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Installation problems of fem-dem coupling #24

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1qq12 opened this issue Jul 13, 2021 · 6 comments
Open

Installation problems of fem-dem coupling #24

1qq12 opened this issue Jul 13, 2021 · 6 comments

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@1qq12
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1qq12 commented Jul 13, 2021

Hi, Jan：
When I install fem-dem coupling, I use the make all command. Based on the answer in (#21), I installed python2 versions with the following code:

sudo apt install python-dev python-ipython python-numpy python-tk python-xlib python-pyqt5 python-minieigen python-pyqt5.qtwebkit python-gts

However I still got the following error:
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/oofem
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/yade
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/install
rm -rf /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source-orig
wget http://www.oofem.org/cgi-bin/OOFEM/download.cgi?download=oofem-2.5.zip -O /home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip
--2021-07-13 13:54:40-- http://www.oofem.org/cgi-bin/OOFEM/download.cgi?download=oofem-2.5.zip
正在解析主机 www.oofem.org (www.oofem.org)... 147.32.130.71
正在连接 www.oofem.org (www.oofem.org)|147.32.130.71|:80... 已连接。
已发出 HTTP 请求，正在等待回应... 302 Found
位置：http://www.oofem.org/download/oofem-2.5.zip [跟随至新的 URL]
--2021-07-13 13:54:47-- http://www.oofem.org/download/oofem-2.5.zip
再次使用存在的到 www.oofem.org:80 的连接。
已发出 HTTP 请求，正在等待回应... 200 OK
长度： 14249792 (14M) [application/zip]
正在保存至: “/home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip”

/home/dadn/dem-fem- 100%[===================>] 13.59M 1.72MB/s 用时 14s

2021-07-13 13:55:02 (968 KB/s) - 已保存 “/home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip” [14249792/14249792])

unzip -q -o /home/dadn/dem-fem-coupling-master/installation/_build/oofem/oofem.zip
mv oofem-2.5 /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source-orig
rm -rf /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
cp -r /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source-orig /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
cd /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source &&
patch -s -p0 < /home/dadn/dem-fem-coupling-master/installation/oofem.diff
mkdir -p /home/dadn/dem-fem-coupling-master/installation/_build/oofem/build
cd /home/dadn/dem-fem-coupling-master/installation/_build/oofem/build &&
cmake -DUSE_PYTHON_BINDINGS=ON /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
-- The CXX compiler identification is GNU 7.5.0
-- The C compiler identification is GNU 7.5.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.17", minimum required is "2.7")
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found suitable version "2.7.17", minimum required is "2.7")
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:567 (message):
Imported targets and dependency information not available for Boost version
(all versions older than 1.33)
Call Stack (most recent call first):
/usr/share/cmake-3.10/Modules/FindBoost.cmake:907 (_Boost_COMPONENT_DEPENDENCIES)
/usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
CMakeLists.txt:507 (find_package)

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
No header defined for python-py27; skipping header check
Call Stack (most recent call first):
CMakeLists.txt:507 (find_package)

CMake Error at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1947 (message):
Unable to find the requested Boost libraries.

Unable to find the Boost header files. Please set BOOST_ROOT to the root
directory containing Boost or BOOST_INCLUDEDIR to the directory containing
Boost's headers.
Call Stack (most recent call first):
CMakeLists.txt:507 (find_package)

-- Looking for C++ include unistd.h
-- Looking for C++ include unistd.h - found
-- Looking for C++ include execinfo.h
-- Looking for C++ include execinfo.h - found
-- Looking for access
-- Looking for access - found
-- Looking for cbrt
-- Looking for cbrt - found
-- Looking for isnan
-- Looking for isnan - not found
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
Boost_INCLUDE_DIR (ADVANCED)
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/oofemlib
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/sm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/tm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm
used as include directory in directory /home/dadn/dem-fem-coupling-master/installation/_build/oofem/source/src/fm

-- Configuring incomplete, errors occurred!
See also "/home/dadn/dem-fem-coupling-master/installation/_build/oofem/build/CMakeFiles/CMakeOutput.log".
See also "/home/dadn/dem-fem-coupling-master/installation/_build/oofem/build/CMakeFiles/CMakeError.log".
Makefile:119: recipe for target 'oofem-cmake' failed
make: *** [oofem-cmake] Error 1
I also got the CMakeOutput.log and CMakeError.log.

CMakeOutput.log
CMakeError.log

So，what should I do next ？
Thanks a lot！！
xue
@stranskyjan
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Owner

Hello,

what is your operating system?

CMake Error at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1947 (message):
Unable to find the requested Boost libraries.

CMake Error: The following variables are used in this project, but they are set to NOTFOUND.

the main problem seems to be here.
What is the output of terminal command apt list *boost*?

Cheers
Jan

@1qq12
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1qq12 commented Jul 14, 2021

Jan,
thank you so much for your very patient guidance!
My operating system is Ubuntu 18.04.5 LTS (Bionic Beaver). Following your answer, I got the following output after typing apt list boost in terminal.

output.txt
Thanks a lot！！
xue

@stranskyjan
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Should work on Ubuntu 18.04 LTS (I am using the same system).

Do you know how you installed boost libraries?

What is the output of dpkg -L libboost-python-dev?

@1qq12
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1qq12 commented Oct 19, 2021

Hello jan,
thank you for your guidance. As you suggested, I checked and found that I did not install libboost-python-dev. so I subsequently installed it. After running the makefile again, it can complete the installation of oofem. But there was a problem again when the program was installing yade.

rm -rf /home/com/dem-fem-coupling-master/installation/_build/yade/source-orig
wget https://launchpad.net/yade/trunk/yade-1.00.0/+download/yade_2019.01a.tar.bz2 -O /home/com/dem-fem-coupling-master/installation/_build/yade/yade.tar.bz2
--2021-10-19 17:06:33-- https://launchpad.net/yade/trunk/yade-1.00.0/+download/yade_2019.01a.tar.bz2
正在解析主机 launchpad.net (launchpad.net)... 91.189.89.222, 91.189.89.223, 2001:67c:1560:8003::8004, ...
正在连接 launchpad.net (launchpad.net)|91.189.89.222|:443... 已连接。
已发出 HTTP 请求，正在等待回应... 303 See Other
位置：https://launchpadlibrarian.net/408954510/yade_2019.01a.tar.bz2 [跟随至新的 URL]
--2021-10-19 17:06:38-- https://launchpadlibrarian.net/408954510/yade_2019.01a.tar.bz2
正在解析主机 launchpadlibrarian.net (launchpadlibrarian.net)... 91.189.89.229, 91.189.89.228, 2001:67c:1560:8003::8008, ...
正在连接 launchpadlibrarian.net (launchpadlibrarian.net)|91.189.89.229|:443... 已连接。
已发出 HTTP 请求，正在等待回应... 200 OK
长度： 6244563 (6.0M) [application/x-tar]
正在保存至: “/home/com/dem-fem-coupling-master/installation/_build/yade/yade.tar.bz2”

/home/com/dem-fem-c 100%[===================>] 5.96M 535KB/s 用时 15s

2021-10-19 17:06:58 (419 KB/s) - 已保存 “/home/com/dem-fem-coupling-master/installation/_build/yade/yade.tar.bz2” [6244563/6244563])

tar xfj /home/com/dem-fem-coupling-master/installation/_build/yade/yade.tar.bz2
mv trunk-2019.01a /home/com/dem-fem-coupling-master/installation/_build/yade/source-orig
rm -rf /home/com/dem-fem-coupling-master/installation/_build/yade/source
cp -r /home/com/dem-fem-coupling-master/installation/_build/yade/source-orig /home/com/dem-fem-coupling-master/installation/_build/yade/source
cd /home/com/dem-fem-coupling-master/installation/_build/yade/source &&
patch -s -p0 < /home/com/dem-fem-coupling-master/installation/yade.diff
mkdir -p /home/com/dem-fem-coupling-master/installation/_build/yade/build
cd /home/com/dem-fem-coupling-master/installation/_build/yade/build &&
cmake
-DCMAKE_INSTALL_PREFIX=/home/com/dem-fem-coupling-master/installation/_build/yade/install
-DENABLE_LINSOLV=OFF
-DENABLE_PFVFLOW=OFF
-DENABLE_LBMFLOW=OFF
-DENABLE_TWOPHASEFLOW=OFF
-DENABLE_GL2PS=OFF
-DNOSUFFIX=ON
/home/com/dem-fem-coupling-master/installation/_build/yade/source
-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at CMakeLists.txt:33 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

-- Found PythonInterp: /usr/bin/python (found version "2.7.17")
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
qmake: could not exec '/usr/lib/x86_64-linux-gnu/qt4/bin/qmake': No such file or directory
-- Found unsuitable Qt version "" from NOTFOUND
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Version is set to 2019.01a
-- Could NOT find OpenGL (missing: OPENGL_opengl_LIBRARY OPENGL_glx_LIBRARY OPENGL_INCLUDE_DIR)
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Could NOT find GL2PS (missing: GL2PS_LIBRARY GL2PS_INCLUDE_DIR)
-- CGAL not found.
-- Found NumPy: version "1.13.3" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Could NOT find Loki (missing: LOKI_INCLUDE_DIR LOKI_LIBRARY)
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
-- 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
CMake Error at /usr/local/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find Boost (missing: thread filesystem iostreams regex
serialization system date_time) (found suitable version "1.65.1", minimum
required is "1.47.0")
Call Stack (most recent call first):
/usr/local/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
/usr/local/share/cmake-3.21/Modules/FindBoost.cmake:2360 (find_package_handle_standard_args)
CMakeLists.txt:102 (FIND_PACKAGE)

-- Configuring incomplete, errors occurred!
See also "/home/com/dem-fem-coupling-master/installation/_build/yade/build/CMakeFiles/CMakeOutput.log".
See also "/home/com/dem-fem-coupling-master/installation/_build/yade/build/CMakeFiles/CMakeError.log".
Makefile:149: recipe for target 'yade-cmake' failed
make: *** [yade-cmake] Error 1

What could be the cause of this? I look forward to your answer.
xue

@1qq12
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1qq12 commented Oct 19, 2021

Here are the error file and output file generated by cmake
CMakeOutput.log
CMakeError.log

.

@stranskyjan
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Could NOT find Boost (missing: thread filesystem iostreams regex serialization system date_time) (found suitable version "1.65.1", minimum required is "1.47.0")

install missing boost libraries: thread, filesystem, iostreams, regex, serialization, system, date_time
e.g. for "iostreams" it is libbost-iostreams-dev

Cheers
Jan

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