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shadowwalkersb avatar shadowwalkersb commented on August 27, 2024

The minimum version of cmake to build eman2 is 3.9, but it should work with higher versions, too. Which branch is the source from?

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samfux84 avatar samfux84 commented on August 27, 2024

I use the release tarball

https://github.com/cryoem/eman2/archive/v2.3.tar.gz

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shadowwalkersb avatar shadowwalkersb commented on August 27, 2024

I have tried a few versions of cmake, 3.14.0, 3.14.5, 3.12.2 and 3.9.4, with the tarball, but can't reproduce this.

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samfux84 avatar samfux84 commented on August 27, 2024

Hi,

Maybe this is due to building the dependencies manually and not with Conda.

When I empty the build directory of EMAN2 and use ccmake to set the variables

ccmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS_RELEASE="-O3 -DNDEBUG -ftree-vectorize -march=core-avx2 -mavx2" -DPYTHON_EXECUTABLE=/cluster/apps/python/2.7.14/bin/python -DCMAKE_INSTALL_PREFIX=/cluster/apps/eman2/2.3/x86_64 -DCMAKE_VERBOSE_MAKEFILE=ON -DENABLE_EMAN_CUDA=ON -DENABLE_OPTIMIZE_X86_64=ON -DFFTW3D_INCLUDE_PATH=/cluster/apps/gcc-4.8.5/fftw-3.3.5-xqwrft73uae7gismovk2xugrzrzjw2oz/include -DFFTW3D_THREADS_INCLUDE_PATH=/cluster/apps/gcc-4.8.5/fftw-3.3.5-xqwrft73uae7gismovk2xugrzrzjw2oz/include -DFFTW3F_INCLUDE_PATH=/cluster/apps/gcc-4.8.5/fftw-3.3.5-xqwrft73uae7gismovk2xugrzrzjw2oz/include -DFFTW3F_THREADS_INCLUDE_PATH=/cluster/apps/gcc-4.8.5/fftw-3.3.5-xqwrft73uae7gismovk2xugrzrzjw2oz/include -DFTGL_INCLUDE_PATH=/cluster/apps/ftgl/2.1.3/x86_64/include -DZLIB_LIBRARY_RELEASE=/cluster/apps/gcc-4.8.5/zlib-1.2.11-bq2w5h6vcd64cmfueygcbug4fksi4eb4/include/lib/libz.so -DPNG_LIBRARY_RELEASE=/cluster/apps/gcc-4.8.5/libpng-1.6.27-d6quyddan2eotsexesxufytusf27xxgz/lib/libpng.so -DGSL_ROOT_DIR=/cluster/apps/gcc-4.8.5/gsl-2.3-xwny6fotw5xcpchcbhl4oyughsocriam -Dpkgcfg_lib_GSL_gsl=/cluster/apps/gcc-4.8.5/gsl-2.3-xwny6fotw5xcpchcbhl4oyughsocriam/lib/libgsl.so -DFTGL_LIBRARY=/cluster/apps/ftgl/2.1.3/x86_64/lib/libftgl.so -DCUDA_VERBOSE_BUILD=ON -DHDF5_INCLUDE_PATH=/cluster/apps/gcc-4.8.5/hdf5-1.10.1-v5tokcw5ende26jt6iufdt25yspgjzw2/include -DFREETYPE_INCLUDE_DIR=/cluster/apps/gcc-4.8.5/freetype-2.7-mhhi2pufcglnyisabx7ha4ylcuyqmf3u/include ..

Then I configure twice by typing "c" in the CMake gui and get the following output:

CMAKE_PREFIX_PATH: /cluster/apps/eman2/2.3/x86_64;/cluster/apps/eman2/2.3/x86_64/..

 PYTHON_EXECUTABLE:   /cluster/apps/python/2.7.14/bin/python

 PYTHON_LIBRARIES:    /cluster/apps/python/2.7.14/lib64/libpython2.7.so

 PYTHON_INCLUDE_DIRS: /cluster/apps/python/2.7.14/include/python2.7

 PYTHON_INCLUDE_PATH: /cluster/apps/python/2.7.14/include/python2.7

 PYTHON_INCLUDE_DIR:  /cluster/apps/python/2.7.14/include/python2.7

 Python site-packages: /cluster/apps/python/2.7.14/lib64/python2.7/site-packages

 NUMPY_INCLUDE_DIR: /cluster/apps/python/2.7.14/lib64/python2.7/site-packages/numpy/core/include

 CMake Warning (dev) at libEM/CMakeLists.txt:109 (find_package):
   Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
   Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
   command to set the policy and suppress this warning.

   Environment variable GSL_ROOT is set to:

     /cluster/apps/gcc-4.8.5/gsl-2.3-xwny6fotw5xcpchcbhl4oyughsocriam

   For compatibility, CMake is ignoring the variable.
 This warning is for project developers.  Use -Wno-dev to suppress it.


 TIFF_LIBRARIES: /cluster/apps/gcc-4.8.5/libtiff-4.0.6-y76bcjaualcxv3hld235ducq3oski7wf/lib/libtiff.so

 CMake Warning (dev) at cmake/JPEG.cmake:1 (find_package):
   Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
   Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
   command to set the policy and suppress this warning.

   Environment variable JPEG_ROOT is set to:

     /cluster/apps/gcc-4.8.5/jpeg-9b-psjvucpx7xwkflb3meatuo6ugdtapkex
 
   For compatibility, CMake is ignoring the variable.
 Call Stack (most recent call first):
   libEM/CMakeLists.txt:127 (include)
 This warning is for project developers.  Use -Wno-dev to suppress it.


 JPEG_LIBRARIES: /cluster/apps/gcc-4.8.5/jpeg-9b-psjvucpx7xwkflb3meatuo6ugdtapkex/lib/libjpeg.so

 HDF5_LIBRARY: /cluster/apps/gcc-4.8.5/hdf5-1.10.1-v5tokcw5ende26jt6iufdt25yspgjzw2/lib/libhdf5.so

 CMake Warning (dev) at /cluster/apps/gcc-4.8.5/cmake-3.12.4-letepnmurt7hl5seixgddx24xniq2rwz/share/cmake-3.12/Modules/FindPNG.cmake:51
 (find_package):
   Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
   Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
   command to set the policy and suppress this warning.

   Environment variable ZLIB_ROOT is set to:

     /cluster/apps/gcc-4.8.5/zlib-1.2.11-bq2w5h6vcd64cmfueygcbug4fksi4eb4

   For compatibility, CMake is ignoring the variable.
 Call Stack (most recent call first):
   cmake/PNG.cmake:1 (find_package)
   libEM/CMakeLists.txt:136 (include)
 This warning is for project developers.  Use -Wno-dev to suppress it.

 PNG_LIBRARIES:
 /cluster/apps/gcc-4.8.5/libpng-1.6.27-d6quyddan2eotsexesxufytusf27xxgz/lib/libpng.so;/cluster/apps/gcc-4.8.5/zlib-1.2.11-bq2w5h6vcd64cmfuey
 gcbug4fksi4eb4/include/lib/libz.so

 CMAKE_LIBRARY_ARCHITECTURE:

 OPENGL_INCLUDE_DIR: /cluster/apps/gcc-4.8.5/mesa-12.0.3-ml7hu2oihsajd36kowkabf4d4zeo5ydm/include

 OPENGL_LIBRARIES:
 /cluster/apps/gcc-4.8.5/mesa-12.0.3-ml7hu2oihsajd36kowkabf4d4zeo5ydm/lib/libGL.so;/cluster/apps/gcc-4.8.5/mesa-glu-9.0.0-dm3qf5nckseq6wbe2v
 h5tubcyfjafcv6/lib/libGLU.so

 CMake Error at /cluster/apps/gcc-4.8.5/cmake-3.12.4-letepnmurt7hl5seixgddx24xniq2rwz/share/cmake-3.12/Modules/FindFreetype.cmake:173
 (set_target_properties):
   set_target_properties can not be used on an ALIAS target.
 Call Stack (most recent call first):
   cmake/Freetype.cmake:1 (find_package)
   cmake/FindFTGL.cmake:27 (include)
   libEM/CMakeLists.txt:180 (find_package)



 CMake Error at /cluster/apps/gcc-4.8.5/cmake-3.12.4-letepnmurt7hl5seixgddx24xniq2rwz/share/cmake-3.12/Modules/FindFreetype.cmake:177
 (set_property):
   set_property can not be used on an ALIAS target.
 Call Stack (most recent call first):
   cmake/Freetype.cmake:1 (find_package)
   cmake/FindFTGL.cmake:27 (include)
   libEM/CMakeLists.txt:180 (find_package)



 CMake Error at /cluster/apps/gcc-4.8.5/cmake-3.12.4-letepnmurt7hl5seixgddx24xniq2rwz/share/cmake-3.12/Modules/FindFreetype.cmake:179
 (set_target_properties):
   set_target_properties can not be used on an ALIAS target.
 Call Stack (most recent call first):
   cmake/Freetype.cmake:1 (find_package)
   cmake/FindFTGL.cmake:27 (include)
   libEM/CMakeLists.txt:180 (find_package)



 FREETYPE_LIBRARIES:    /cluster/apps/gcc-4.8.5/freetype-2.7-mhhi2pufcglnyisabx7ha4ylcuyqmf3u/lib/libfreetype.so

 FREETYPE_INCLUDE_DIRS: /cluster/apps/gcc-4.8.5/freetype-2.7-mhhi2pufcglnyisabx7ha4ylcuyqmf3u/include/freetype2

 Boost_LIBRARIES:   /cluster/apps/gcc-4.8.5/boost-1.64.0-unobzlo4mdmdkthumilwexlles6eral4/lib/libboost_python-mt.so

 Boost_INCLUDE_DIR: /cluster/apps/gcc-4.8.5/boost-1.64.0-unobzlo4mdmdkthumilwexlles6eral4/include

I guess you can't provide any support since building EMAN2 without using Conda is not supported any more, but I would like to document this issues for other people also trying to build EMAN2 without Conda.

I will provide an update if I can resolve this problem

Best regards

Sam

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sludtke42 avatar sludtke42 commented on August 27, 2024

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samfux84 avatar samfux84 commented on August 27, 2024

Hi Steven,

Thank you for your reply.

Now after installing all dependencies without Conda (for instance installing PyQT5 for Python 2.7.14) I start to get a better understanding why you switched to Conda. As I am quite experienced setting up software on a HPC cluster, I wanted to take the challenge getting EMAN2 installed without using Conda (which worked quite well for all dependencies). Also because I am always trying to use already installed software instead of making redundant installations. Especially for OpenMPI I prefer to use the version that we installed, because it was compiled with support for our batch system (LSF).

Thank you for the hint of looking at an older version of CMakeLists.txt.

Currently, the modification that I did was replacing

# Set EMAN_PREFIX
if("$ENV{CONDA_BUILD_STATE}" STREQUAL "BUILD" )
        message("ENV{CONDA_BUILD_STATE}: $ENV{CONDA_BUILD_STATE}")
        if(NOT WIN32)
                set(EMAN_PREFIX $ENV{PREFIX})
        else()
                set(EMAN_PREFIX $ENV{LIBRARY_PREFIX})
        endif()
else()
        find_package(Conda REQUIRED)

        if(CONDA_PREFIX)
                if(NOT WIN32)
                        set(EMAN_PREFIX ${CONDA_PREFIX})
                else()
                        set(EMAN_PREFIX ${CONDA_PREFIX}/Library)
                endif()
        endif()
endif()

set(EMAN_PREFIX_INC      ${EMAN_PREFIX}/include)
set(EMAN_PREFIX_LIB      ${EMAN_PREFIX}/lib)
set(CMAKE_INSTALL_PREFIX ${EMAN_PREFIX} CACHE PATH "installation prefix" FORCE)
set(CMAKE_PREFIX_PATH    ${EMAN_PREFIX} ${EMAN_PREFIX}/..)
message_var(CMAKE_PREFIX_PATH)

with

set(CMAKE_INSTALL_PREFIX "/cluster/apps/eman2/2.3/x86_64")
set(EMAN_PREFIX          ${CMAKE_INSTALL_PREFIX})
set(EMAN_PREFIX_INC      ${EMAN_PREFIX}/include)
set(EMAN_PREFIX_LIB      ${EMAN_PREFIX}/lib)
set(CMAKE_PREFIX_PATH    ${EMAN_PREFIX} ${EMAN_PREFIX}/..)
message_var(CMAKE_PREFIX_PATH)

I will have a look at an older CMakeLists.txt file and try to resolve the issue. If I can't find a solution until the end of this week, then I will go with the Conda setup.

Thank you for your help.

Best regards

Sam

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shadowwalkersb avatar shadowwalkersb commented on August 27, 2024

If you specify the necessary variables to point to the right libraries and include directories, you shouldn't need conda related stuff in cmake. I don't think the problem you are seeing is conda related. Looks like with cmake 3.10, findFreetype defines imported targets which are not supposed to be modified. I am not sure why I am not seeing the same errors when I use newer cmake versions, but I believe, your problem can be fixed by just removing the whole if-block setting the Freetype target,

eman2/cmake/Freetype.cmake

Lines 6 to 14 in 6aaac88

if(Freetype_FOUND AND NOT TARGET Freetype)
add_library(Freetype INTERFACE)
add_library(Freetype::Freetype ALIAS Freetype)
set_target_properties(Freetype
PROPERTIES
INTERFACE_INCLUDE_DIRECTORIES "${FREETYPE_INCLUDE_DIRS}"
INTERFACE_LINK_LIBRARIES "${FREETYPE_LIBRARIES}"
)
endif()
. So, Freetype.cmake becomes

find_package(Freetype REQUIRED)

message("FREETYPE_LIBRARIES:    ${FREETYPE_LIBRARIES}")
message("FREETYPE_INCLUDE_DIRS: ${FREETYPE_INCLUDE_DIRS}")

I don't know, if other targets will cause similar problems after fixing this.

Hope this helps.

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shadowwalkersb avatar shadowwalkersb commented on August 27, 2024

Or, if you can, use cmake 3.9, maybe.

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samfux84 avatar samfux84 commented on August 27, 2024

I could fix the issue.

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