Could NOT find OpenGL (missing: OPENGL_opengl

TeQiang Zou

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Nov 17, 2020, 10:17:27 PM11/17/20

to EMAN2

When I used cmake to build the EMAN2, I got this error. The complete info is below:

(eman2) icecreamzou@ubuntu:/mnt/newdisk/eman2/eman2/eman2-build$ cmake .. -DENABLE_OPTIMIZE_MACHINE=ON

-- The CXX compiler identification is GNU 7.3.0

-- Check for working CXX compiler: /mnt/newdisk/miniconda3/envs/eman2/bin/x86_64-conda_cos6-linux-gnu-c++

-- Check for working CXX compiler: /mnt/newdisk/miniconda3/envs/eman2/bin/x86_64-conda_cos6-linux-gnu-c++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Looking for fseek64

-- Looking for fseek64 - not found

-- Looking for fseeko

-- Looking for fseeko - found

-- Looking for ftell64

-- Looking for ftell64 - not found

-- Looking for ftello

-- Looking for ftello - found

-- Found Conda: /mnt/newdisk/miniconda3/envs/eman2

-- CMAKE_PREFIX_PATH="/mnt/newdisk/miniconda3/envs/eman2;/mnt/newdisk/miniconda3/envs/eman2/.."

-- Found PythonInterp: /mnt/newdisk/miniconda3/envs/eman2/bin/python (found version "3.7.7")

-- Found PythonLibs: /mnt/newdisk/miniconda3/envs/eman2/lib/libpython3.7m.so (found version "3.7.7")

PYTHON_EXECUTABLE: /mnt/newdisk/miniconda3/envs/eman2/bin/python

PYTHON_LIBRARIES: /mnt/newdisk/miniconda3/envs/eman2/lib/libpython3.7m.so

PYTHON_INCLUDE_DIRS: /mnt/newdisk/miniconda3/envs/eman2/include/python3.7m

PYTHON_INCLUDE_PATH: /mnt/newdisk/miniconda3/envs/eman2/include/python3.7m

PYTHON_INCLUDE_DIR: /mnt/newdisk/miniconda3/envs/eman2/include/python3.7m

Python site-packages: /mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages

-- PYTHON_LIB_SHARED="0"

-- CMAKE_CXX_COMPILER_ID="GNU"

-- Found Python: /mnt/newdisk/miniconda3/envs/eman2/bin/python

-- NUMPY_INCLUDE_DIR="/mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/numpy/core/include"

-- Found NumPy: /mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/numpy/core/include

-- Found Nosetests: /mnt/newdisk/miniconda3/envs/eman2/bin/nosetests

CMake Warning at /mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/cmake/data/share/cmake-3.14/Modules/FindBoost.cmake:905 (message):

New Boost version may have incorrect or missing dependencies and imported

targets

Call Stack (most recent call first):

/mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/cmake/data/share/cmake-3.14/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)

/mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/cmake/data/share/cmake-3.14/Modules/FindBoost.cmake:1709 (_Boost_MISSING_DEPENDENCIES)

cmake/Boost.cmake:3 (find_package)

cmake/find_all.cmake:7 (include)

CMakeLists.txt:77 (include)

CMake Warning at /mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/cmake/data/share/cmake-3.14/Modules/FindBoost.cmake:905 (message):

New Boost version may have incorrect or missing dependencies and imported

targets

Call Stack (most recent call first):

/mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/cmake/data/share/cmake-3.14/Modules/FindBoost.cmake:1027 (_Boost_COMPONENT_DEPENDENCIES)

/mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/cmake/data/share/cmake-3.14/Modules/FindBoost.cmake:1709 (_Boost_MISSING_DEPENDENCIES)

cmake/Boost.cmake:3 (find_package)

cmake/find_all.cmake:7 (include)

CMakeLists.txt:77 (include)

-- Boost version: 1.74.0

-- Found the following Boost libraries:

-- python37

-- numpy37

Boost_LIBRARIES: /mnt/newdisk/miniconda3/envs/eman2/lib/libboost_python37.so;/mnt/newdisk/miniconda3/envs/eman2/lib/libboost_numpy37.so

Boost_INCLUDE_DIR: /mnt/newdisk/miniconda3/envs/eman2/include

-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")

-- Found GSL: /mnt/newdisk/miniconda3/envs/eman2/include (found version "2.4")

-- HDF5_LIBRARY="/mnt/newdisk/miniconda3/envs/eman2/lib/libhdf5.so"

-- Found HDF5: /mnt/newdisk/miniconda3/envs/eman2/lib/libhdf5.so

-- Found FFTW3: /mnt/newdisk/miniconda3/envs/eman2/include

-- Found TIFF: /mnt/newdisk/miniconda3/envs/eman2/lib/libtiff.so (found version "4.0.9")

-- TIFF_LIBRARIES="/mnt/newdisk/miniconda3/envs/eman2/lib/libtiff.so"

-- Found JPEG: /mnt/newdisk/miniconda3/envs/eman2/lib/libjpeg.so (found version "90")

-- JPEG_LIBRARIES="/mnt/newdisk/miniconda3/envs/eman2/lib/libjpeg.so"

-- Found ZLIB: /mnt/newdisk/miniconda3/envs/eman2/lib/libz.so (found version "1.2.11")

-- Found PNG: /mnt/newdisk/miniconda3/envs/eman2/lib/libpng.so (found version "1.6.37")

-- PNG_LIBRARIES="/mnt/newdisk/miniconda3/envs/eman2/lib/libpng.so;/mnt/newdisk/miniconda3/envs/eman2/lib/libz.so"

CMake Error at /mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/cmake/data/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:137 (message):

Could NOT find OpenGL (missing: OPENGL_opengl_LIBRARY OpenGL)

Call Stack (most recent call first):

/mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/cmake/data/share/cmake-3.14/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)

/mnt/newdisk/miniconda3/envs/eman2/lib/python3.7/site-packages/cmake/data/share/cmake-3.14/Modules/FindOpenGL.cmake:397 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)

cmake/OpenGL.cmake:3 (find_package)

libEM/CMakeLists.txt:161 (include)

-- Configuring incomplete, errors occurred!

See also "/mnt/newdisk/eman2/eman2/eman2-build/CMakeFiles/CMakeOutput.log".

See also "/mnt/newdisk/eman2/eman2/eman2-build/CMakeFiles/CMakeError.log".

How can I fix this problem?

I have installed mesa, libgl1-mesa-dev, libglu1-mesa-dev, libglu1-mesa-dev, freeglut3-dev, g++. And I'm using VMware on Windows, Unbuntu 20.04 TLS.

Thanks!

TeQiang Zou

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Nov 17, 2020, 10:32:55 PM11/17/20

to EMAN2

And I start to wonder if I could use EMAN2 on the VMware since there is no real graphics driver on it....Which means couldn't run large 3D software.

shadow walker

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Nov 17, 2020, 10:51:45 PM11/17/20

to em...@googlegroups.com

Unfortunately, currently we can't use anaconda compilers to build EMAN2 from source. CMake not finding OpenGL is one of the problems that occurs with anaconda compilers. So, I suggest using the system compilers. Now, I see two problems in the output posted. How were the compilers installed in the first place? Did you follow the instructions on the Wiki? The second problem I see is the version of Boost. It's supposed to be 1.69 not 1.74.

What is the output of "conda list" and "conda info -a"?

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TeQiang Zou

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Nov 18, 2020, 2:30:50 AM11/18/20

to em...@googlegroups.com

For the first problem, I completely follow the wiki instructions(https://blake.bcm.edu/emanwiki/EMAN2/COMPILE_EMAN2_ANACONDA) to install the eman2. And due to internet issues (I'm in China), I download the python packages which eman2 need manually(the depencies are from eman-deps, eman-deps-cli, eman-deps-cxx, eman-deps-dev, version 25.3). So the first compiler is installed by conda.

And I am really puzzled why there is cmake on dependency file emam-deps-dev-25.3.json since you say that I should use system compilers. In https://blake.bcm.edu/emanwiki/EMAN2/COMPILE_EMAN2_ANACONDA, it tells to activate environment eman2 before cmake build, doesn't it mean to let me use anaconda cmake(but not system cmake)? I suspect that maybe I misunderstood something...

The emam-deps-dev-25.3.json is below:

{
  "arch": "x86_64",
  "build": "hfe7c423_0",
  "build_number": 0,
  "channel": "<unknown>",
  "constrains": [],
  "depends": [
    "cmake 3.14.*",
    "compilers",
    "eman-deps 25.3 hfe7c423_0",
    "libglu",
    "mesa-libgl-devel-cos6-x86_64"
  ],
  "extracted_package_dir": "/home/icecreamzou/Software/miniconda3/pkgs/eman-deps-dev-25.3-hfe7c423_0",
  "features": "",
  "files": [],
  "fn": "eman-deps-dev-25.3-hfe7c423_0.tar.bz2",
  "link": {
    "source": "/home/icecreamzou/Software/miniconda3/pkgs/eman-deps-dev-25.3-hfe7c423_0",
    "type": 1
  },
  "md5": "815f0a658ee732679bb248fbef92957c",
  "name": "eman-deps-dev",
  "package_tarball_full_path": "/home/icecreamzou/Software/miniconda3/pkgs/eman-deps-dev-25.3-hfe7c423_0.tar.bz2",
  "paths_data": {
    "paths": [],
    "paths_version": 1
  },
  "platform": "linux",
  "requested_spec": "eman-deps-dev[url=file:///home/icecreamzou/Software/eman-deps-dev-25.3-hfe7c423_0.tar.bz2]",
  "subdir": "linux-64",
  "timestamp": 1604432293592,
  "track_features": "",
  "url": "file:///home/icecreamzou/Software/eman-deps-dev-25.3-hfe7c423_0.tar.bz2",
  "version": "25.3"
}

For the second problem, I have reinstalled the 1.69 version of boost. The warning disappeared.

-- Boost version: 1.69.0

The output of conda list:
(eman2) icecreamzou@ubuntu:/mnt/newdisk/eman2/eman2/eman2-build$ conda list
# packages in environment at /mnt/newdisk/miniconda3/envs/eman2:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
absl-py 0.11.0 pypi_0 pypi
astunparse 1.6.3 pypi_0 pypi
backcall 0.2.0 pyh9f0ad1d_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
backports 1.0 py_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
backports.functools_lru_cache 1.6.1 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
binutils 2.33.1 h53a641e_7 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
binutils_impl_linux-64 2.33.1 he6710b0_7 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
binutils_linux-64 2.33.1 h9595d00_15 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
blas 1.0 mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
boost 1.69.0 py37h8619c78_1001 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
boost-cpp 1.69.0 ha2d47e9_1001 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bsddb3 6.2.6 py37h516909a_1000 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bzip2 1.0.8 h516909a_3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
c-ares 1.11.0 h470a237_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
c-compiler 1.1.1 h516909a_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ca-certificates 2020.10.14 0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
cachetools 4.1.1 pypi_0 pypi
certifi 2020.11.8 py37h89c1867_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
chardet 3.0.4 pypi_0 pypi
cmake 3.14.3 pypi_0 pypi
colorama 0.4.4 pyh9f0ad1d_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
compilers 1.1.1 0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
configparser 5.0.1 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cudatoolkit 8.0 3 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cudnn 6.0.21 cuda8.0_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/free
cxx-compiler 1.1.1 hc9558a2_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
cycler 0.10.0 py_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
dbus 1.13.6 hfdff14a_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
decorator 4.4.2 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
eman-deps 25.3 hfe7c423_0 <unknown>
eman-deps-cli 25.3 hfe7c423_0 <unknown>
eman-deps-cxx 25.3 he982023_0 <unknown>
eman-deps-dev 25.3 hfe7c423_0 <unknown>
expat 2.2.9 he1b5a44_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fftw 3.3.8 mpi_openmpi_h6dd7431_1005 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fontconfig 2.13.1 he4413a7_1000 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fortran-compiler 1.1.1 he991be0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
freetype 2.10.4 h7ca028e_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ftgl 2.4.0 hc56bac0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
future 0.18.2 py37h89c1867_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gast 0.3.3 pypi_0 pypi
gcc_impl_linux-64 7.3.0 habb00fd_1 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
gcc_linux-64 7.3.0 h553295d_15 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
gettext 0.19.8.1 hf34092f_1004 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gfortran_impl_linux-64 7.3.0 hdf63c60_1 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
gfortran_linux-64 7.3.0 h553295d_15 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
glib 2.66.2 h58526e2_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
google-auth 1.23.0 pypi_0 pypi
google-auth-oauthlib 0.4.2 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
grpcio 1.33.2 pypi_0 pypi
gsl 2.4 h294904e_1006 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gstreamer 1.14.5 h36ae1b5_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gxx_impl_linux-64 7.3.0 hdf63c60_1 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
gxx_linux-64 7.3.0 h553295d_15 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
h5py 2.10.0 pypi_0 pypi
hdf5 1.8.18 3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
icu 58.2 hf484d3e_1000 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
idna 2.10 pypi_0 pypi
importlib-metadata 2.0.0 pypi_0 pypi
intel-openmp 2020.2 254 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
ipython 7.19.0 py37h888b3d9_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ipython_genutils 0.2.0 py_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jedi 0.17.0 py37_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
joblib 0.17.0 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
jpeg 9d h36c2ea0_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
keras-preprocessing 1.1.2 pypi_0 pypi
kernel-headers_linux-64 2.6.32 h77966d4_13 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
kiwisolver 1.3.1 py37hc928c03_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
krb5 1.17.1 hfafb76e_3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ld_impl_linux-64 2.33.1 h53a641e_7 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libblas 3.8.0 20_mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libcblas 3.8.0 20_mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libclang 10.0.1 default_hde54327_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libcurl 7.71.1 hcdd3856_8 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libdb 6.1.26 0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
libdrm-cos6-x86_64 2.4.65 h9d98e8f_1104 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libedit 3.1.20191231 h14c3975_1 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libev 4.33 h516909a_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libevent 2.1.10 hcdb4288_3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libffi 3.2.1 hf484d3e_1007 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgcc 7.2.0 h69d50b8_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgcc-ng 9.1.0 hdf63c60_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libgfortran 3.0.0 1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgfortran-ng 7.3.0 hdf63c60_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libglib 2.66.2 hbe7bbb4_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libglu 9.0.0 he1b5a44_1001 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libiconv 1.16 h516909a_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
liblapack 3.8.0 20_mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
liblapacke 3.8.0 20_mkl http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libllvm10 10.0.1 he513fc3_3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libnghttp2 1.41.0 hab1572f_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libopenblas 0.3.10 pthreads_hb3c22a3_4 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpng 1.6.37 h21135ba_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libpq 12.3 h5513abc_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libssh2 1.9.0 hab1572f_5 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
libtiff 4.0.9 h648cc4a_1002 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libuuid 2.32.1 h14c3975_1000 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libwebp-base 1.1.0 h36c2ea0_3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libx11-common-cos6-x86_64 1.6.4 h9d98e8f_1104 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libx11-cos6-x86_64 1.6.4 h9d98e8f_1104 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxcb 1.13 h14c3975_1002 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxkbcommon 0.10.0 he1b5a44_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxml2 2.9.9 h13577e0_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
llvm-openmp 11.0.0 hfc4b9b4_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lz4-c 1.9.2 he1b5a44_3 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
markdown 3.3.3 pypi_0 pypi
matplotlib 3.2.2 1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
matplotlib-base 3.2.2 py37hef1b27d_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mesa-dri-drivers-cos6-x86_64 11.0.7 h9d98e8f_1104 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mesa-dri1-drivers-cos6-x86_64 7.11 h9d98e8f_1104 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mesa-libgl-cos6-x86_64 11.0.7 h9d98e8f_1104 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mesa-libgl-devel-cos6-x86_64 11.0.7 h9d98e8f_1104 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mkl 2020.2 256 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl-service 2.3.0 py37he904b0f_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl_fft 1.2.0 py37h23d657b_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mkl_random 1.1.1 py37h0573a6f_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
mpi 1.0 openmpi http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mysql-common 8.0.21 2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mysql-libs 8.0.21 hf3661c5_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ncurses 6.2 he6710b0_1 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
nose 1.3.7 py_1006 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
nspr 4.29 he1b5a44_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
nss 3.58 h27285de_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
numpy 1.17.4 py37hc1035e2_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
numpy-base 1.17.4 py37hde5b4d6_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
oauthlib 3.1.0 pypi_0 pypi
olefile 0.46 pyh9f0ad1d_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openmpi 3.1.4 hc99cbb1_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
openssl 1.1.1h h7b6447c_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
opt-einsum 3.3.0 pypi_0 pypi
pandas 1.1.4 py37h10a2094_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
parso 0.8.0 py_1 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pcre 8.44 he1b5a44_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pickleshare 0.7.5 py_1003 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pillow 6.1.0 py37he7afcd5_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pip 20.2.4 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
prompt-toolkit 3.0.8 pyha770c72_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
protobuf 3.14.0 pypi_0 pypi
pthread-stubs 0.4 h14c3975_1001 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
ptyprocess 0.6.0 py_1001 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyasn1 0.4.8 pypi_0 pypi
pyasn1-modules 0.2.8 pypi_0 pypi
pydusa 1.15 py37h414ee2b_17 <unknown>
pygments 2.7.2 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyopengl 3.1.5 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyqt 5.9.2 py37hcca6a23_4 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python 3.7.7 hcf32534_0_cpython http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
python-dateutil 2.8.1 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python_abi 3.7 1_cp37m http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytz 2020.4 pyhd8ed1ab_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
qt 5.9.7 h52cfd70_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
readline 8.0 h7b6447c_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
requests 2.25.0 pypi_0 pypi
requests-oauthlib 1.3.0 pypi_0 pypi
rsa 4.6 pypi_0 pypi
scikit-learn 0.23.2 py37hddcf8d6_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
scipy 1.5.2 py37hb14ef9d_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
setuptools 49.6.0 py37he5f6b98_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
sip 4.19.8 py37hf484d3e_1000 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
six 1.15.0 py_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
sqlite 3.33.0 h62c20be_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
sysroot_linux-64 2.12 h77966d4_13 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
system 5.8 2 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tensorboard 2.4.0 pypi_0 pypi
tensorboard-plugin-wit 1.7.0 pypi_0 pypi
tensorflow-estimator 2.3.0 pypi_0 pypi
tensorflow-gpu 2.3.1 pypi_0 pypi
termcolor 1.1.0 pypi_0 pypi
threadpoolctl 2.1.0 pyh5ca1d4c_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tk 8.6.10 hbc83047_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
tornado 6.1 py37h4abf009_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tqdm 4.51.0 pyh9f0ad1d_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
traitlets 5.0.5 py_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tzdata 2020d h516909a_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
urllib3 1.26.2 pypi_0 pypi
wcwidth 0.2.5 pyh9f0ad1d_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
werkzeug 1.0.1 pypi_0 pypi
wheel 0.35.1 pyh9f0ad1d_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
wrapt 1.12.1 pypi_0 pypi
xorg-libxau 1.0.9 h14c3975_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz 5.2.5 h7b6447c_0 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zipp 3.4.0 pypi_0 pypi
zlib 1.2.11 h7b6447c_3 http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main
zstd 1.4.5 h6597ccf_2 http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge

The output of conda info -a:
active environment : eman2
active env location : /mnt/newdisk/miniconda3/envs/eman2
shell level : 1
user config file : /home/icecreamzou/.condarc
populated config files : /home/icecreamzou/.condarc
conda version : 4.6.14
conda-build version : not installed
python version : 3.7.3.final.0
base environment : /mnt/newdisk/miniconda3 (writable)
channel URLs : http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/linux-64
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/noarch
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo/linux-64
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo/noarch
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/linux-64
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/noarch
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64
http://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch
http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/free/linux-64
http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/free/noarch
http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main/linux-64
http://mirror.tuna.tsinghua.edu.cn/anaconda/pkgs/main/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /mnt/newdisk/miniconda3/pkgs
/home/icecreamzou/.conda/pkgs
envs directories : /mnt/newdisk/miniconda3/envs
/home/icecreamzou/.conda/envs
platform : linux-64
user-agent : conda/4.6.14 requests/2.21.0 CPython/3.7.3 Linux/5.4.0-53-generic ubuntu/20.04.1 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False

# conda environments:
#
base /mnt/newdisk/miniconda3
eman2 * /mnt/newdisk/miniconda3/envs/eman2
test /mnt/newdisk/miniconda3/envs/test

sys.version: 3.7.3 (default, Mar 27 2019, 22:11:17)
...
sys.prefix: /mnt/newdisk/miniconda3
sys.executable: /mnt/newdisk/miniconda3/bin/python
conda location: /mnt/newdisk/miniconda3/lib/python3.7/site-packages/conda
conda-build: None
conda-env: /mnt/newdisk/miniconda3/bin/conda-env
user site dirs:

CIO_TEST: <not set>
CMAKE_PREFIX_PATH: /mnt/newdisk/miniconda3/envs/eman2:/mnt/newdisk/miniconda3/envs/eman2/x86_64-conda_cos6-linux-gnu/sysroot/usr
CONDA_BACKUP_F90: /mnt/newdisk/miniconda3/envs/eman2/bin/x86_64-conda_cos6-linux-gnu-gfortran
CONDA_BACKUP_HOST: x86_64-conda_cos6-linux-gnu
CONDA_BACKUP_LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/mnt/newdisk/miniconda3/envs/eman2/lib -Wl,-rpath-link,/mnt/newdisk/miniconda3/envs/eman2/lib -L/mnt/newdisk/miniconda3/envs/eman2/lib
CONDA_BUILD_SYSROOT: /mnt/newdisk/miniconda3/envs/eman2/x86_64-conda_cos6-linux-gnu/sysroot
CONDA_DEFAULT_ENV: eman2
CONDA_EXE: /mnt/newdisk/miniconda3/bin/conda
CONDA_MKL_INTERFACE_LAYER_BACKUP:
CONDA_PREFIX: /mnt/newdisk/miniconda3/envs/eman2
CONDA_PROMPT_MODIFIER: (eman2)
CONDA_PYTHON_EXE: /mnt/newdisk/miniconda3/bin/python
CONDA_ROOT: /mnt/newdisk/miniconda3
CONDA_SHLVL: 1
NO_PROXY: <set>
PATH: /mnt/newdisk/miniconda3/bin:/mnt/newdisk/miniconda3/envs/eman2/bin:/mnt/newdisk/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
REQUESTS_CA_BUNDLE: <not set>
SSL_CERT_FILE: <not set>
WINDOWPATH: 2
no_proxy: <set>

Thanks!

shadow walker <shadoww...@gmail.com> 于2020年11月18日周三上午11:51写道：

You received this message because you are subscribed to a topic in the Google Groups "EMAN2" group.
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To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAMkj2EmxAWmMhV54d7mRoaQTeH6%3DnQq-%3DGg5y_8qpKXLsuZfGw%40mail.gmail.com.

shadow walker

unread,

Nov 18, 2020, 12:13:11 PM11/18/20

to em...@googlegroups.com

Installing the dependencies manually is not "following the instructions". This whole system of building has been designed so that users get the right dependencies without any hassle. I'm aware of similar reports where conda can have issues in China. One solution could be posting an environment file, but we don't offer environment files at the moment.

To make things work here install dependencies listed in v24.1 of eman-deps-dev, eman-deps, eman-deps-cxx and eman-deps-cli. The version you got here is marked as dev version to avoid accidental installs. With v24.1 you shouldn't get any compilers into your environment and cmake will use the system compilers.

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CA%2BPutqro820Ta%3DL77t%2Bag10-dWM0d8A8P7HVJ%2BDYRkfuvkfpoQ%40mail.gmail.com.

--

shadow_walker

TeQiang Zou

unread,

Dec 4, 2020, 8:46:28 AM12/4/20

to em...@googlegroups.com

Thank you for your suggestion. I want to make sure that if I should use cmake of anaconda or of system. Now I'm using cmake installed by conda. And error still occurred...

shadow walker <shadoww...@gmail.com> 于2020年11月19日周四上午1:13写道：

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAMkj2E%3De1TCQCoyt6OFQtqeXqfo%2BLqfcoi%3DoQ99Og24oFcaC3A%40mail.gmail.com.

Steve Ludtke

unread,

Dec 4, 2020, 10:40:49 AM12/4/20

to em...@googlegroups.com

Hi. You should use cmake from Anaconda (though if it's the same version I don't think this should matter much), and you should use system-installed compilers (as Tunay said previously). You should not have compilers installed in your EMAN2 environment. Here is the complete conda list output from the environment I'm currently using to build. I'm not saying you have to have an exact match (I haven't updated my conda environment in a while), but this does work for me right now:

(e3) id> conda list

# packages in environment at /home/stevel/EMAN2/miniconda3/envs/e3:

#

# Name Version Build Channel

_libgcc_mutex 0.1 main

_tflow_select 2.1.0 gpu

absl-py 0.9.0 py37_0

asn1crypto 1.4.0 py_0

astor 0.8.0 py37_0

attrs 19.3.0 py_0

backcall 0.1.0 py37_0

backports 1.0 py_2

backports.weakref 1.0.post1 py_1

blas 1.0 mkl

bleach 3.1.0 py_0

blinker 1.4 py37_0

boost 1.69.0 py37h3e44d54_0 conda-forge

boost-cpp 1.69.0 h3a22d5f_0 conda-forge

brotlipy 0.7.0 py37h7b6447c_1000

bsddb3 6.2.7 py37h516909a_0 conda-forge

bzip2 1.0.8 h7b6447c_0

c-ares 1.15.0 h7b6447c_1001

ca-certificates 2020.1.1 0

cachetools 4.1.1 py_0

certifi 2020.6.20 py37_0

cffi 1.14.0 py37h2e261b9_0

chardet 3.0.4 py37_1003

click 7.1.2 py_0

cmake 3.14.0 h52cb24c_0

configparser 3.7.4 py37_0

cryptography 2.8 py37h1ba5d50_0

cudatoolkit 10.1.243 h6bb024c_0

cudnn 7.6.5 cuda10.1_0

cupti 10.1.168 0

cycler 0.10.0 py37_0

dbus 1.13.12 h746ee38_0

decorator 4.4.1 py_0

defusedxml 0.6.0 py_0

eman-deps 19.1 0 cryoem

eman-deps-cli 19.1 h5ca1d4c_0 cryoem

eman-deps-cxx 19.1 h5ca1d4c_0 cryoem

eman-deps-dev 19.1 0 cryoem

entrypoints 0.3 py37_0

expat 2.2.6 he6710b0_0

fftw 3.3.8 mpi_openmpi_h6dd7431_1005 conda-forge

fftw-mpi 3.3.6 openmpi3_4 cryoem

fontconfig 2.13.0 h9420a91_0

freetype 2.9.1 h8a8886c_1

ftgl 2.1.3 1 cryoem

future 0.18.2 py37_0

gast 0.2.2 py37_0

glib 2.63.1 h5a9c865_0

gmp 6.1.2 h6c8ec71_1

google-auth 1.21.0 py_0

google-auth-oauthlib 0.4.1 py_2

google-pasta 0.1.8 py_0

grpcio 1.27.2 py37hf8bcb03_0

gsl 2.4 h14c3975_4

gst-plugins-base 1.14.0 hbbd80ab_1

gstreamer 1.14.0 hb453b48_1

h5py 2.8.0 py37h39dcb92_0

hdf5 1.8.18 h6792536_1

html5lib 1.0.1 py_0

icu 58.2 h9c2bf20_1

idna 2.10 py_0

importlib-metadata 1.6.0 py37_0

importlib_metadata 1.6.0 0

intel-openmp 2019.4 243

ipykernel 5.1.4 py37h39e3cac_0

ipython 7.12.0 py37h5ca1d4c_0

ipython_genutils 0.2.0 py37_0

ipywidgets 7.5.1 py_0

jedi 0.17.1 py37_0

jinja2 2.11.2 py_0

joblib 0.14.1 py_0

jpeg 9b h024ee3a_2

json5 0.9.5 py_0

jsonschema 3.2.0 py37_0

jupyter 1.0.0 py37_7

jupyter_client 6.1.3 py_0

jupyter_console 6.1.0 py_0

jupyter_core 4.6.3 py37_0

jupyterlab 2.2.6 py_0

jupyterlab_server 1.2.0 py_0

keras-applications 1.0.8 py_0

keras-preprocessing 1.1.0 py_1

kiwisolver 1.1.0 py37he6710b0_0

krb5 1.16.1 h173b8e3_7

ld_impl_linux-64 2.33.1 h53a641e_7

libaec 1.0.4 hf484d3e_0 conda-forge

libcurl 7.67.0 h20c2e04_0

libdb 6.1.26 he6710b0_0

libedit 3.1.20181209 hc058e9b_0

libffi 3.2.1 hd88cf55_4

libgcc-ng 9.1.0 hdf63c60_0

libgfortran-ng 7.3.0 hdf63c60_0

libpng 1.6.37 hbc83047_0

libprotobuf 3.10.1 hd408876_0

libsodium 1.0.16 h1bed415_0

libssh2 1.8.2 h1ba5d50_0

libstdcxx-ng 9.1.0 hdf63c60_0

libtiff 4.0.9 he85c1e1_2

libuuid 1.0.3 h1bed415_2

libxcb 1.13 h1bed415_1

libxml2 2.9.9 hea5a465_1

markdown 3.1.1 py37_0

markupsafe 1.1.1 py37h7b6447c_0

matplotlib 3.1.3 py37_0

matplotlib-base 3.1.3 py37hef1b27d_0

mistune 0.8.4 py37h7b6447c_0

mkl 2019.4 243

mkl-service 2.3.0 py37he904b0f_0

mkl_fft 1.0.15 py37ha843d7b_0

mkl_random 1.1.0 py37hd6b4f25_0

mock 4.0.1 py_0

mpi 1.0 openmpi

nbconvert 5.6.1 py37_0

nbformat 5.0.6 py_0

ncurses 6.1 he6710b0_1

nose 1.3.7 py37_2

notebook 6.0.3 py37_0

numpy 1.17.4 py37hc1035e2_0

numpy-base 1.17.4 py37hde5b4d6_0

oauthlib 3.1.0 py_0

openmpi 3.1.4 hc99cbb1_0 conda-forge

openssl 1.1.1d h7b6447c_3

opt_einsum 3.1.0 py_0

pandoc 2.2.3.2 0

pandocfilters 1.4.2 py37_1

parso 0.7.0 py_0

pcre 8.43 he6710b0_0

pexpect 4.8.0 py37_0

pickleshare 0.7.5 py37_0

pip 20.0.2 py37_1

prometheus_client 0.7.1 py_0

prompt_toolkit 3.0.2 py_0

protobuf 3.10.1 py37he6710b0_0

ptyprocess 0.6.0 py37_0

pyasn1 0.4.8 py_0

pyasn1-modules 0.2.7 py_0

pycparser 2.20 py_2

pydusa 1.15 numpy1.17_15 cryoem

pygments 2.5.2 py_0

pyjwt 1.7.1 py37_0

pyopengl 3.1.5 py_0 conda-forge

pyopenssl 19.1.0 py_1

pyparsing 2.4.5 py_0

pyqt 5.9.2 py37h05f1152_2

pyreadline 2.1 pypi_0 pypi

pyrsistent 0.16.0 py37h7b6447c_0

pysocks 1.7.1 py37_1

python 3.7.6 h0371630_2

python-dateutil 2.8.1 py_0

pytz 2019.3 py_0

pyzmq 18.1.1 py37he6710b0_0

qt 5.9.7 h5867ecd_1

qtconsole 4.7.4 py_0

qtpy 1.9.0 py_0

readline 7.0 h7b6447c_5

requests 2.24.0 py_0

requests-oauthlib 1.3.0 py_0

rhash 1.3.8 h1ba5d50_0

rsa 4.6 py_0

scikit-learn 0.22.1 py37hd81dba3_0

scipy 1.4.1 py37h0b6359f_0

send2trash 1.5.0 py37_0

setuptools 45.2.0 py37_0

sip 4.19.8 py37hf484d3e_0

six 1.14.0 py37_0

sphire 1.4.0 pypi_0 pypi

sqlite 3.30.1 h7b6447c_0

tbb 2020.0 hfd86e86_0

tbb4py 2020.0 py37hfd86e86_0

tensorboard 2.2.1 pyh532a8cf_0

tensorboard-plugin-wit 1.6.0 py_0

tensorflow 2.1.0 gpu_py37h7a4bb67_0

tensorflow-base 2.1.0 gpu_py37h6c5654b_0

tensorflow-estimator 2.1.0 pyhd54b08b_0

tensorflow-gpu 2.1.0 h0d30ee6_0

termcolor 1.1.0 py37_1

terminado 0.8.3 py37_0

testpath 0.4.4 py_0

tk 8.6.8 hbc83047_0

tornado 6.0.3 py37h7b6447c_3

tqdm 4.40.0 py_0

traitlets 4.3.3 py37_0

urllib3 1.25.10 py_0

wcwidth 0.1.8 py_0

webencodings 0.5.1 py37_1

werkzeug 0.16.0 py_0

wheel 0.34.2 py37_0

widgetsnbextension 3.5.1 py37_0

wrapt 1.11.2 py37h7b6447c_0

xz 5.2.4 h14c3975_4

zeromq 4.3.1 he6710b0_3

zipp 3.1.0 py_0

zlib 1.2.11 h7b6447c_3

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CA%2BPutqqJXfPay2nF%2Ba6T%3DtqpZFCopbiAbafD28ipizKjQHR1MQ%40mail.gmail.com.

TeQiang Zou

unread,

Dec 4, 2020, 9:09:16 PM12/4/20

to em...@googlegroups.com

Thanks, you are really helpful. I will try again!

Steve Ludtke <slud...@gmail.com> 于2020年12月4日周五下午11:40写道：

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/6DDE0078-43E3-44A2-954B-00D9359933A6%40gmail.com.

TeQiang Zou

unread,

Dec 5, 2020, 5:46:30 AM12/5/20

to em...@googlegroups.com

I feel really happy that I have built the eman2 successfully, the output is below:

(eman2) icecreamzou@ubuntu:/mnt/newdisk/eman2-build$ cmake ../eman2 -DENABLE_OPTIMIZE_MACHINE=ON
-- The CXX compiler identification is GNU 9.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works

-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so found components: OpenGL
-- OPENGL_INCLUDE_DIR="/usr/include"
-- OPENGL_LIBRARIES="/usr/lib/x86_64-linux-gnu/libOpenGL.so;/usr/lib/x86_64-linux-gnu/libGLX.so;/usr/lib/x86_64-linux-gnu/libGLU.so"
-- OPENGL_glu_LIBRARY="/usr/lib/x86_64-linux-gnu/libGLU.so"
-- OPENGL_opengl_LIBRARY="/usr/lib/x86_64-linux-gnu/libOpenGL.so"
-- OPENGL_gl_LIBRARY=""
-- OPENGL_FOUND="TRUE"
-- OPENGL_GLU_FOUND="YES"
-- OpenGL_OpenGL_FOUND="TRUE"
-- OPENGL_opengl_LIBRARY="/usr/lib/x86_64-linux-gnu/libOpenGL.so"
-- OPENGL_gl_LIBRARY=""
Target OpenGL exists.
Target OpenGL::OpenGL exists.
Target OpenGL::GL exists.
Target OpenGL::GLU exists.
-- Found FTGL: /mnt/newdisk/miniconda3/envs/eman2/include
-- Found Freetype: /mnt/newdisk/miniconda3/envs/eman2/lib/libfreetype.so (found version "2.10.4")
FREETYPE_LIBRARIES: /mnt/newdisk/miniconda3/envs/eman2/lib/libfreetype.so
FREETYPE_INCLUDE_DIRS: /mnt/newdisk/miniconda3/envs/eman2/include/freetype2
-- EMAN_GITDIR="/mnt/newdisk/eman2"
-- CMAKE_SOURCE_DIR="/mnt/newdisk/eman2"
-- Configuring done
-- Generating done
-- Build files have been written to: /mnt/newdisk/eman2-build

Since this is the furthest step I have ever reached, I am really excited. However, when I make it using "make -j 16", 2 error still occured, which made me feel upset again. Would you like to help me find out what the cause is this time? The output of make -j 16 is below:

(eman2) icecreamzou@ubuntu:/mnt/newdisk/eman2-build$ make -j 16
Scanning dependencies of target EM2
[ 0%] Building CXX object libEM/CMakeFiles/EM2.dir/byteorder.cpp.o
[ 1%] Building CXX object libEM/CMakeFiles/EM2.dir/boxingtools.cpp.o
[ 2%] Building CXX object libEM/CMakeFiles/EM2.dir/emfft.cpp.o
[ 2%] Building CXX object libEM/CMakeFiles/EM2.dir/log.cpp.o
[ 3%] Building CXX object libEM/CMakeFiles/EM2.dir/emobject.cpp.o
[ 5%] Building CXX object libEM/CMakeFiles/EM2.dir/util.cpp.o
[ 5%] Building CXX object libEM/CMakeFiles/EM2.dir/io/imageio.cpp.o
[ 5%] Building CXX object libEM/CMakeFiles/EM2.dir/emutil.cpp.o
[ 6%] Building CXX object libEM/CMakeFiles/EM2.dir/interp.cpp.o
[ 7%] Building CXX object libEM/CMakeFiles/EM2.dir/quaternion.cpp.o
[ 7%] Building CXX object libEM/CMakeFiles/EM2.dir/transform.cpp.o
[ 8%] Building CXX object libEM/CMakeFiles/EM2.dir/symmetry.cpp.o
[ 9%] Building CXX object libEM/CMakeFiles/EM2.dir/geometry.cpp.o
[ 10%] Building CXX object libEM/CMakeFiles/EM2.dir/pointarray.cpp.o
[ 10%] Building CXX object libEM/CMakeFiles/EM2.dir/pdbreader.cpp.o
[ 11%] Building CXX object libEM/CMakeFiles/EM2.dir/io/mrcio.cpp.o
[ 12%] Building CXX object libEM/CMakeFiles/EM2.dir/io/eerio.cpp.o
[ 13%] Building CXX object libEM/CMakeFiles/EM2.dir/io/dm3io.cpp.o
[ 13%] Building CXX object libEM/CMakeFiles/EM2.dir/io/dm4io.cpp.o
[ 14%] Building CXX object libEM/CMakeFiles/EM2.dir/io/tifio.cpp.o
[ 15%] Building CXX object libEM/CMakeFiles/EM2.dir/io/hdfio.cpp.o
[ 15%] Building CXX object libEM/CMakeFiles/EM2.dir/io/hdfio2.cpp.o
[ 16%] Building CXX object libEM/CMakeFiles/EM2.dir/io/jpegio.cpp.o
In file included from /mnt/newdisk/miniconda3/envs/eman2/include/boost/config/header_deprecated.hpp:18,
from /mnt/newdisk/miniconda3/envs/eman2/include/boost/pending/integer_log2.hpp:5,
from /mnt/newdisk/miniconda3/envs/eman2/include/boost/random/detail/integer_log2.hpp:19,
from /mnt/newdisk/miniconda3/envs/eman2/include/boost/random/detail/large_arithmetic.hpp:19,
from /mnt/newdisk/miniconda3/envs/eman2/include/boost/random/detail/const_mod.hpp:23,
from /mnt/newdisk/miniconda3/envs/eman2/include/boost/random/linear_congruential.hpp:30,
from /mnt/newdisk/miniconda3/envs/eman2/include/boost/random/additive_combine.hpp:27,
from /mnt/newdisk/miniconda3/envs/eman2/include/boost/random.hpp:36,
from /mnt/newdisk/eman2/libEM/pointarray.cpp:38:
/mnt/newdisk/miniconda3/envs/eman2/include/boost/pending/integer_log2.hpp:7:1: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
7 | BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
| ^~~~~~~~~~~~~~~~~~~~~~~
[ 17%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata.cpp.o
[ 18%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_io.cpp.o
[ 18%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_core.cpp.o
[ 19%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_cuda.cpp.o
[ 20%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_modular.cpp.o
[ 21%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_metadata.cpp.o
[ 21%] Building CXX object libEM/CMakeFiles/EM2.dir/emdata_transform.cpp.o
[ 22%] Building CXX object libEM/CMakeFiles/EM2.dir/io/pifio.cpp.o
[ 23%] Building CXX object libEM/CMakeFiles/EM2.dir/io/v4l2io.cpp.o
[ 23%] Building CXX object libEM/CMakeFiles/EM2.dir/io/vtkio.cpp.o
[ 24%] Building CXX object libEM/CMakeFiles/EM2.dir/io/spiderio.cpp.o
[ 25%] Building CXX object libEM/CMakeFiles/EM2.dir/io/sspiderio.cpp.o
[ 26%] Building CXX object libEM/CMakeFiles/EM2.dir/io/pgmio.cpp.o
[ 26%] Building CXX object libEM/CMakeFiles/EM2.dir/io/fitsio.cpp.o
[ 27%] Building CXX object libEM/CMakeFiles/EM2.dir/io/icosio.cpp.o
[ 28%] Building CXX object libEM/CMakeFiles/EM2.dir/io/lstio.cpp.o
[ 28%] Building CXX object libEM/CMakeFiles/EM2.dir/io/lstfastio.cpp.o
[ 29%] Building CXX object libEM/CMakeFiles/EM2.dir/io/pngio.cpp.o
[ 30%] Building CXX object libEM/CMakeFiles/EM2.dir/io/salio.cpp.o
[ 31%] Building CXX object libEM/CMakeFiles/EM2.dir/io/amiraio.cpp.o
[ 31%] Building CXX object libEM/CMakeFiles/EM2.dir/io/xplorio.cpp.o
[ 32%] Building CXX object libEM/CMakeFiles/EM2.dir/io/gatan2io.cpp.o
[ 33%] Building CXX object libEM/CMakeFiles/EM2.dir/io/emio.cpp.o
[ 34%] Building CXX object libEM/CMakeFiles/EM2.dir/io/imagicio.cpp.o
[ 34%] Building CXX object libEM/CMakeFiles/EM2.dir/io/imagicio2.cpp.o
[ 35%] Building CXX object libEM/CMakeFiles/EM2.dir/io/df3io.cpp.o
[ 36%] Building CXX object libEM/CMakeFiles/EM2.dir/io/omapio.cpp.o
[ 36%] Building CXX object libEM/CMakeFiles/EM2.dir/io/situsio.cpp.o
[ 37%] Building CXX object libEM/CMakeFiles/EM2.dir/io/serio.cpp.o
[ 38%] Building CXX object libEM/CMakeFiles/EM2.dir/emcache.cpp.o
[ 39%] Building CXX object libEM/CMakeFiles/EM2.dir/ctf.cpp.o
[ 39%] Building CXX object libEM/CMakeFiles/EM2.dir/xydata.cpp.o
[ 40%] Building CXX object libEM/CMakeFiles/EM2.dir/processor.cpp.o
[ 41%] Building CXX object libEM/CMakeFiles/EM2.dir/aligner.cpp.o
[ 42%] Building CXX object libEM/CMakeFiles/EM2.dir/projector.cpp.o
[ 42%] Building CXX object libEM/CMakeFiles/EM2.dir/cmp.cpp.o
[ 43%] Building CXX object libEM/CMakeFiles/EM2.dir/averager.cpp.o
[ 44%] Building CXX object libEM/CMakeFiles/EM2.dir/reconstructor.cpp.o
[ 44%] Building CXX object libEM/CMakeFiles/EM2.dir/reconstructor_tools.cpp.o
[ 45%] Building CXX object libEM/CMakeFiles/EM2.dir/exception.cpp.o
[ 46%] Building CXX object libEM/CMakeFiles/EM2.dir/testutil.cpp.o
[ 47%] Building CXX object libEM/CMakeFiles/EM2.dir/analyzer.cpp.o
[ 47%] Building CXX object libEM/CMakeFiles/EM2.dir/randnum.cpp.o
[ 48%] Building CXX object libEM/CMakeFiles/EM2.dir/io/hdf_filecache.cpp.o
[ 49%] Building CXX object libEM/CMakeFiles/EM2.dir/polardata.cpp.o
[ 50%] Building CXX object libEM/CMakeFiles/EM2.dir/tomoseg.cpp.o
[ 50%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/grid_queue.cpp.o
[ 51%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/grid_queue2.cpp.o
[ 52%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/volume_data.cpp.o
[ 52%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/volume.cpp.o
[ 53%] Building CXX object libEM/CMakeFiles/EM2.dir/gorgon/skeletonizer.cpp.o
[ 54%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/emdata_sparx.cpp.o
[ 55%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/fundamentals.cpp.o
[ 55%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/fourierfilter.cpp.o
[ 56%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/rsconvolution.cpp.o
[ 57%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/native_fft.cpp.o
[ 57%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/util_sparx.cpp.o
[ 58%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/lapackblas.cpp.o
[ 59%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/pca.cpp.o
[ 60%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/varimax.cpp.o
[ 61%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/steepest.cpp.o
[ 61%] Building CXX object libEM/CMakeFiles/EM2.dir/sparx/lbfgsb.cpp.o
[ 62%] Building CXX object libEM/CMakeFiles/EM2.dir/sphire/emdata_sphire.cpp.o
[ 63%] Building CXX object libEM/CMakeFiles/EM2.dir/sphire/util_sphire.cpp.o
[ 63%] Linking CXX shared library libEM2.so
[ 63%] Built target EM2
Scanning dependencies of target pyGLUtils2
Scanning dependencies of target pyAligner2
Scanning dependencies of target pyMarchingCubes2
Scanning dependencies of target pyTransform2
Scanning dependencies of target pyPointArray2
Scanning dependencies of target pyFundamentals2
Scanning dependencies of target pyEMObject2
Scanning dependencies of target pyEMData2
Scanning dependencies of target pyTomoSeg2
Scanning dependencies of target pyProcessor2
Scanning dependencies of target pyUtils2
Scanning dependencies of target pyPDBReader2
Scanning dependencies of target pyProjector2
Scanning dependencies of target pyAverager2
Scanning dependencies of target pyCmp2
Scanning dependencies of target pyReconstructor2
[ 64%] Building CXX object libpyEM/CMakeFiles/pyTransform2.dir/libpyTransform2.cpp.o
[ 65%] Building CXX object libpyEM/CMakeFiles/pyFundamentals2.dir/libpyFundamentals2.cpp.o
[ 66%] Building CXX object libpyEM/CMakeFiles/pyPointArray2.dir/libpyPointArray2.cpp.o
[ 66%] Building CXX object libpyEM/CMakeFiles/pyGLUtils2.dir/libpyGLUtils2.cpp.o
[ 67%] Building CXX object libpyEM/CMakeFiles/pyEMObject2.dir/libpyEMObject2.cpp.o
[ 67%] Building CXX object libpyEM/CMakeFiles/pyAligner2.dir/libpyAligner2.cpp.o
[ 67%] Building CXX object libpyEM/CMakeFiles/pyEMData2.dir/libpyEMData2.cpp.o
[ 67%] Building CXX object libpyEM/CMakeFiles/pyMarchingCubes2.dir/libpyMarchingCubes2.cpp.o
[ 68%] Building CXX object libpyEM/CMakeFiles/pyProcessor2.dir/libpyProcessor2.cpp.o
[ 68%] Building CXX object libpyEM/CMakeFiles/pyProjector2.dir/libpyProjector2.cpp.o
[ 68%] Building CXX object libpyEM/CMakeFiles/pyTomoSeg2.dir/libpyTomoSeg2.cpp.o
[ 68%] Building CXX object libpyEM/CMakeFiles/pyUtils2.dir/libpyUtils2.cpp.o
[ 69%] Building CXX object libpyEM/CMakeFiles/pyAverager2.dir/libpyAverager2.cpp.o
[ 70%] Building CXX object libpyEM/CMakeFiles/pyPDBReader2.dir/libpyPDBReader2.cpp.o
[ 71%] Building CXX object libpyEM/CMakeFiles/pyCmp2.dir/libpyCmp2.cpp.o
[ 72%] Building CXX object libpyEM/CMakeFiles/pyReconstructor2.dir/libpyReconstructor2.cpp.o
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyPointArray2.dir/build.make:63: libpyEM/CMakeFiles/pyPointArray2.dir/libpyPointArray2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyPointArray2.dir/libpyPointArray2.cpp.o'
make[1]: *** [CMakeFiles/Makefile2:484: libpyEM/CMakeFiles/pyPointArray2.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 73%] Building CXX object libpyEM/CMakeFiles/pyGLUtils2.dir/__/libEM/emftgl.cpp.o
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyTransform2.dir/build.make:63: libpyEM/CMakeFiles/pyTransform2.dir/libpyTransform2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyTransform2.dir/libpyTransform2.cpp.o'
make[1]: *** [CMakeFiles/Makefile2:521: libpyEM/CMakeFiles/pyTransform2.dir/all] Error 2
[ 74%] Building CXX object libpyEM/CMakeFiles/pyMarchingCubes2.dir/__/libEM/marchingcubes.cpp.o
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyGLUtils2.dir/build.make:63: libpyEM/CMakeFiles/pyGLUtils2.dir/libpyGLUtils2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyGLUtils2.dir/libpyGLUtils2.cpp.o'
make[2]: *** Waiting for unfinished jobs....
[ 75%] Building CXX object libpyEM/CMakeFiles/pyEMData2.dir/emdata_wrapitems.cpp.o
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyFundamentals2.dir/build.make:63: libpyEM/CMakeFiles/pyFundamentals2.dir/libpyFundamentals2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyFundamentals2.dir/libpyFundamentals2.cpp.o'
make[1]: *** [CMakeFiles/Makefile2:558: libpyEM/CMakeFiles/pyFundamentals2.dir/all] Error 2
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyUtils2.dir/build.make:63: libpyEM/CMakeFiles/pyUtils2.dir/libpyUtils2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyUtils2.dir/libpyUtils2.cpp.o'
make[1]: *** [CMakeFiles/Makefile2:891: libpyEM/CMakeFiles/pyUtils2.dir/all] Error 2
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyAverager2.dir/build.make:63: libpyEM/CMakeFiles/pyAverager2.dir/libpyAverager2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyAverager2.dir/libpyAverager2.cpp.o'
make[1]: *** [CMakeFiles/Makefile2:928: libpyEM/CMakeFiles/pyAverager2.dir/all] Error 2
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyEMData2.dir/build.make:63: libpyEM/CMakeFiles/pyEMData2.dir/libpyEMData2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyEMData2.dir/libpyEMData2.cpp.o'
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:595: libpyEM/CMakeFiles/pyGLUtils2.dir/all] Error 2
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyTomoSeg2.dir/build.make:63: libpyEM/CMakeFiles/pyTomoSeg2.dir/libpyTomoSeg2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyTomoSeg2.dir/libpyTomoSeg2.cpp.o'
make[1]: *** [CMakeFiles/Makefile2:743: libpyEM/CMakeFiles/pyTomoSeg2.dir/all] Error 2
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyProjector2.dir/build.make:63: libpyEM/CMakeFiles/pyProjector2.dir/libpyProjector2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyProjector2.dir/libpyProjector2.cpp.o'
make[1]: *** [CMakeFiles/Makefile2:854: libpyEM/CMakeFiles/pyProjector2.dir/all] Error 2
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyReconstructor2.dir/build.make:63: libpyEM/CMakeFiles/pyReconstructor2.dir/libpyReconstructor2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyReconstructor2.dir/libpyReconstructor2.cpp.o'
make[1]: *** [CMakeFiles/Makefile2:1039: libpyEM/CMakeFiles/pyReconstructor2.dir/all] Error 2
c++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make[2]: *** [libpyEM/CMakeFiles/pyMarchingCubes2.dir/build.make:63: libpyEM/CMakeFiles/pyMarchingCubes2.dir/libpyMarchingCubes2.cpp.o] Error 1
make[2]: *** Deleting file 'libpyEM/CMakeFiles/pyMarchingCubes2.dir/libpyMarchingCubes2.cpp.o'
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:669: libpyEM/CMakeFiles/pyMarchingCubes2.dir/all] Error 2
[ 76%] Linking CXX shared library libpyEMObject2.so
[ 76%] Linking CXX shared library libpyPDBReader2.so
[ 76%] Built target pyPDBReader2
[ 76%] Built target pyEMObject2
make[1]: *** [CMakeFiles/Makefile2:706: libpyEM/CMakeFiles/pyEMData2.dir/all] Error 2
[ 77%] Linking CXX shared library libpyProcessor2.so
[ 77%] Built target pyProcessor2
[ 78%] Linking CXX shared library libpyCmp2.so
[ 78%] Built target pyCmp2
[ 79%] Linking CXX shared library libpyAligner2.so
[ 79%] Built target pyAligner2
make: *** [Makefile:141: all] Error 2

Thanks!

TeQiang Zou <xdt...@gmail.com> 于2020年12月5日周六上午10:08写道：

TeQiang Zou

unread,

Dec 5, 2020, 7:34:11 AM12/5/20

to em...@googlegroups.com

I have solved it. It's simply because I ran out of my memory. I just chang to "make" which will choose the suitable j for me. And then I make the eman2 successfully!

TeQiang Zou <xdt...@gmail.com> 于2020年12月5日周六下午6:46写道：

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