-- ************************************************************************** -- Starting configuration of Amber version 20.0.0... -- CMake Version: 3.17.3 -- 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 7.5.0 -- The CXX compiler identification is GNU 5.5.0 -- The Fortran compiler identification is GNU 7.5.0 -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc - works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/g++ -- Check for working CXX compiler: /usr/bin/g++ - works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working Fortran compiler: /usr/bin/gfortran -- Check for working Fortran compiler: /usr/bin/gfortran - works -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Checking whether /usr/bin/gfortran supports Fortran 90 -- Checking whether /usr/bin/gfortran supports Fortran 90 - yes -- Testing if stdlib.h can be included... -- Testing if stdlib.h can be included... yes -- Looking for pthread.h -- Looking for pthread.h - found -- 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-9.0 (found version "9.0") -- 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/progs/amber20_src/build/CMakeFiles/miniconda/download/Miniconda3-latest-Linux-x86_64.sh ##O=- # # 0.3% # 1.0% ##### 2.6% ####### 3.6% ######### 5.0% ############ 6.4% ############### 7.8% ################## 9.3% #################### 10.6% ####################### 11.8% ######################### 13.2% ############################ 14.7% ############################### 15.9% ################################# 17.2% #################################### 18.4% ###################################### 19.7% ######################################### 20.9% ########################################### 22.2% ############################################## 23.5% ################################################ 24.6% ################################################## 25.9% ##################################################### 27.1% 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##################################################################################################################################################################################################### 100.0% Installing Miniconda Python. PREFIX=/home/progs/amber20_src/build/CMakeFiles/miniconda/install Unpacking payload ... 0%| | 0/36 [00:00 2020.12.8-h06a4308_0 certifi pkgs/main/noarch::certifi-2020.6.20-p~ --> pkgs/main/linux-64::certifi-2020.12.5-py38h06a4308_0 cffi 1.14.3-py38h261ae71_2 --> 1.14.4-py38h261ae71_0 chardet 3.0.4-py38h06a4308_1003 --> 4.0.0-py38h06a4308_1003 cryptography 3.2.1-py38h3c74f83_1 --> 3.3.1-py38h3c74f83_0 openssl 1.1.1h-h7b6447c_0 --> 1.1.1i-h27cfd23_0 pip 20.2.4-py38h06a4308_0 --> 20.3.3-py38h06a4308_0 pyopenssl 19.1.0-pyhd3eb1b0_1 --> 20.0.1-pyhd3eb1b0_1 requests 2.24.0-py_0 --> 2.25.1-pyhd3eb1b0_0 setuptools 50.3.1-py38h06a4308_1 --> 51.0.0-py38h06a4308_2 tqdm 4.51.0-pyhd3eb1b0_0 --> 4.54.1-pyhd3eb1b0_0 urllib3 1.25.11-py_0 --> 1.26.2-pyhd3eb1b0_0 wheel 0.35.1-pyhd3eb1b0_0 --> 0.36.2-pyhd3eb1b0_0 Downloading and Extracting Packages tqdm-4.54.1 | 55 KB | | 0% tqdm-4.54.1 | 55 KB | ########## | 100% tqdm-4.54.1 | 55 KB | ########## | 100% ca-certificates-2020 | 121 KB | | 0% ca-certificates-2020 | 121 KB | ########## | 100% cffi-1.14.4 | 226 KB | | 0% cffi-1.14.4 | 226 KB | ########## | 100% cffi-1.14.4 | 226 KB | ########## | 100% cryptography-3.3.1 | 566 KB | | 0% cryptography-3.3.1 | 566 KB | ########## | 100% cryptography-3.3.1 | 566 KB | ########## | 100% requests-2.25.1 | 52 KB | | 0% requests-2.25.1 | 52 KB | ########## | 100% pip-20.3.3 | 1.8 MB | | 0% pip-20.3.3 | 1.8 MB | ##4 | 25% pip-20.3.3 | 1.8 MB | ########## | 100% pip-20.3.3 | 1.8 MB | ########## | 100% openssl-1.1.1i | 2.5 MB | | 0% openssl-1.1.1i | 2.5 MB | ###1 | 32% openssl-1.1.1i | 2.5 MB | #######6 | 77% openssl-1.1.1i | 2.5 MB | ########## | 100% openssl-1.1.1i | 2.5 MB | ########## | 100% pyopenssl-20.0.1 | 49 KB | | 0% pyopenssl-20.0.1 | 49 KB | ########## | 100% certifi-2020.12.5 | 141 KB | | 0% certifi-2020.12.5 | 141 KB | ########## | 100% wheel-0.36.2 | 33 KB | | 0% wheel-0.36.2 | 33 KB | ########## | 100% urllib3-1.26.2 | 105 KB | | 0% urllib3-1.26.2 | 105 KB | ########## | 100% setuptools-51.0.0 | 726 KB | | 0% setuptools-51.0.0 | 726 KB | ########## | 100% setuptools-51.0.0 | 726 KB | ########## | 100% chardet-4.0.0 | 194 KB | | 0% chardet-4.0.0 | 194 KB | ########## | 100% chardet-4.0.0 | 194 KB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Requirement already satisfied: pip in ./CMakeFiles/miniconda/install/lib/python3.8/site-packages (20.3.3) Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/progs/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 blas-1.0 | 46 KB | | 0% blas-1.0 | 46 KB | ########## | 100% nomkl-3.0 | 46 KB | | 0% nomkl-3.0 | 46 KB | ########## | 100% Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve. Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... Warning: 2 possible package resolutions (only showing differing packages): - defaults/linux-64::jedi-0.17.0-py38_0, defaults/noarch::parso-0.8.1-pyhd3eb1b0_0 - defaults/linux-64::jedi-0.17.2-py38h06a4308_1, defaults/noarch::parso-0.7.0-py_0done ## Package Plan ## environment location: /home/progs/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 ---------------------------|----------------- argon2-cffi-20.1.0 | py38h7b6447c_1 46 KB async_generator-1.10 | py_0 24 KB attrs-20.3.0 | pyhd3eb1b0_0 43 KB backcall-0.2.0 | py_0 15 KB beautifulsoup4-4.9.3 | pyhb0f4dca_0 91 KB bleach-3.2.1 | py_0 112 KB bzip2-1.0.8 | h7b6447c_0 78 KB conda-build-3.20.5 | py38_1 548 KB cython-0.29.21 | py38h2531618_0 2.0 MB decorator-4.4.2 | py_0 14 KB defusedxml-0.6.0 | py_0 23 KB entrypoints-0.3 | py38_0 10 KB filelock-3.0.12 | py_0 13 KB glob2-0.7 | py_0 15 KB icu-58.2 | he6710b0_3 10.5 MB importlib-metadata-2.0.0 | py_1 35 KB importlib_metadata-2.0.0 | 1 11 KB iniconfig-1.1.1 | py_0 9 KB ipykernel-5.3.4 | py38h5ca1d4c_0 183 KB ipython-7.19.0 | py38hb070fc8_0 982 KB ipython_genutils-0.2.0 | pyhd3eb1b0_1 27 KB jedi-0.17.0 | py38_0 780 KB jinja2-2.11.2 | py_0 103 KB jsonschema-3.2.0 | py_2 47 KB jupyter_client-6.1.7 | py_0 77 KB jupyter_core-4.7.0 | py38h06a4308_0 68 KB jupyterlab_pygments-0.1.2 | py_0 8 KB libarchive-3.4.2 | h62408e4_0 796 KB libgfortran-ng-7.3.0 | hdf63c60_0 1006 KB liblief-0.10.1 | he6710b0_0 1.7 MB libopenblas-0.3.10 | h5a2b251_0 4.5 MB libsodium-1.0.18 | h7b6447c_0 244 KB libxml2-2.9.10 | hb55368b_3 1.2 MB lz4-c-1.9.2 | heb0550a_3 175 KB markupsafe-1.1.1 | py38h7b6447c_0 33 KB mistune-0.8.4 |py38h7b6447c_1000 55 KB more-itertools-8.6.0 | pyhd3eb1b0_0 40 KB nbclient-0.5.1 | py_0 58 KB nbconvert-6.0.7 | py38_0 481 KB nbformat-5.0.8 | py_0 88 KB nest-asyncio-1.4.3 | pyhd3eb1b0_0 11 KB notebook-6.1.6 | py38h06a4308_0 4.1 MB numpy-1.19.2 | py38h6163131_0 22 KB numpy-base-1.19.2 | py38h75fe3a5_0 4.2 MB packaging-20.8 | pyhd3eb1b0_0 36 KB pandoc-2.11 | hb0f4dca_0 9.6 MB pandocfilters-1.4.3 | py38h06a4308_1 14 KB parso-0.8.1 | pyhd3eb1b0_0 69 KB patchelf-0.12 | h2531618_1 88 KB pexpect-4.8.0 | pyhd3eb1b0_3 53 KB pickleshare-0.7.5 | pyhd3eb1b0_1003 13 KB pkginfo-1.6.1 | py38h06a4308_0 43 KB pluggy-0.13.1 | py38_0 33 KB prometheus_client-0.9.0 | pyhd3eb1b0_0 45 KB prompt-toolkit-3.0.8 | py_0 248 KB psutil-5.7.2 | py38h7b6447c_0 330 KB ptyprocess-0.6.0 | pyhd3eb1b0_2 20 KB py-1.10.0 | pyhd3eb1b0_0 76 KB py-lief-0.10.1 | py38h403a769_0 1.0 MB pygments-2.7.3 | pyhd3eb1b0_0 676 KB pyparsing-2.4.7 | py_0 65 KB pyrsistent-0.17.3 | py38h7b6447c_0 90 KB pytest-6.2.1 | py38h06a4308_0 423 KB python-dateutil-2.8.1 | py_0 215 KB python-libarchive-c-2.9 | py_0 46 KB pytz-2020.4 | pyhd3eb1b0_0 180 KB pyyaml-5.3.1 | py38h7b6447c_1 185 KB pyzmq-20.0.0 | py38h2531618_1 447 KB ripgrep-12.1.1 | 0 1.4 MB scipy-1.5.2 | py38habc2bb6_0 14.5 MB send2trash-1.5.0 | pyhd3eb1b0_1 14 KB soupsieve-2.1 | pyhd3eb1b0_0 31 KB terminado-0.9.1 | py38_0 27 KB testpath-0.4.4 | py_0 82 KB toml-0.10.1 | py_0 20 KB tornado-6.1 | py38h27cfd23_0 588 KB traitlets-5.0.5 | py_0 83 KB wcwidth-0.2.5 | py_0 29 KB webencodings-0.5.1 | py38_1 20 KB zeromq-4.3.3 | he6710b0_3 500 KB zipp-3.4.0 | pyhd3eb1b0_0 15 KB zstd-1.4.5 | h9ceee32_0 619 KB ------------------------------------------------------------ Total: 66.2 MB The following NEW packages will be INSTALLED: argon2-cffi pkgs/main/linux-64::argon2-cffi-20.1.0-py38h7b6447c_1 async_generator pkgs/main/noarch::async_generator-1.10-py_0 attrs pkgs/main/noarch::attrs-20.3.0-pyhd3eb1b0_0 backcall pkgs/main/noarch::backcall-0.2.0-py_0 beautifulsoup4 pkgs/main/noarch::beautifulsoup4-4.9.3-pyhb0f4dca_0 bleach pkgs/main/noarch::bleach-3.2.1-py_0 bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 conda-build pkgs/main/linux-64::conda-build-3.20.5-py38_1 cython pkgs/main/linux-64::cython-0.29.21-py38h2531618_0 decorator pkgs/main/noarch::decorator-4.4.2-py_0 defusedxml pkgs/main/noarch::defusedxml-0.6.0-py_0 entrypoints pkgs/main/linux-64::entrypoints-0.3-py38_0 filelock pkgs/main/noarch::filelock-3.0.12-py_0 glob2 pkgs/main/noarch::glob2-0.7-py_0 icu pkgs/main/linux-64::icu-58.2-he6710b0_3 importlib-metadata pkgs/main/noarch::importlib-metadata-2.0.0-py_1 importlib_metadata pkgs/main/noarch::importlib_metadata-2.0.0-1 iniconfig pkgs/main/noarch::iniconfig-1.1.1-py_0 ipykernel pkgs/main/linux-64::ipykernel-5.3.4-py38h5ca1d4c_0 ipython pkgs/main/linux-64::ipython-7.19.0-py38hb070fc8_0 ipython_genutils pkgs/main/noarch::ipython_genutils-0.2.0-pyhd3eb1b0_1 jedi pkgs/main/linux-64::jedi-0.17.0-py38_0 jinja2 pkgs/main/noarch::jinja2-2.11.2-py_0 jsonschema pkgs/main/noarch::jsonschema-3.2.0-py_2 jupyter_client pkgs/main/noarch::jupyter_client-6.1.7-py_0 jupyter_core pkgs/main/linux-64::jupyter_core-4.7.0-py38h06a4308_0 jupyterlab_pygmen~ pkgs/main/noarch::jupyterlab_pygments-0.1.2-py_0 libarchive pkgs/main/linux-64::libarchive-3.4.2-h62408e4_0 libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0 liblief pkgs/main/linux-64::liblief-0.10.1-he6710b0_0 libopenblas pkgs/main/linux-64::libopenblas-0.3.10-h5a2b251_0 libsodium pkgs/main/linux-64::libsodium-1.0.18-h7b6447c_0 libxml2 pkgs/main/linux-64::libxml2-2.9.10-hb55368b_3 lz4-c pkgs/main/linux-64::lz4-c-1.9.2-heb0550a_3 markupsafe pkgs/main/linux-64::markupsafe-1.1.1-py38h7b6447c_0 mistune pkgs/main/linux-64::mistune-0.8.4-py38h7b6447c_1000 more-itertools pkgs/main/noarch::more-itertools-8.6.0-pyhd3eb1b0_0 nbclient pkgs/main/noarch::nbclient-0.5.1-py_0 nbconvert pkgs/main/linux-64::nbconvert-6.0.7-py38_0 nbformat pkgs/main/noarch::nbformat-5.0.8-py_0 nest-asyncio pkgs/main/noarch::nest-asyncio-1.4.3-pyhd3eb1b0_0 notebook pkgs/main/linux-64::notebook-6.1.6-py38h06a4308_0 numpy pkgs/main/linux-64::numpy-1.19.2-py38h6163131_0 numpy-base pkgs/main/linux-64::numpy-base-1.19.2-py38h75fe3a5_0 packaging pkgs/main/noarch::packaging-20.8-pyhd3eb1b0_0 pandoc pkgs/main/linux-64::pandoc-2.11-hb0f4dca_0 pandocfilters pkgs/main/linux-64::pandocfilters-1.4.3-py38h06a4308_1 parso pkgs/main/noarch::parso-0.8.1-pyhd3eb1b0_0 patchelf pkgs/main/linux-64::patchelf-0.12-h2531618_1 pexpect pkgs/main/noarch::pexpect-4.8.0-pyhd3eb1b0_3 pickleshare pkgs/main/noarch::pickleshare-0.7.5-pyhd3eb1b0_1003 pkginfo pkgs/main/linux-64::pkginfo-1.6.1-py38h06a4308_0 pluggy pkgs/main/linux-64::pluggy-0.13.1-py38_0 prometheus_client pkgs/main/noarch::prometheus_client-0.9.0-pyhd3eb1b0_0 prompt-toolkit pkgs/main/noarch::prompt-toolkit-3.0.8-py_0 psutil pkgs/main/linux-64::psutil-5.7.2-py38h7b6447c_0 ptyprocess pkgs/main/noarch::ptyprocess-0.6.0-pyhd3eb1b0_2 py pkgs/main/noarch::py-1.10.0-pyhd3eb1b0_0 py-lief pkgs/main/linux-64::py-lief-0.10.1-py38h403a769_0 pygments pkgs/main/noarch::pygments-2.7.3-pyhd3eb1b0_0 pyparsing pkgs/main/noarch::pyparsing-2.4.7-py_0 pyrsistent pkgs/main/linux-64::pyrsistent-0.17.3-py38h7b6447c_0 pytest pkgs/main/linux-64::pytest-6.2.1-py38h06a4308_0 python-dateutil pkgs/main/noarch::python-dateutil-2.8.1-py_0 python-libarchive~ pkgs/main/noarch::python-libarchive-c-2.9-py_0 pytz pkgs/main/noarch::pytz-2020.4-pyhd3eb1b0_0 pyyaml pkgs/main/linux-64::pyyaml-5.3.1-py38h7b6447c_1 pyzmq pkgs/main/linux-64::pyzmq-20.0.0-py38h2531618_1 ripgrep pkgs/main/linux-64::ripgrep-12.1.1-0 scipy pkgs/main/linux-64::scipy-1.5.2-py38habc2bb6_0 send2trash pkgs/main/noarch::send2trash-1.5.0-pyhd3eb1b0_1 soupsieve pkgs/main/noarch::soupsieve-2.1-pyhd3eb1b0_0 terminado pkgs/main/linux-64::terminado-0.9.1-py38_0 testpath pkgs/main/noarch::testpath-0.4.4-py_0 toml pkgs/main/noarch::toml-0.10.1-py_0 tornado pkgs/main/linux-64::tornado-6.1-py38h27cfd23_0 traitlets pkgs/main/noarch::traitlets-5.0.5-py_0 wcwidth pkgs/main/noarch::wcwidth-0.2.5-py_0 webencodings pkgs/main/linux-64::webencodings-0.5.1-py38_1 zeromq pkgs/main/linux-64::zeromq-4.3.3-he6710b0_3 zipp pkgs/main/noarch::zipp-3.4.0-pyhd3eb1b0_0 zstd pkgs/main/linux-64::zstd-1.4.5-h9ceee32_0 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting matplotlib Downloading matplotlib-3.3.3-cp38-cp38-manylinux1_x86_64.whl (11.6 MB) Requirement already satisfied: python-dateutil>=2.1 in ./CMakeFiles/miniconda/install/lib/python3.8/site-packages (from matplotlib) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in ./CMakeFiles/miniconda/install/lib/python3.8/site-packages (from matplotlib) (2.4.7) Requirement already satisfied: numpy>=1.15 in ./CMakeFiles/miniconda/install/lib/python3.8/site-packages (from matplotlib) (1.19.2) Collecting cycler>=0.10 Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Requirement already satisfied: six in ./CMakeFiles/miniconda/install/lib/python3.8/site-packages (from cycler>=0.10->matplotlib) (1.15.0) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.3.1-cp38-cp38-manylinux1_x86_64.whl (1.2 MB) Collecting pillow>=6.2.0 Downloading Pillow-8.0.1-cp38-cp38-manylinux1_x86_64.whl (2.2 MB) Installing collected packages: pillow, kiwisolver, cycler, matplotlib Successfully installed cycler-0.10.0 kiwisolver-1.3.1 matplotlib-3.3.3 pillow-8.0.1 Cache location: /home/progs/amber20_src/build/CMakeFiles/miniconda/install/pkgs Will remove the following tarballs: /home/progs/amber20_src/build/CMakeFiles/miniconda/install/pkgs --------------------------------------------------------------- libopenblas-0.3.10-h5a2b251_0.conda 4.5 MB py-1.10.0-pyhd3eb1b0_0.conda 76 KB packaging-20.8-pyhd3eb1b0_0.conda 36 KB nest-asyncio-1.4.3-pyhd3eb1b0_0.conda 11 KB jedi-0.17.0-py38_0.conda 780 KB ca-certificates-2020.10.14-0.conda 121 KB ruamel_yaml-0.15.87-py38h7b6447c_1.conda 249 KB 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libedit-3.1.20191231-h14c3975_1.conda Removed nbformat-5.0.8-py_0.conda Removed zlib-1.2.11-h7b6447c_3.conda Removed certifi-2020.6.20-pyhd3eb1b0_3.conda Removed libgcc-ng-9.1.0-hdf63c60_0.conda Removed requests-2.24.0-py_0.conda Removed readline-8.0-h7b6447c_0.conda Removed pycparser-2.20-py_2.conda Removed libstdcxx-ng-9.1.0-hdf63c60_0.conda Removed cffi-1.14.4-py38h261ae71_0.conda Removed send2trash-1.5.0-pyhd3eb1b0_1.conda Removed libsodium-1.0.18-h7b6447c_0.conda Removed cryptography-3.3.1-py38h3c74f83_0.conda Removed prometheus_client-0.9.0-pyhd3eb1b0_0.conda Removed pandoc-2.11-hb0f4dca_0.conda Removed beautifulsoup4-4.9.3-pyhb0f4dca_0.conda Removed brotlipy-0.7.0-py38h27cfd23_1003.conda Removed bleach-3.2.1-py_0.conda Removed patchelf-0.12-h2531618_1.conda Removed python-3.8.5-h7579374_1.conda Removed parso-0.8.1-pyhd3eb1b0_0.conda Removed pyyaml-5.3.1-py38h7b6447c_1.conda Removed pygments-2.7.3-pyhd3eb1b0_0.conda Removed pyzmq-20.0.0-py38h2531618_1.conda Removed liblief-0.10.1-he6710b0_0.conda Removed iniconfig-1.1.1-py_0.conda Removed ipykernel-5.3.4-py38h5ca1d4c_0.conda Removed pysocks-1.7.1-py38h06a4308_0.conda Removed wcwidth-0.2.5-py_0.conda Removed blas-1.0-openblas.conda Removed libarchive-3.4.2-h62408e4_0.conda Removed toml-0.10.1-py_0.conda Removed attrs-20.3.0-pyhd3eb1b0_0.conda Removed yaml-0.2.5-h7b6447c_0.conda Removed webencodings-0.5.1-py38_1.conda Removed decorator-4.4.2-py_0.conda Removed glob2-0.7-py_0.conda Removed ptyprocess-0.6.0-pyhd3eb1b0_2.conda WARNING: /home/haoxili/.conda/pkgs does not exist Cache location: /home/progs/amber20_src/build/CMakeFiles/miniconda/install/pkgs Will remove the following packages: /home/progs/amber20_src/build/CMakeFiles/miniconda/install/pkgs --------------------------------------------------------------- cryptography-3.2.1-py38h3c74f83_1 3.5 MB blas-1.0-openblas 281 KB wheel-0.35.1-pyhd3eb1b0_0 135 KB certifi-2020.6.20-pyhd3eb1b0_3 328 KB nomkl-3.0-0 281 KB setuptools-50.3.1-py38h06a4308_1 3.8 MB urllib3-1.25.11-py_0 412 KB numpy-1.19.2-py38h6163131_0 68 KB ca-certificates-2020.10.14-0 227 KB cffi-1.14.3-py38h261ae71_2 862 KB tqdm-4.51.0-pyhd3eb1b0_0 271 KB requests-2.24.0-py_0 218 KB chardet-3.0.4-py38h06a4308_1003 847 KB importlib_metadata-2.0.0-1 37 KB pip-20.2.4-py38h06a4308_0 7.9 MB pyopenssl-19.1.0-pyhd3eb1b0_1 247 KB openssl-1.1.1h-h7b6447c_0 13.4 MB _libgcc_mutex-0.1-main 7 KB --------------------------------------------------- Total: 32.8 MB removing cryptography-3.2.1-py38h3c74f83_1 removing blas-1.0-openblas removing wheel-0.35.1-pyhd3eb1b0_0 removing certifi-2020.6.20-pyhd3eb1b0_3 removing nomkl-3.0-0 removing setuptools-50.3.1-py38h06a4308_1 removing urllib3-1.25.11-py_0 removing numpy-1.19.2-py38h6163131_0 removing ca-certificates-2020.10.14-0 removing cffi-1.14.3-py38h261ae71_2 removing tqdm-4.51.0-pyhd3eb1b0_0 removing requests-2.24.0-py_0 removing chardet-3.0.4-py38h06a4308_1003 removing importlib_metadata-2.0.0-1 removing pip-20.2.4-py38h06a4308_0 removing pyopenssl-19.1.0-pyhd3eb1b0_1 removing openssl-1.1.1h-h7b6447c_0 removing _libgcc_mutex-0.1-main -- Miniconda install successful! -- Found PythonLibs: /home/progs/amber20_src/build/CMakeFiles/miniconda/install/lib/libpython3.8.so (found version "3.8.5") -- Checking for Python package numpy -- found -- Checking for Python package scipy -- found Matplotlib created a temporary config/cache directory at /tmp/matplotlib-0dh44h37 because the default path (/home/haoxili/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. -- 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/python3.8/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 "3.0.4") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.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 -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found Perl: /usr/bin/perl (found version "5.26.1") -- Found perl make: /usr/bin/make -- Perl modules well be installed to AMBERHOME/lib/perl -- Running updater... -- >>> Preparing to apply updates... please wait. -- >>> Downloading updates for AmberTools 20 -- >>> 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Downloading AmberTools 20/update.11 (889 Bytes) -- >>> Applying AmberTools 20/update.11 -- >>> Downloading AmberTools 20/update.12 (2.00 KB) -- >>> Applying AmberTools 20/update.12 -- >>> Downloading updates for Amber 20 -- >>> Downloading Amber 20/update.1 (4.89 KB) -- >>> Applying Amber 20/update.1 -- >>> Downloading Amber 20/update.2 (3.43 KB) -- >>> Applying Amber 20/update.2 -- >>> Downloading Amber 20/update.3 (1.83 KB) -- >>> Applying Amber 20/update.3 -- >>> Downloading Amber 20/update.4 (32.28 KB) -- >>> Applying Amber 20/update.4 -- >>> Downloading Amber 20/update.5 (22.48 KB) -- >>> Applying Amber 20/update.5 -- >>> Downloading Amber 20/update.6 (2.38 KB) -- >>> Applying Amber 20/update.6 -- >>> Downloading Amber 20/update.7 (1.60 KB) -- >>> Applying Amber 20/update.7 -- >>> Downloading Amber 20/update.8 (4.49 KB) -- >>> Applying Amber 20/update.8 -- >>> 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_IS_LINKABLE) -- Looking for tgetent in termcap -- Looking for tgetent in termcap - found -- Found Termcap: /usr/lib/x86_64-linux-gnu/libtermcap.so -- 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 /home/progs/cmake-3.17.3-Linux-x86_64/share/cmake-3.17/Modules/FindPackageHandleStandardArgs.cmake:272 (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:221 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_C: -fopenmp (found version "4.5") CMake Warning (dev) at /home/progs/cmake-3.17.3-Linux-x86_64/share/cmake-3.17/Modules/FindPackageHandleStandardArgs.cmake:272 (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:221 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_CXX: -fopenmp (found version "4.0") CMake Warning (dev) at /home/progs/cmake-3.17.3-Linux-x86_64/share/cmake-3.17/Modules/FindPackageHandleStandardArgs.cmake:272 (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:221 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Performing Test SUPPORTS_NO_AS_NEEDED -- Performing Test SUPPORTS_NO_AS_NEEDED - Success -- Could NOT find MKL (missing: MKL_INTERFACE_LIBRARY MKL_GFORTRAN_INTERFACE_LIBRARY MKL_GNU_THREADING_LIBRARY MKL_CORE_LIBRARY) -- Looking for fftw_execute in fftw3 -- Looking for fftw_execute in fftw3 - found -- Looking for fftw_cleanup in fftw3 -- Looking for fftw_cleanup in fftw3 - found -- Found FFTW: //home/progs/amber16/lib/libfftw3.so -- Looking for nc_strerror in netcdf -- Looking for nc_strerror in netcdf - found -- Failed to find NetCDF interface for F77 (NetCDF_INCLUDES_F77 = NetCDF_INCLUDES_F77-NOTFOUND, NetCDF_LIBRARIES_F77 = //home/progs/amber16/lib/libnetcdff.so) -- Failed to find NetCDF interface for F90 (NetCDF_INCLUDES_F90 = NetCDF_INCLUDES_F90-NOTFOUND, NetCDF_LIBRARIES_F90 = //home/progs/amber16/lib/libnetcdff.so) -- Could NOT find NetCDF (missing: NetCDF_INCLUDES) -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- A library with BLAS API found. -- Looking for Fortran cheev -- Looking for Fortran cheev - not found -- A library with LAPACK API not found. Please specify library location. -- Looking for dsaupd in arpack -- Looking for dsaupd in arpack - not found -- Detailed information about why this check failed can be found in /home/progs/amber20_src/build/CMakeFiles/CMakeError.log -- The ARPACK library was found, but //home/progs/amber16/lib/libarpack.a is not linkable. Perhaps it was built with an incompatible Fortran compiler? Please set ARPACK_LIBRARY to point to a working ARPACK library. (missing: 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, 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_MALOC_LIB APBS_WORKS APBS_INCLUDES) CMake Warning (dev) at /home/progs/cmake-3.17.3-Linux-x86_64/share/cmake-3.17/Modules/FindPackageHandleStandardArgs.cmake:272 (message): The package name passed to `find_package_handle_standard_args` (JNI) does not match the name of the calling package (JNIFixed). 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/FindJNIFixed.cmake:323 (FIND_PACKAGE_HANDLE_STANDARD_ARGS) cmake/FindPUPIL.cmake:19 (find_package) cmake/3rdPartyTools.cmake:368 (find_package) CMakeLists.txt:194 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find JNI (missing: JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH) -- Could not find the Java development libraries, so PUPIL can't be used. (missing: PUPIL_MAIN_LIB PUPIL_BLIND_LIB PUPIL_TIME_LIB) -- Could not find lio. If you want to use it, set LIO_HOME to point to a built lio source directory. -- 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 "1.2.11") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- 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 -- 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/5.26/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) -- Could NOT find MBX (missing: MBX_DIR) -- Could not find MBX. To locate it, add its install dir to the prefix path. -- Cannot find PLUMED. You will still be able to load it at runtime. If you want to link it at build time, set PLUMED_ROOT to where you installed it. -- Performing Test SUPPORTS_WNO_UNUSED_LOCAL_TYPEDEFS -- Performing Test SUPPORTS_WNO_UNUSED_LOCAL_TYPEDEFS - Success -- Looking for mkstemp -- Looking for mkstemp - found -- Generating amber source scripts -- Configuring subdirs... -- Looking for termcap.h -- Looking for termcap.h - found -- Looking for dirent.h -- Looking for dirent.h - found -- Looking for langinfo.h -- Looking for langinfo.h - found -- Looking for pwd.h -- Looking for pwd.h - found -- Looking for unistd.h -- Looking for unistd.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for varargs.h -- Looking for varargs.h - not found -- Looking for stdarg.h -- Looking for stdarg.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for limits.h -- Looking for limits.h - found -- Looking for sys/ptem.h -- Looking for sys/ptem.h - not found -- Looking for sys/pte.h -- Looking for sys/pte.h - not found -- Looking for sys/stream.h -- Looking for sys/stream.h - not found -- Looking for sys/select.h -- Looking for sys/select.h - found -- Looking for termios.h -- Looking for termios.h - found -- Looking for termio.h -- Looking for termio.h - found -- Looking for sys/file.h -- Looking for sys/file.h - found -- Looking for locale.h -- Looking for locale.h - found -- Looking for memory.h -- Looking for memory.h - found -- Looking for wchar.h -- Looking for wchar.h - found -- Looking for wctype.h -- Looking for wctype.h - found -- Looking for lstat -- Looking for lstat - found -- Looking for memmove -- Looking for memmove - found -- Looking for putenv -- Looking for putenv - found -- Looking for select -- Looking for select - found -- Looking for setenv -- Looking for setenv - found -- Looking for setlocale -- Looking for setlocale - found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strpbrk -- Looking for strpbrk - found -- Looking for tcgetattr -- Looking for tcgetattr - found -- Looking for vsnprintf -- Looking for vsnprintf - found -- Looking for isascii -- Looking for isascii - found -- Looking for isxdigit -- Looking for isxdigit - found -- Looking for wcwidth -- Looking for wcwidth - found -- Looking for wctomb -- Looking for wctomb - found -- Looking for strcoll -- Looking for strcoll - found -- Looking for TIOCGWINSZ -- Looking for TIOCGWINSZ - found -- Looking for TIOCSTAT -- Looking for TIOCSTAT - not found -- Looking for FIONREAD -- Looking for FIONREAD - found -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Searching 16 bit integer - Using unsigned short -- Check if the system is big endian - little endian -- Performing Test LIBTOOL_HAS_NO_UNDEFINED -- Performing Test LIBTOOL_HAS_NO_UNDEFINED - Success -- Performing Test CC_HAS_WCONVERSION -- Performing Test CC_HAS_WCONVERSION - Success -- Performing Test CC_HAS_SHORTEN_64_32 -- Performing Test CC_HAS_SHORTEN_64_32 - Failed -- Looking for math.h -- Looking for math.h - found -- Looking for alloca.h -- Looking for alloca.h - found -- Looking for malloc.h -- Looking for malloc.h - found -- Looking for fcntl.h -- Looking for fcntl.h - found -- Looking for getopt.h -- Looking for getopt.h - found -- Looking for stdio.h -- Looking for stdio.h - found -- Looking for signal.h -- Looking for signal.h - found -- Looking for sys/param.h -- Looking for sys/param.h - found -- Looking for sys/stat.h -- Looking for sys/stat.h - found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for sys/mman.h -- Looking for sys/mman.h - found -- Looking for sys/resource.h -- Looking for sys/resource.h - found -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for pstdint.h -- Looking for pstdint.h - found -- Looking for endian.h -- Looking for endian.h - found -- Looking for BaseTsd.h -- Looking for BaseTsd.h - not found -- Looking for winsock2.h -- Looking for winsock2.h - not found -- Looking for ftw.h -- Looking for ftw.h - found -- Looking for libgen.h -- Looking for libgen.h - found -- Looking for isfinite -- Looking for isfinite - found -- Looking for isnan -- Looking for isnan - found -- Looking for isinf -- Looking for isinf - found -- Looking for st_blksize -- Looking for st_blksize - not found -- Looking for alloca -- Looking for alloca - found -- Looking for snprintf -- Looking for snprintf - found -- Check size of char -- Check size of char - done -- Check size of double -- Check size of double - done -- Check size of float -- Check size of float - done -- Check size of int -- Check size of int - done -- Check size of uint -- Check size of uint - done -- Check size of schar -- Check size of schar - failed -- Check size of long -- Check size of long - done -- Check size of long long -- Check size of long long - done -- Check size of unsigned long long -- Check size of unsigned long long - done -- Check size of off_t -- Check size of off_t - done -- Check size of off64_t -- Check size of off64_t - done -- Check size of short -- Check size of short - done -- Check size of ushort -- Check size of ushort - done -- Check size of _Bool -- Check size of _Bool - done -- Check size of size_t -- Check size of size_t - done -- Check size of ssize_t -- Check size of ssize_t - done -- Check size of __int64 -- Check size of __int64 - failed -- Check size of int64_t -- Check size of int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Check size of unsigned char -- Check size of unsigned char - done -- Check size of unsigned short int -- Check size of unsigned short int - done -- Check size of unsigned int -- Check size of unsigned int - done -- Check size of long long -- Check size of long long - done -- Check size of unsigned long long -- Check size of unsigned long long - done -- Looking for fsync -- Looking for fsync - found -- Looking for strlcat -- Looking for strlcat - not found -- Looking for strdup -- Looking for strdup - found -- Looking for strndup -- Looking for strndup - found -- Looking for strtoll -- Looking for strtoll - found -- Looking for strtoull -- Looking for strtoull - found -- Looking for mktemp -- Looking for mktemp - found -- Looking for random -- Looking for random - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for MPI_Comm_f2c -- Looking for MPI_Comm_f2c - not found -- Looking for getpagesize -- Looking for getpagesize - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for getrlimit -- Looking for getrlimit - found -- Looking for _filelengthi64 -- Looking for _filelengthi64 - not found -- Looking for mremap -- Looking for mremap - found -- Found bash: /bin/bash -- netcdf-fortran: Detected TS29113 support in Fortran compiler -- Check size of signed char -- Check size of signed char - done -- Reticulating splines... -- Looking for sscanf -- Looking for sscanf - found -- Looking for stat -- Looking for stat - found -- Check size of long double -- Check size of long double - done -- Looking for getline -- Looking for getline - found -- Performing Test SUPPORTS_WNO_UNUSED_RESULT -- Performing Test SUPPORTS_WNO_UNUSED_RESULT - Success -- Looking for backtrace -- Looking for backtrace - found -- Looking for sys/dir.h -- Looking for sys/dir.h - found -- Looking for stdbool.h -- Looking for stdbool.h - found -- Looking for Windows.h -- Looking for Windows.h - not found -- Looking for X11/Xmd.h -- Looking for X11/Xmd.h - found -- Looking for toupper -- Looking for toupper - found -- Looking for tolower -- Looking for tolower - found -- Check size of BOOL -- Check size of BOOL - done If you can't see the following build report, then you need to turn off COLOR_CMAKE_MESSAGES -- ************************************************************************** -- Build Report -- Compiler Flags: -- C No-Opt:   -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -O0 -- C Optimized:   -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native -- -- CXX No-Opt:   -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O0 -- CXX Optimized:   -Wall -Wno-unused-function -Wno-unknown-pragmas -Wno-unused-local-typedefs -Wno-unused-variable -Wno-unused-but-set-variable -O3 -mtune=native -- -- Fortran No-Opt:   -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O0 -- Fortran Optimized:  -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none -Wno-unused-dummy-argument -Wno-unused-variable -O3 -mtune=native -- -- 3rd Party Libraries -- ---building bundled: ----------------------------------------------------- -- lapack - for fundamental linear algebra calculations -- arpack - for fundamental linear algebra calculations -- ucpp - used as a preprocessor for the NAB compiler -- netcdf - for creating trajectory data files -- netcdf-fortran - for creating trajectory data files from Fortran -- readline - used for the console functionality of cpptraj -- boost - C++ support library -- perlmol - chemistry library used by FEW -- ---using installed: ------------------------------------------------------ -- blas - for fundamental linear algebra calculations -- fftw - used to do Fourier transforms very quickly -- xblas - used for high-precision linear algebra calculations -- zlib - for various compression and decompression tasks -- libbz2 - for bzip2 compression in cpptraj -- libm - for fundamental math routines if they are not contained in the C library -- ---disabled: ------------------------------------------------ -- c9x-complex - used as a support library on systems that do not have C99 complex.h support -- lio - used by Sander to run certain QM routines on the GPU -- apbs - used by Sander as an alternate Poisson-Boltzmann equation solver -- pupil - used by Sander as an alternate user interface -- plumed - used as an alternate MD backend for Sander -- mkl - alternate implementation of lapack and blas that is tuned for speed -- mbx - computes energies and forces for pmemd with the MB-pol model -- Features: -- MPI: OFF -- OpenMP: OFF -- CUDA: OFF -- Build Shared Libraries: ON -- Build GUI Interfaces: ON -- Build Python Programs: ON -- -Python Interpreter: Internal Miniconda (version 3.8) -- Build Perl Programs: ON -- Build configuration: RELEASE -- Target Processor: x86_64 -- Build Documentation: OFF -- Sander Variants: normal LES API LES-API -- Install location: /home/progs/amber20/ -- Installation of Tests: ON -- Compilers: --  C: GNU 7.5.0 (/usr/bin/gcc) --  CXX: GNU 5.5.0 (/usr/bin/g++) --  Fortran: GNU 7.5.0 (/usr/bin/gfortran) -- Building Tools: -- addles amberlite ambpdb antechamber cifparse cphstats cpptraj emil etc few gbnsr6 gem.pmemd leap lib mdgx mm_pbsa mmpbsa_py moft nab ndiff-2.00 nfe-umbrella-slice nmode nmr_aux packmol_memgen paramfit parmed pbsa pdb4amber pmemd pymsmt pysander pytraj reduce rism sander saxs sebomd sff sqm xray xtalutil -- NOT Building Tools: -- quick - In-development programs are disabled. -- pymdgx - In-development programs are disabled. -- gpu_utils - Requires CUDA -- ************************************************************************** -- Environment resource files are provided to set the proper environment -- variables to use AMBER and AmberTools. This is required to run any Python -- programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj) -- -- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the -- /home/progs/amber20//amber.sh file in your shell. Consider adding the line -- test -f /home/progs/amber20//amber.sh && source /home/progs/amber20//amber.sh -- to your startup file (e.g., ~/.bashrc) -- -- If you use a C shell (e.g., csh, tcsh), source the -- /home/progs/amber20//amber.csh file in your shell. Consider adding the line -- test -f /home/progs/amber20//amber.csh && source /home/progs/amber20//amber.csh -- to your startup file (e.g., ~/.cshrc) -- -- Amber will be installed to /home/progs/amber20/ -- Configuring done -- Generating done -- Build files have been written to: /home/progs/amber20_src/build