0 2.3 MB debugpy-1.6.7 | py312h6a678d5_0 2.0 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 | py312h06a4308_0 24 KB iniconfig-1.1.1 | pyhd3eb1b0_0 8 KB ipykernel-6.28.0 | py312h06a4308_0 241 KB ipython-8.20.0 | py312h06a4308_0 1.4 MB jedi-0.18.1 | py312h06a4308_1 1.1 MB jinja2-3.1.3 | py312h06a4308_0 330 KB json5-0.9.6 | pyhd3eb1b0_0 21 KB jsonschema-4.19.2 | py312h06a4308_0 177 KB jsonschema-specifications-2023.7.1| py312h06a4308_0 15 KB jupyter-lsp-2.2.0 | py312h06a4308_0 100 KB jupyter_client-8.6.0 | py312h06a4308_0 221 KB jupyter_core-5.5.0 | py312h06a4308_0 87 KB jupyter_events-0.8.0 | py312h06a4308_0 40 KB jupyter_server-2.10.0 | py312h06a4308_0 540 KB jupyter_server_terminals-0.4.4| py312h06a4308_1 27 KB jupyterlab-4.0.11 | py312h06a4308_0 4.3 MB jupyterlab_pygments-0.1.2 | py_0 8 KB jupyterlab_server-2.25.1 | py312h06a4308_0 104 KB liblief-0.12.3 | h6a678d5_0 1.9 MB libsodium-1.0.18 | h7b6447c_0 244 KB markupsafe-2.1.3 | py312h5eee18b_0 25 KB matplotlib-inline-0.1.6 | py312h06a4308_0 18 KB mistune-2.0.4 | py312h06a4308_0 105 KB more-itertools-10.1.0 | py312h06a4308_0 96 KB nbclient-0.8.0 | py312h06a4308_0 110 KB nbconvert-7.10.0 | py312h06a4308_0 486 KB nbformat-5.9.2 | py312h06a4308_0 149 KB nest-asyncio-1.6.0 | py312h06a4308_0 16 KB notebook-7.0.8 | py312h06a4308_0 3.0 MB notebook-shim-0.2.3 | py312h06a4308_0 25 KB overrides-7.4.0 | py312h06a4308_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 | py312h06a4308_0 58 KB prometheus_client-0.14.1 | py312h06a4308_0 117 KB prompt-toolkit-3.0.43 | py312h06a4308_0 732 KB prompt_toolkit-3.0.43 | hd3eb1b0_0 5 KB psutil-5.9.0 | py312h5eee18b_0 449 KB ptyprocess-0.7.0 | pyhd3eb1b0_2 17 KB pure_eval-0.2.2 | pyhd3eb1b0_0 14 KB py-lief-0.12.3 | py312h6a678d5_0 1.3 MB pygments-2.15.1 | py312h06a4308_1 1.7 MB pytest-7.4.0 | py312h06a4308_0 645 KB python-fastjsonschema-2.16.2| py312h06a4308_0 244 KB python-json-logger-2.0.7 | py312h06a4308_0 17 KB python-libarchive-c-2.9 | pyhd3eb1b0_1 47 KB pyyaml-6.0.1 | py312h5eee18b_0 186 KB pyzmq-25.1.2 | py312h6a678d5_0 533 KB referencing-0.30.2 | py312h06a4308_0 73 KB rfc3339-validator-0.1.4 | py312h06a4308_0 9 KB rfc3986-validator-0.1.1 | py312h06a4308_0 9 KB rpds-py-0.10.6 | py312hb02cf49_0 921 KB scipy-1.12.0 | py312h2809609_0 23.3 MB send2trash-1.8.2 | py312h06a4308_0 31 KB sniffio-1.3.0 | py312h06a4308_0 16 KB soupsieve-2.5 | py312h06a4308_0 84 KB stack_data-0.2.0 | pyhd3eb1b0_0 22 KB terminado-0.17.1 | py312h06a4308_0 38 KB tinycss2-1.2.1 | py312h06a4308_0 44 KB tornado-6.3.3 | py312h5eee18b_0 787 KB traitlets-5.7.1 | py312h06a4308_0 254 KB typing-extensions-4.9.0 | py312h06a4308_1 9 KB typing_extensions-4.9.0 | py312h06a4308_1 68 KB wcwidth-0.2.5 | pyhd3eb1b0_0 26 KB webencodings-0.5.1 | py312h06a4308_2 25 KB websocket-client-0.58.0 | py312h06a4308_4 83 KB yaml-0.2.5 | h7b6447c_0 75 KB zeromq-4.3.5 | h6a678d5_0 366 KB ------------------------------------------------------------ Total: 60.1 MB The following NEW packages will be INSTALLED: anyio pkgs/main/linux-64::anyio-4.2.0-py312h06a4308_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-py312h5eee18b_0 asttokens pkgs/main/noarch::asttokens-2.0.5-pyhd3eb1b0_0 async-lru pkgs/main/linux-64::async-lru-2.0.4-py312h06a4308_0 attrs pkgs/main/linux-64::attrs-23.1.0-py312h06a4308_0 babel pkgs/main/linux-64::babel-2.11.0-py312h06a4308_0 beautifulsoup4 pkgs/main/linux-64::beautifulsoup4-4.12.2-py312h06a4308_0 bleach pkgs/main/noarch::bleach-4.1.0-pyhd3eb1b0_0 chardet pkgs/main/linux-64::chardet-4.0.0-py312h06a4308_1003 click pkgs/main/linux-64::click-8.1.7-py312h06a4308_0 comm pkgs/main/linux-64::comm-0.2.1-py312h06a4308_0 conda-build pkgs/main/linux-64::conda-build-24.3.0-py312h06a4308_0 conda-index pkgs/main/noarch::conda-index-0.4.0-pyhd3eb1b0_0 cython pkgs/main/linux-64::cython-0.29.36-py312h5eee18b_0 debugpy pkgs/main/linux-64::debugpy-1.6.7-py312h6a678d5_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-py312h06a4308_0 iniconfig pkgs/main/noarch::iniconfig-1.1.1-pyhd3eb1b0_0 ipykernel pkgs/main/linux-64::ipykernel-6.28.0-py312h06a4308_0 ipython pkgs/main/linux-64::ipython-8.20.0-py312h06a4308_0 jedi pkgs/main/linux-64::jedi-0.18.1-py312h06a4308_1 jinja2 pkgs/main/linux-64::jinja2-3.1.3-py312h06a4308_0 json5 pkgs/main/noarch::json5-0.9.6-pyhd3eb1b0_0 jsonschema pkgs/main/linux-64::jsonschema-4.19.2-py312h06a4308_0 jsonschema-specif~ pkgs/main/linux-64::jsonschema-specifications-2023.7.1-py312h06a4308_0 jupyter-lsp pkgs/main/linux-64::jupyter-lsp-2.2.0-py312h06a4308_0 jupyter_client pkgs/main/linux-64::jupyter_client-8.6.0-py312h06a4308_0 jupyter_core pkgs/main/linux-64::jupyter_core-5.5.0-py312h06a4308_0 jupyter_events pkgs/main/linux-64::jupyter_events-0.8.0-py312h06a4308_0 jupyter_server pkgs/main/linux-64::jupyter_server-2.10.0-py312h06a4308_0 jupyter_server_te~ pkgs/main/linux-64::jupyter_server_terminals-0.4.4-py312h06a4308_1 jupyterlab pkgs/main/linux-64::jupyterlab-4.0.11-py312h06a4308_0 jupyterlab_pygmen~ pkgs/main/noarch::jupyterlab_pygments-0.1.2-py_0 jupyterlab_server pkgs/main/linux-64::jupyterlab_server-2.25.1-py312h06a4308_0 liblief pkgs/main/linux-64::liblief-0.12.3-h6a678d5_0 libsodium pkgs/main/linux-64::libsodium-1.0.18-h7b6447c_0 markupsafe pkgs/main/linux-64::markupsafe-2.1.3-py312h5eee18b_0 matplotlib-inline pkgs/main/linux-64::matplotlib-inline-0.1.6-py312h06a4308_0 mistune pkgs/main/linux-64::mistune-2.0.4-py312h06a4308_0 more-itertools pkgs/main/linux-64::more-itertools-10.1.0-py312h06a4308_0 nbclient pkgs/main/linux-64::nbclient-0.8.0-py312h06a4308_0 nbconvert pkgs/main/linux-64::nbconvert-7.10.0-py312h06a4308_0 nbformat pkgs/main/linux-64::nbformat-5.9.2-py312h06a4308_0 nest-asyncio pkgs/main/linux-64::nest-asyncio-1.6.0-py312h06a4308_0 notebook pkgs/main/linux-64::notebook-7.0.8-py312h06a4308_0 notebook-shim pkgs/main/linux-64::notebook-shim-0.2.3-py312h06a4308_0 overrides pkgs/main/linux-64::overrides-7.4.0-py312h06a4308_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-py312h06a4308_0 prometheus_client pkgs/main/linux-64::prometheus_client-0.14.1-py312h06a4308_0 prompt-toolkit pkgs/main/linux-64::prompt-toolkit-3.0.43-py312h06a4308_0 prompt_toolkit pkgs/main/noarch::prompt_toolkit-3.0.43-hd3eb1b0_0 psutil pkgs/main/linux-64::psutil-5.9.0-py312h5eee18b_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-py312h6a678d5_0 pygments pkgs/main/linux-64::pygments-2.15.1-py312h06a4308_1 pytest pkgs/main/linux-64::pytest-7.4.0-py312h06a4308_0 python-fastjsonsc~ pkgs/main/linux-64::python-fastjsonschema-2.16.2-py312h06a4308_0 python-json-logger pkgs/main/linux-64::python-json-logger-2.0.7-py312h06a4308_0 python-libarchive~ pkgs/main/noarch::python-libarchive-c-2.9-pyhd3eb1b0_1 pyyaml pkgs/main/linux-64::pyyaml-6.0.1-py312h5eee18b_0 pyzmq pkgs/main/linux-64::pyzmq-25.1.2-py312h6a678d5_0 referencing pkgs/main/linux-64::referencing-0.30.2-py312h06a4308_0 rfc3339-validator pkgs/main/linux-64::rfc3339-validator-0.1.4-py312h06a4308_0 rfc3986-validator pkgs/main/linux-64::rfc3986-validator-0.1.1-py312h06a4308_0 rpds-py pkgs/main/linux-64::rpds-py-0.10.6-py312hb02cf49_0 scipy pkgs/main/linux-64::scipy-1.12.0-py312h2809609_0 send2trash pkgs/main/linux-64::send2trash-1.8.2-py312h06a4308_0 sniffio pkgs/main/linux-64::sniffio-1.3.0-py312h06a4308_0 soupsieve pkgs/main/linux-64::soupsieve-2.5-py312h06a4308_0 stack_data pkgs/main/noarch::stack_data-0.2.0-pyhd3eb1b0_0 terminado pkgs/main/linux-64::terminado-0.17.1-py312h06a4308_0 tinycss2 pkgs/main/linux-64::tinycss2-1.2.1-py312h06a4308_0 tornado pkgs/main/linux-64::tornado-6.3.3-py312h5eee18b_0 traitlets pkgs/main/linux-64::traitlets-5.7.1-py312h06a4308_0 typing-extensions pkgs/main/linux-64::typing-extensions-4.9.0-py312h06a4308_1 typing_extensions pkgs/main/linux-64::typing_extensions-4.9.0-py312h06a4308_1 wcwidth pkgs/main/noarch::wcwidth-0.2.5-pyhd3eb1b0_0 webencodings pkgs/main/linux-64::webencodings-0.5.1-py312h06a4308_2 websocket-client pkgs/main/linux-64::websocket-client-0.58.0-py312h06a4308_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-3.8.3-cp312-cp312-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-cp312-cp312-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-4.50.0-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (159 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 159.4/159.4 kB 811.5 kB/s eta 0:00:00 Collecting kiwisolver>=1.3.1 (from matplotlib) Downloading kiwisolver-1.4.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB) Requirement already satisfied: numpy<2,>=1.21 in ./CMakeFiles/miniconda/install/lib/python3.12/site-packages (from matplotlib) (1.26.4) Requirement already satisfied: packaging>=20.0 in ./CMakeFiles/miniconda/install/lib/python3.12/site-packages (from matplotlib) (23.1) Collecting pillow>=8 (from matplotlib) Downloading pillow-10.2.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (9.7 kB) Collecting pyparsing>=2.3.1 (from matplotlib) Downloading pyparsing-3.1.2-py3-none-any.whl.metadata (5.1 kB) Requirement already satisfied: python-dateutil>=2.7 in ./CMakeFiles/miniconda/install/lib/python3.12/site-packages (from matplotlib) (2.8.2) Requirement already satisfied: six>=1.5 in ./CMakeFiles/miniconda/install/lib/python3.12/site-packages (from python-dateutil>=2.7->matplotlib) (1.16.0) Downloading matplotlib-3.8.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.6/11.6 MB 407.2 kB/s eta 0:00:00 Downloading contourpy-1.2.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (303 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 303.9/303.9 kB 732.3 kB/s eta 0:00:00 Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB) Downloading fonttools-4.50.0-cp312-cp312-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.9 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.9/4.9 MB 1.2 MB/s eta 0:00:00 Downloading kiwisolver-1.4.5-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.5/1.5 MB 331.4 kB/s eta 0:00:00 Downloading pillow-10.2.0-cp312-cp312-manylinux_2_28_x86_64.whl (4.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 1.4 MB/s eta 0:00:00 Downloading pyparsing-3.1.2-py3-none-any.whl (103 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.2/103.2 kB 598.1 kB/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-4.50.0 kiwisolver-1.4.5 matplotlib-3.8.3 pillow-10.2.0 pyparsing-3.1.2 Will remove 187 (202.7 MB) tarball(s). Will remove 1 index cache(s). Will remove 19 (63.4 MB) package(s). There are no tempfile(s) to remove. There are no logfile(s) to remove. -- Miniconda install successful! CMake Warning (dev) at cmake/PythonBuildConfig.cmake:13 (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): CMakeLists.txt:121 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonLibs: /home/lcmvar/SOFT/amber22_src/build/CMakeFiles/miniconda/install/lib/libpython3.12.so (found version "3.12.1") -- 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 -- Python relative site-packages location: /lib/python3.12/site-packages -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Found BISON: /usr/bin/bison (found version "3.8.2") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Found Perl: /usr/bin/perl (found version "5.36.0") -- Found perl make: /usr/bin/make -- Perl modules well be installed to AMBERHOME/lib/perl -- Running updater... /home/lcmvar/SOFT/amber22_src/updateutils/patch.py:135: SyntaxWarning: invalid escape sequence '\d' delfile = re.compile('deleted file mode (\d{3})+') -- >>> Preparing to apply updates... please wait. -- >>> Downloading updates for AmberTools 23 -- >>> Downloading AmberTools 23/update.1 (1.82 KB) -- >>> Applying AmberTools 23/update.1 -- >>> Downloading AmberTools 23/update.2 (431.73 KB) -- >>> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0% Done. -- >>> Applying AmberTools 23/update.2 -- >>> Downloading AmberTools 23/update.3 (9.18 MB) -- >>> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0% Done. -- >>> Applying AmberTools 23/update.3 -- >>> Downloading AmberTools 23/update.4 (20.03 KB) -- >>> Applying AmberTools 23/update.4 -- >>> Downloading AmberTools 23/update.5 (2.11 MB) -- >>> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0% Done. -- >>> Applying AmberTools 23/update.5 -- >>> Downloading AmberTools 23/update.6 (23.77 KB) -- >>> Applying AmberTools 23/update.6 -- >>> Downloading updates for Amber 22 -- >>> Downloading Amber 22/update.1 (1.94 KB) -- >>> Applying Amber 22/update.1 -- >>> Downloading Amber 22/update.2 (10.78 MB) -- >>> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0% Done. -- >>> Applying Amber 22/update.2 -- >>> Downloading Amber 22/update.3 (238.18 KB) -- >>> Downloading: [::::::::::::::::::::::::::::::::::::::::::::::::::] 100.0% Done. -- >>> Applying Amber 22/update.3 -- >>> Downloading Amber 22/update.4 (3.57 KB) -- >>> Applying Amber 22/update.4 -- >>> Downloading Amber 22/update.5 (46.83 KB) -- >>> Applying Amber 22/update.5 -- >>> NOTE: update_amber only updates the raw source code! You must recompile if you want -- >>> any changes to take effect! -- Updater done. If you want to install updates, then set the APPLY_UPDATES variable to true. -- Checking whether to use built-in libraries... -- Looking for complex.h -- Looking for complex.h - found -- Could NOT find Readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY READLINE_WORKS) -- Unable to locate MKL_HOME for your system. To use MKL, set MKL_HOME to point to your MKL installation location. CMake Warning (dev) at /usr/share/cmake-3.27/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (OpenMP_C) does not match the name of the calling package (OpenMPFixed). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args) cmake/hanjianwei/FindMKL.cmake:194 (find_package) cmake/3rdPartyTools.cmake:227 (find_package) CMakeLists.txt:206 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find OpenMP_C (missing: OpenMP_pthread_LIBRARY) (found version "4.5") CMake Warning (dev) at /usr/share/cmake-3.27/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (OpenMP_CXX) does not match the name of the calling package (OpenMPFixed). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args) cmake/hanjianwei/FindMKL.cmake:194 (find_package) cmake/3rdPartyTools.cmake:227 (find_package) CMakeLists.txt:206 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find OpenMP_CXX (missing: OpenMP_pthread_LIBRARY) (found version "4.5") CMake Warning (dev) at /usr/share/cmake-3.27/Modules/FindPackageHandleStandardArgs.cmake:438 (message): The package name passed to `find_package_handle_standard_args` (OpenMP_Fortran) does not match the name of the calling package (OpenMPFixed). This can lead to problems in calling code that expects `find_package` result variables (e.g., `_FOUND`) to follow a certain pattern. Call Stack (most recent call first): cmake/patched-cmake-modules/FindOpenMPFixed.cmake:408 (find_package_handle_standard_args) cmake/hanjianwei/FindMKL.cmake:194 (find_package) cmake/3rdPartyTools.cmake:227 (find_package) CMakeLists.txt:206 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find OpenMP_Fortran (missing: OpenMP_pthread_LIBRARY) (found version "4.5") -- Performing Test SUPPORTS_NO_AS_NEEDED -- Performing Test SUPPORTS_NO_AS_NEEDED - Success -- Performing Test CMath_LINKS_WITHOUT_M -- Performing Test CMath_LINKS_WITHOUT_M - Failed -- Performing Test CMath_LINKS_WITH_M -- Performing Test CMath_LINKS_WITH_M - Success -- Found CMath: /usr/lib/x86_64-linux-gnu/libm.so -- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY OpenMP_C_FOUND MKL_WORKS MKL_FORTRAN_WORKS) -- hints given to look for KMMD in DIR: -- found KMMD?: KMMD_LIB-NOTFOUND -- found INCLUDES?: -- Did not find an external KMMD library, should be able to use bundled. If you have a custom version then set the path with -DKMMD_DIR (missing: KMMD_LIB) -- Cannot search for FFTW Fortran headers because the serial headers were not found -- Could NOT find FFTW (missing: FFTW_LIBRARY_SERIAL FFTW_WORKS FFTW_INCLUDES_SERIAL FFTW_FORTRAN_WORKS) -- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 = NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 = NetCDF_LIBRARIES_F77-NOTFOUND) -- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 = NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 = NetCDF_LIBRARIES_F90-NOTFOUND) -- Could NOT find NetCDF (missing: NetCDF_C_WORKS NetCDF_LIBRARIES NetCDF_INCLUDES) -- Could NOT find Protobuf (missing: Protobuf_LIBRARIES Protobuf_INCLUDE_DIR) -- Could NOT find XBLAS (missing: XBLAS_LIBRARY XBLAS_C_WORKS XBLAS_FORTRAN_WORKS) -- A library with BLAS API not found. Please specify library location. -- LAPACK requires BLAS -- A library with LAPACK API not found. Please specify library location. -- The ARPACK library was not found. Please set ARPACK_LIBRARY to point to it. (missing: ARPACK_LIBRARY ARPACK_WORKS) -- Could not find some or all of the five main APBS libraries. Please set APBS_GENERIC_LIB, APBS_ROUTINES_LIB, APBS_PMGC_LIB, APBS_MG_LIB, APBS_MC_LIB, APBS_FEM_LIB, UMFPACK_LIB, and APBS_MALOC_LIB to point to the correct libraries (missing: APBS_API_LIB APBS_ROUTINES_LIB APBS_MG_LIB APBS_PMGC_LIB APBS_GENERIC_LIB APBS_FEM_LIB APBS_MC_LIB UMFPACK_LIB APBS_MALOC_LIB APBS_WORKS APBS_INCLUDES) -- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 AWT) -- Could NOT find PUPIL (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB JNI_FOUND PUPIL_WORKS) -- Could NOT find LIO (missing: LIO_G2G_LIBRARY LIO_AMBER_LIBRARY LIO_WORKS) -- Could NOT find PLUMED (missing: PLUMED_LIBRARY PLUMED_KERNEL_LIBRARY PLUMED_INCLUDES PLUMED_WORKS) (Required is at least version "2.5") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR) -- Checking for perl module Chemistry::Mol -- Checking for perl module Chemistry::Mol - failed -- Checking for perl module ExtUtils::MakeMaker -- Checking for perl module ExtUtils::MakeMaker - found at /usr/share/perl/5.36/ExtUtils/MakeMaker.pm -- Failed to find Perl modules: Chemistry::Mol (missing: PERLMODULES_CHEMISTRY_MOL_MODULE) -- Could NOT find Boost (missing: Boost_INCLUDE_DIR thread system program_options iostreams regex timer chrono filesystem graph) -- Unable to build internal Boost without zlib and libbz2 CMake Error at cmake/3rdPartyTools.cmake:108 (message): 3rd party program boost is required to build Amber, but it is disabled (likely because it was not found). Call Stack (most recent call first): cmake/3rdPartyTools.cmake:570 (set_3rdparty) CMakeLists.txt:206 (include) -- Configuring incomplete, errors occurred! If errors are reported, search for 'CMake Error' in the cmake.log file. If the cmake build report looks OK, you should now do the following: make install source /home/lcmvar/SOFT/amber22/amber.sh Consider adding the last line to your login startup script, e.g. ~/.bashrc