OpenGL issue upon compiling from source

[oligegilo]

Hi, I work on a Red Hat Linux system and would like to install the latest version of SmartPeak from source but ran into issues regarding OpenGL when compiling with cmake.

cmake -DUSE_SUPERBUILD=ON -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Debug ~/SmartPeak make -j4

works fine, but the next step

cmake -DEIGEN_USE_GPU=OFF -DUSE_SUPERBUILD=OFF -DBOOST_USE_STATIC=OFF -G "Unix Makefiles" -DCMAKE_PREFIX_PATH=$HOME/OpenMS-build/ -DPLOG_INCLUDE_DIR=$HOME/SmartPeak_superbuild/Dependencies/Source/plog/include -DIMGUI_DIR=$HOME/SmartPeak_superbuild/Dependencies/Source/imgui -DIMPLOT_DIR=$HOME/SmartPeak_superbuild/Dependencies/Source/implot -DCMAKE_BUILD_TYPE=Debug ~/SmartPeak

crashes like so:

CMake Error at /home/USER/Transcriptomics/software/cmake-3.21.0-rc2-linux-x86_64/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find OpenGL (missing: OPENGL_opengl_LIBRARY OPENGL_glx_LIBRARY OPENGL_INCLUDE_DIR) Call Stack (most recent call first): /home/USER/Transcriptomics/software/cmake-3.21.0-rc2-linux-x86_64/share/cmake-3.21/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE) /home/USER/Transcriptomics/software/cmake-3.21.0-rc2-linux-x86_64/share/cmake-3.21/Modules/FindOpenGL.cmake:443 (FIND_PACKAGE_HANDLE_STANDARD_ARGS) src/tests/class_tests/smartpeak/CMakeLists.txt:91 (find_package)

I am aware that I am missing the OpenGL header and libs - I tried to pull recommended packages in via Conda (mesa-libgl-cos6-x86_64, libglu and mesa) and link it within the DCMAKE_PREFIX_PATH but doesn't work. Could you point me into the right direction in how to properly get OpenGL to work to use SmartPeak? Thanks!

[dmccloskey]

Hi,

At least on Ubuntu systems, if OpenGL is installed, CMAKE should be able to locate it by default without having to manually specify the paths using additional arguments. I would recommend trying to install OpenGL using the Red Hat Linux package manager instead of via Conda (e.g., https://access.redhat.com/solutions/56301) and see if that fixes the problem.

Out of curiosity, have you tried installing and running the linux version of SmartPeak provided in the releases?

[oligegilo]

Hi, last but not least we installed OpenGL globally and that did the job. I installed the Linux release yes. However, when I finally like to build SmartPeak 'make -j4 runs' into a missing 'plog/Log.h' error - any idea how to solve this issue?

[ 1%] Building CXX object _deps/googletest-build/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o [ 2%] Building CXX object src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/ApplicationProcessor.cpp.o [ 2%] Building CXX object src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/CastValue.cpp.o [ 3%] Building CXX object src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/ConsoleHandler.cpp.o In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/CastValue.cpp:24: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/CastValue.h:29:10: fatal error: plog/Log.h: No such file or directory

include <plog/Log.h>

      ^~~~~~~~~~~~

compilation terminated. make[2]: [src/smartpeak/CMakeFiles/SmartPeak.dir/build.make:90: src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/CastValue.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ConsoleHandler.cpp:23: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ConsoleHandler.h:29:10: fatal error: plog/Log.h: No such file or directory

include <plog/Log.h>

      ^~~~~~~~~~~~

compilation terminated. make[2]: *** [src/smartpeak/CMakeFiles/SmartPeak.dir/build.make:104: src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/ConsoleHandler.cpp.o] Error 1 In file included from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/RawDataHandler.h:35, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/RawDataProcessor.h:28, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationHandler.h:27, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/ApplicationProcessor.h:26, from /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/source/core/ApplicationProcessor.cpp:24: /home/USER/Metabolomics/software/SmartPeak/src/smartpeak/include/SmartPeak/core/CastValue.h:29:10: fatal error: plog/Log.h: No such file or directory

include <plog/Log.h>

      ^~~~~~~~~~~~

compilation terminated. make[2]: [src/smartpeak/CMakeFiles/SmartPeak.dir/build.make:76: src/smartpeak/CMakeFiles/SmartPeak.dir/source/core/ApplicationProcessor.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:1097: src/smartpeak/CMakeFiles/SmartPeak.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... [ 3%] Linking CXX static library ../../../lib/libgtestd.a [ 3%] Built target gtest make: [Makefile:166: all] Error 2

[bertrandboudaud]

Hi,

I never tried to compile on redhat. however, it is recommended, for ubuntu build to follow the script used by circleci: .circleci/config.yml

on the ubuntu section, you will find there is a step named "Installing SmartPeak SuperBuild". It is supposed to get and build some dependencies like: imgui, implot, plog (which you are looking for now), sqlite.

as you can see the command to get and build is as follow:

cd ~/SmartPeak
mkdir -p superbuild
cd superbuild
cmake -DUSE_SUPERBUILD=ON -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release ~/SmartPeak
make -j4

you may try that (and in general follow this config.yml)

[oligegilo]

Hi, thanks in fact I did the superbuild but as you already mentioned RedHat did not accept it for some reason. For the record I solved it by locally installing imgui, implot and plog and then just pointed out the respective locations under the DCMAKE_PREFIX_PATH.

[dmccloskey]

OK great to hear. Please get back if you run into any other issues.