2023-03-08T08:58:40,440 Created temporary directory: /tmp/pip-ephem-wheel-cache-sbxj48m1
2023-03-08T08:58:40,442 Created temporary directory: /tmp/pip-build-tracker-mfb63xxp
2023-03-08T08:58:40,443 Initialized build tracking at /tmp/pip-build-tracker-mfb63xxp
2023-03-08T08:58:40,443 Created build tracker: /tmp/pip-build-tracker-mfb63xxp
2023-03-08T08:58:40,443 Entered build tracker: /tmp/pip-build-tracker-mfb63xxp
2023-03-08T08:58:40,444 Created temporary directory: /tmp/pip-wheel-hdpmzx09
2023-03-08T08:58:40,448 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2023-03-08T08:58:40,451 Created temporary directory: /tmp/pip-ephem-wheel-cache-e0k7v8p1
2023-03-08T08:58:40,480 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-03-08T08:58:40,483 2 location(s) to search for versions of ambermdrun:
2023-03-08T08:58:40,483 * https://pypi.org/simple/ambermdrun/
2023-03-08T08:58:40,483 * https://www.piwheels.org/simple/ambermdrun/
2023-03-08T08:58:40,484 Fetching project page and analyzing links: https://pypi.org/simple/ambermdrun/
2023-03-08T08:58:40,484 Getting page https://pypi.org/simple/ambermdrun/
2023-03-08T08:58:40,486 Found index url https://pypi.org/simple
2023-03-08T08:58:40,538 Fetched page https://pypi.org/simple/ambermdrun/ as application/vnd.pypi.simple.v1+json
2023-03-08T08:58:40,539   Found link https://files.pythonhosted.org/packages/d6/db/18b74901842877c76f511fc9f2a0ed7f2ac8a09b72bc8926a79aa8e3613d/AmberMDrun-0.0.1.tar.gz (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.6), version: 0.0.1
2023-03-08T08:58:40,540 Fetching project page and analyzing links: https://www.piwheels.org/simple/ambermdrun/
2023-03-08T08:58:40,540 Getting page https://www.piwheels.org/simple/ambermdrun/
2023-03-08T08:58:40,541 Found index url https://www.piwheels.org/simple
2023-03-08T08:58:40,705 Fetched page https://www.piwheels.org/simple/ambermdrun/ as text/html
2023-03-08T08:58:40,707 Skipping link: not a file: https://www.piwheels.org/simple/ambermdrun/
2023-03-08T08:58:40,707 Skipping link: not a file: https://pypi.org/simple/ambermdrun/
2023-03-08T08:58:40,733 Given no hashes to check 1 links for project 'ambermdrun': discarding no candidates
2023-03-08T08:58:40,758 Collecting ambermdrun==0.0.1
2023-03-08T08:58:40,761   Created temporary directory: /tmp/pip-unpack-8cx9p72f
2023-03-08T08:58:40,824   Downloading AmberMDrun-0.0.1.tar.gz (904 kB)
2023-03-08T08:58:41,712   Added ambermdrun==0.0.1 from https://files.pythonhosted.org/packages/d6/db/18b74901842877c76f511fc9f2a0ed7f2ac8a09b72bc8926a79aa8e3613d/AmberMDrun-0.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-mfb63xxp'
2023-03-08T08:58:41,719   Created temporary directory: /tmp/pip-build-env-mr9kdf3z
2023-03-08T08:58:41,730   Installing build dependencies: started
2023-03-08T08:58:41,731   Running command pip subprocess to install build dependencies
2023-03-08T08:58:42,923   Using pip 23.0.1 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9)
2023-03-08T08:58:43,497   DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2023-03-08T08:58:43,523   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-03-08T08:58:45,227   Collecting setuptools>=42
2023-03-08T08:58:45,400     Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.5.1-py3-none-any.whl (1.1 MB)
2023-03-08T08:58:45,672   Collecting wheel
2023-03-08T08:58:45,689     Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB)
2023-03-08T08:58:46,025   Collecting ninja
2023-03-08T08:58:46,060     Using cached https://www.piwheels.org/simple/ninja/ninja-1.11.1-cp39-cp39-linux_armv7l.whl (132 kB)
2023-03-08T08:58:46,810   Collecting cmake>=3.12
2023-03-08T08:58:48,394     Using cached https://www.piwheels.org/simple/cmake/cmake-3.25.2-cp39-cp39-linux_armv7l.whl (17.3 MB)
2023-03-08T08:58:51,040   Installing collected packages: ninja, cmake, wheel, setuptools
2023-03-08T08:58:51,113     Creating /tmp/pip-build-env-mr9kdf3z/overlay/bin
2023-03-08T08:58:51,115     changing mode of /tmp/pip-build-env-mr9kdf3z/overlay/bin/ninja to 755
2023-03-08T08:58:58,302     changing mode of /tmp/pip-build-env-mr9kdf3z/overlay/bin/cmake to 755
2023-03-08T08:58:58,306     changing mode of /tmp/pip-build-env-mr9kdf3z/overlay/bin/cpack to 755
2023-03-08T08:58:58,309     changing mode of /tmp/pip-build-env-mr9kdf3z/overlay/bin/ctest to 755
2023-03-08T08:58:58,524     changing mode of /tmp/pip-build-env-mr9kdf3z/overlay/bin/wheel to 755
2023-03-08T08:59:01,141   Successfully installed cmake-3.25.2 ninja-1.11.1 setuptools-67.5.1 wheel-0.38.4
2023-03-08T08:59:01,672   Installing build dependencies: finished with status 'done'
2023-03-08T08:59:01,678   Getting requirements to build wheel: started
2023-03-08T08:59:01,679   Running command Getting requirements to build wheel
2023-03-08T08:59:02,283   running egg_info
2023-03-08T08:59:02,289   writing AmberMDrun.egg-info/PKG-INFO
2023-03-08T08:59:02,291   writing dependency_links to AmberMDrun.egg-info/dependency_links.txt
2023-03-08T08:59:02,293   writing entry points to AmberMDrun.egg-info/entry_points.txt
2023-03-08T08:59:02,294   writing requirements to AmberMDrun.egg-info/requires.txt
2023-03-08T08:59:02,295   writing top-level names to AmberMDrun.egg-info/top_level.txt
2023-03-08T08:59:02,342   reading manifest file 'AmberMDrun.egg-info/SOURCES.txt'
2023-03-08T08:59:02,392   reading manifest template 'MANIFEST.in'
2023-03-08T08:59:02,426   adding license file 'LICENSE'
2023-03-08T08:59:02,444   writing manifest file 'AmberMDrun.egg-info/SOURCES.txt'
2023-03-08T08:59:02,508   Getting requirements to build wheel: finished with status 'done'
2023-03-08T08:59:02,519   Created temporary directory: /tmp/pip-modern-metadata-9tbzvhrp
2023-03-08T08:59:02,522   Preparing metadata (pyproject.toml): started
2023-03-08T08:59:02,522   Running command Preparing metadata (pyproject.toml)
2023-03-08T08:59:03,053   running dist_info
2023-03-08T08:59:03,073   creating /tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun.egg-info
2023-03-08T08:59:03,079   writing /tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun.egg-info/PKG-INFO
2023-03-08T08:59:03,082   writing dependency_links to /tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun.egg-info/dependency_links.txt
2023-03-08T08:59:03,084   writing entry points to /tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun.egg-info/entry_points.txt
2023-03-08T08:59:03,086   writing requirements to /tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun.egg-info/requires.txt
2023-03-08T08:59:03,087   writing top-level names to /tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun.egg-info/top_level.txt
2023-03-08T08:59:03,089   writing manifest file '/tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun.egg-info/SOURCES.txt'
2023-03-08T08:59:03,112   reading manifest file '/tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun.egg-info/SOURCES.txt'
2023-03-08T08:59:03,114   reading manifest template 'MANIFEST.in'
2023-03-08T08:59:03,136   adding license file 'LICENSE'
2023-03-08T08:59:03,149   writing manifest file '/tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun.egg-info/SOURCES.txt'
2023-03-08T08:59:03,151   creating '/tmp/pip-modern-metadata-9tbzvhrp/AmberMDrun-0.0.1.dist-info'
2023-03-08T08:59:03,400   Preparing metadata (pyproject.toml): finished with status 'done'
2023-03-08T08:59:03,407   Source in /tmp/pip-wheel-hdpmzx09/ambermdrun_c254c72303c24d0b970e202833aaf8c9 has version 0.0.1, which satisfies requirement ambermdrun==0.0.1 from https://files.pythonhosted.org/packages/d6/db/18b74901842877c76f511fc9f2a0ed7f2ac8a09b72bc8926a79aa8e3613d/AmberMDrun-0.0.1.tar.gz
2023-03-08T08:59:03,408   Removed ambermdrun==0.0.1 from https://files.pythonhosted.org/packages/d6/db/18b74901842877c76f511fc9f2a0ed7f2ac8a09b72bc8926a79aa8e3613d/AmberMDrun-0.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-mfb63xxp'
2023-03-08T08:59:03,414 Created temporary directory: /tmp/pip-unpack-t0qprvgh
2023-03-08T08:59:03,414 Building wheels for collected packages: ambermdrun
2023-03-08T08:59:03,419   Created temporary directory: /tmp/pip-wheel-4yr0tdva
2023-03-08T08:59:03,419   Destination directory: /tmp/pip-wheel-4yr0tdva
2023-03-08T08:59:03,422   Building wheel for ambermdrun (pyproject.toml): started
2023-03-08T08:59:03,423   Running command Building wheel for ambermdrun (pyproject.toml)
2023-03-08T08:59:04,054   running bdist_wheel
2023-03-08T08:59:04,072   running build
2023-03-08T08:59:04,072   running build_py
2023-03-08T08:59:04,081   creating build
2023-03-08T08:59:04,081   creating build/lib.linux-armv7l-cpython-39
2023-03-08T08:59:04,082   creating build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-03-08T08:59:04,083   copying AmberMDrun/equil.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-03-08T08:59:04,085   copying AmberMDrun/version.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-03-08T08:59:04,087   copying AmberMDrun/mmpbsa.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-03-08T08:59:04,089   copying AmberMDrun/__init__.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-03-08T08:59:04,090   copying AmberMDrun/pyamber.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-03-08T08:59:04,093   copying AmberMDrun/main.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-03-08T08:59:04,095   running build_ext
2023-03-08T08:59:04,578   -- The CXX compiler identification is GNU 10.2.1
2023-03-08T08:59:04,634   -- Detecting CXX compiler ABI info
2023-03-08T08:59:05,001   -- Detecting CXX compiler ABI info - done
2023-03-08T08:59:05,040   -- Check for working CXX compiler: /usr/bin/c++ - skipped
2023-03-08T08:59:05,042   -- Detecting CXX compile features
2023-03-08T08:59:05,044   -- Detecting CXX compile features - done
2023-03-08T08:59:05,055   -- current platform: Linux
2023-03-08T08:59:05,076   -- pybind11 v2.10.1
2023-03-08T08:59:05,144   -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6")
2023-03-08T08:59:05,675   -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so
2023-03-08T08:59:05,685   -- Performing Test HAS_FLTO
2023-03-08T08:59:06,150   -- Performing Test HAS_FLTO - Success
2023-03-08T08:59:06,157   -- Configuring done
2023-03-08T08:59:06,200   -- Generating done
2023-03-08T08:59:06,230   -- Build files have been written to: /tmp/pip-wheel-hdpmzx09/ambermdrun_c254c72303c24d0b970e202833aaf8c9/build/temp.linux-armv7l-cpython-39/AmberMDrun
2023-03-08T08:59:12,875   [1/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o
2023-03-08T08:59:22,988   [2/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/SystemInfo.cpp.o
2023-03-08T08:59:29,674   [3/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/npt.cpp.o
2023-03-08T08:59:32,549   [4/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/base.cpp.o
2023-03-08T08:59:32,777   [5/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/format.cc.o
2023-03-08T08:59:33,568   [6/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/md.cpp.o
2023-03-08T08:59:35,942   [7/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/min.cpp.o
2023-03-08T08:59:37,444   [8/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/nvt.cpp.o
2023-03-08T08:59:37,641   [9/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/os.cc.o
2023-03-08T08:59:38,606   [10/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/gamd.cpp.o
2023-03-08T08:59:39,212   [11/16] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/smd.cpp.o
2023-03-08T08:59:39,405   [12/16] Linking CXX static library AmberMDrun/libambermd.a
2023-03-08T08:59:46,803   [13/16] Building CXX object AmberMDrun/CMakeFiles/amberMd.dir/main.cpp.o
2023-03-08T08:59:48,142   [14/16] Linking CXX executable AmberMDrun/amberMd
2023-03-08T08:59:55,962   [15/16] Building CXX object AmberMDrun/CMakeFiles/_pyamber.dir/pyamber.cpp.o
2023-03-08T09:00:15,911   [16/16] Linking CXX shared module /tmp/pip-wheel-hdpmzx09/ambermdrun_c254c72303c24d0b970e202833aaf8c9/build/lib.linux-armv7l-cpython-39/AmberMDrun/_pyamber.cpython-39-arm-linux-gnueabihf.so
2023-03-08T09:00:15,950   installing to build/bdist.linux-armv7l/wheel
2023-03-08T09:00:15,950   running install
2023-03-08T09:00:15,976   running install_lib
2023-03-08T09:00:15,985   creating build/bdist.linux-armv7l
2023-03-08T09:00:15,986   creating build/bdist.linux-armv7l/wheel
2023-03-08T09:00:15,987   creating build/bdist.linux-armv7l/wheel/AmberMDrun
2023-03-08T09:00:15,989   copying build/lib.linux-armv7l-cpython-39/AmberMDrun/equil.py -> build/bdist.linux-armv7l/wheel/AmberMDrun
2023-03-08T09:00:15,991   copying build/lib.linux-armv7l-cpython-39/AmberMDrun/_pyamber.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/AmberMDrun
2023-03-08T09:00:16,057   copying build/lib.linux-armv7l-cpython-39/AmberMDrun/version.py -> build/bdist.linux-armv7l/wheel/AmberMDrun
2023-03-08T09:00:16,059   copying build/lib.linux-armv7l-cpython-39/AmberMDrun/mmpbsa.py -> build/bdist.linux-armv7l/wheel/AmberMDrun
2023-03-08T09:00:16,061   copying build/lib.linux-armv7l-cpython-39/AmberMDrun/__init__.py -> build/bdist.linux-armv7l/wheel/AmberMDrun
2023-03-08T09:00:16,063   copying build/lib.linux-armv7l-cpython-39/AmberMDrun/pyamber.py -> build/bdist.linux-armv7l/wheel/AmberMDrun
2023-03-08T09:00:16,065   copying build/lib.linux-armv7l-cpython-39/AmberMDrun/main.py -> build/bdist.linux-armv7l/wheel/AmberMDrun
2023-03-08T09:00:16,067   running install_egg_info
2023-03-08T09:00:16,099   running egg_info
2023-03-08T09:00:16,105   writing AmberMDrun.egg-info/PKG-INFO
2023-03-08T09:00:16,107   writing dependency_links to AmberMDrun.egg-info/dependency_links.txt
2023-03-08T09:00:16,109   writing entry points to AmberMDrun.egg-info/entry_points.txt
2023-03-08T09:00:16,111   writing requirements to AmberMDrun.egg-info/requires.txt
2023-03-08T09:00:16,112   writing top-level names to AmberMDrun.egg-info/top_level.txt
2023-03-08T09:00:16,122   reading manifest file 'AmberMDrun.egg-info/SOURCES.txt'
2023-03-08T09:00:16,190   reading manifest template 'MANIFEST.in'
2023-03-08T09:00:16,223   adding license file 'LICENSE'
2023-03-08T09:00:16,249   writing manifest file 'AmberMDrun.egg-info/SOURCES.txt'
2023-03-08T09:00:16,252   Copying AmberMDrun.egg-info to build/bdist.linux-armv7l/wheel/AmberMDrun-0.0.1-py3.9.egg-info
2023-03-08T09:00:16,266   running install_scripts
2023-03-08T09:00:16,312   creating build/bdist.linux-armv7l/wheel/AmberMDrun-0.0.1.dist-info/WHEEL
2023-03-08T09:00:16,315   creating '/tmp/pip-wheel-4yr0tdva/.tmp-pe7b3t2l/AmberMDrun-0.0.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-03-08T09:00:16,318   adding 'AmberMDrun/__init__.py'
2023-03-08T09:00:16,611   adding 'AmberMDrun/_pyamber.cpython-39-arm-linux-gnueabihf.so'
2023-03-08T09:00:16,623   adding 'AmberMDrun/equil.py'
2023-03-08T09:00:16,625   adding 'AmberMDrun/main.py'
2023-03-08T09:00:16,626   adding 'AmberMDrun/mmpbsa.py'
2023-03-08T09:00:16,628   adding 'AmberMDrun/pyamber.py'
2023-03-08T09:00:16,629   adding 'AmberMDrun/version.py'
2023-03-08T09:00:16,631   adding 'AmberMDrun-0.0.1.dist-info/LICENSE'
2023-03-08T09:00:16,632   adding 'AmberMDrun-0.0.1.dist-info/METADATA'
2023-03-08T09:00:16,633   adding 'AmberMDrun-0.0.1.dist-info/WHEEL'
2023-03-08T09:00:16,635   adding 'AmberMDrun-0.0.1.dist-info/entry_points.txt'
2023-03-08T09:00:16,636   adding 'AmberMDrun-0.0.1.dist-info/top_level.txt'
2023-03-08T09:00:16,636   adding 'AmberMDrun-0.0.1.dist-info/RECORD'
2023-03-08T09:00:16,649   removing build/bdist.linux-armv7l/wheel
2023-03-08T09:00:16,741   Building wheel for ambermdrun (pyproject.toml): finished with status 'done'
2023-03-08T09:00:16,760   Created wheel for ambermdrun: filename=AmberMDrun-0.0.1-cp39-cp39-linux_armv7l.whl size=589984 sha256=9d7e6f27bf8ed40c3dedf66ef4e92029d07387a88d52cc1879d0fb0cdceecb78
2023-03-08T09:00:16,761   Stored in directory: /tmp/pip-ephem-wheel-cache-e0k7v8p1/wheels/eb/e3/d5/1637f4fd7c9d66019d935a0ad85f5d1b5b13841281bf49429c
2023-03-08T09:00:16,773 Successfully built ambermdrun
2023-03-08T09:00:16,799 Removed build tracker: '/tmp/pip-build-tracker-mfb63xxp'