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mandelbrot-project / spectral_lib_builder

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update to CFM-4 #1

Closed Adafede closed 2 years ago

Adafede commented 2 years ago

See

https://hub.docker.com/r/wishartlab/cfmid

https://bitbucket.org/wishartlab/cfm-id-code/src/master

oolonek commented 2 years ago

Compiling from source is doable but its a real pain. On my side it was necessary because parallel jobs handling was not OK starting from docker cfm.

Of course I dont have clean install instruction but in case it can help these are some notes I had taken while installing. You can block some hours for the install !

installing cfm on server mapp

Thursday 14 October 2021

See instructions here https://bitbucket.org/wishartlab/cfm-id-code/src/master/cfm/INSTALL.md

tar -zxvf RDKit_2017_09_3.tgz
cd ../..
mkdir build
cd build
cmake .. \
    -DRDK_PGSQL_STATIC=OFF\
    -DRDK_BUILD_PYTHON_WRAPPERS=OFF\
    -DRDK_BUILD_CPP_TESTS=OFF\
    -DRDK_BUILD_DESCRIPTORS3D=OFF\
    -DRDK_INSTALL_STATIC_LIBS=OFF\
    -DRDK_INSTALL_INTREE=OFF\
    -DRDK_BUILD_INCHI_SUPPORT=ON\
    -DRDK_OPTIMIZE_NATIVE=ON\
    -DCMAKE_CXX_STANDARD=11\
    -DCMAKE_BUILD_TYPE=Release
make install

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH::~/Programs/rdkit-Release_2017_09_3/lib:~/Programs/lp_solve_5.5/lpsolve55/bin/ux64

beware no spaces across equal sign

cmake  ..  
    -DINCLUDE_TESTS=${BUILD_CFM_TEST}\
    -DINCLUDE_TRAIN=${BUILD_CFM_TRAIN}\
    -DLPSOLVE_INCLUDE_DIR=/usr/local/include/lp_solve\
    -DLPSOLVE_LIBRARY_DIR=/usr/local/lib\
    -DRDKIT_INCLUDE_DIR=/usr/local/include/rdkit\
    -DRDKIT_INCLUDE_EXT_DIR=/usr/local/include/rdkit/External\
    -DRDKIT_LIBRARY_DIR=/usr/local/lib\
    -DCMAKE_CXX_STANDARD=11;\

cmake  .. \
    -DINCLUDE_TESTS=${BUILD_CFM_TEST}\
    -DINCLUDE_TRAIN=${BUILD_CFM_TRAIN}\
    -DLPSOLVE_INCLUDE_DIR=/home/allardpm/Programs/lp_solve_5.5\
    -DLPSOLVE_LIBRARY_DIR=/home/allardpm/Programs/lp_solve_5.5/lpsolve55/bin/ux64\
    -DRDKIT_INCLUDE_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/Code\
    -DRDKIT_INCLUDE_EXT_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/External\
    -DRDKIT_LIBRARY_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/lib\
    -DCMAKE_CXX_STANDARD=11;\

cmake  .. \
    -DLPSOLVE_INCLUDE_DIR=/home/allardpm/Programs/lp_solve_5.5 \
    -DLPSOLVE_LIBRARY_DIR=/home/allardpm/Programs/lp_solve_5.5/lpsolve55/bin/ux64 \
    -DRDKIT_INCLUDE_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3 \
    -DRDKIT_INCLUDE_EXT_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/External \
    -DRDKIT_LIBRARY_DIR=/home/allardpm/Programs/rdkit-Release_2017_09_3/lib \
    -DCMAKE_CXX_STANDARD=11; \

    export RDBASE=~/Programs/rdkit-Release_2017_09_3/

    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:
INCHI_LIB (ADVANCED)
    linked by target "cfm-code" in directory /home/allardpm/Programs/cfm-id-code/cfm/cfm-code
RDINCHI_LIB (ADVANCED)
    linked by target "cfm-code" in directory /home/allardpm/Programs/cfm-id-code/cfm/cfm-code

/usr/local/include/rdkit/

cmake  .. \
    -DINCLUDE_TESTS=${BUILD_CFM_TEST}\
    -DINCLUDE_TRAIN=${BUILD_CFM_TRAIN}\
    -DLPSOLVE_INCLUDE_DIR=/home/allardpm/Programs/lp_solve_5.5\
    -DLPSOLVE_LIBRARY_DIR=/home/allardpm/Programs/lp_solve_5.5/lpsolve55/bin/ux64\
    -DRDKIT_INCLUDE_DIR=/usr/local/include/rdkit\
    -DRDKIT_INCLUDE_EXT_DIR=/usr/local/include/rdkit/External\
    -DRDKIT_LIBRARY_DIR=/usr/local/lib\
    -DCMAKE_CXX_STANDARD=11;\
Adafede commented 2 years ago

There is actually no more need to compile from scratch, which makes everything much easier! 😊

Adafede commented 2 years ago

Done :)