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'