Notes for linux

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Don't use rm

Move file to trash and empty trash periodically instead of using rm

# ban rm
echo -e "\nalias 'rm'='echo "The use of rm is banned on this system."'" >> ~/.bashrc
source ~/.bashrc
# move file to transh
gio trash path/to/your/files

Parallel compression

Compress files parallelly using pgiz

tar cf - /path/to/directory | pigz -p 4 > directory.tar.gz

In this command:

• tar cf - /path/to/directory creates an archive of the specified directory and outputs it to standard output (-).
• pigz -p 4 takes the tar output from standard input and compresses it using 4 cores (-p 4 option).
• > directory.tar.gz redirects the compressed output to a file named directory.tar.gz.

Zip file extraction

Check the content of the compressed file

unzip -l file.zip

Extract part of the compressed file

unzip file/in/zip directory/in/zip/*

Upgrade gcc for Cantera and OpenFOAM compiliation

The compilation of OpenFOAM requires GCC version 5.4 or above (support c++14), Linux cluster based on CentOS Linux usually has default gcc version 4.8.5. To upgrade gcc,

1. get source code from website,

    wget 'https://mirrors.tuna.tsinghua.edu.cn/gnu/gcc/gcc-9.3.0/gcc-9.3.0.tar.gz'
    or
    wget 'https://ftp.gnu.org/gnu/gcc/gcc-9.3.0/gcc-9.3.0.tar.gz'
   

2. uncompress it the download dependencies:

    tar xzf gcc-9.3.0.tar.gz
    cd gcc-9.3.0 
    ./contrib/download_prerequisites
   

3. build the source code and install

    mkdir build && cd build/
    ../configure --prefix=/dir/to/install/gcc-9.5.0 --disable-multilib # build only 64bit lib
    make -j 16 && make install
   

4. (option) Update the environmental

    export PATH=$PATH:/dir/to/install/gcc-9.3.0/bin
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/dir/to/install/gcc-9.3.0/lib:/dir/to/install/gcc-9.3.0/lib64:/dir/to/install/gcc-9.3.0/libexec
    export INCLUDE=$INCLUDE:/dir/to/install/gcc-9.3.0/include
    # check installation
    /dir/to/install/gcc-9.3.0/bin/gcc --version
   

5. specify g++ and gcc version used for compilation

   For OpenFOAM, in directory ‘~/OpenFOAM/OpenFOAM-9/wmake/rules/linux64Gcc/’,

    # in c
    cc          = /dir/to/install/gcc-9.3.0/bin/gcc -m64
    # in c++
    CC          = /dir/to/install/gcc-9.3.0/bin/g++ -std=c++14 -m64
   

   For Cantera, change CC and CXX environmental varibles in SConstruct

    # ************************************
    # *** Compiler Configuration Tests ***
    # ************************************
    env['CC']='/dir/to/install/gcc-9.3.0/bin/gcc'
    env['CXX']='/dir/to/install/gcc-9.3.0/bin/g++'
   

Install openmpi for OpenFOAM compiliation

1. get source code from website,

    wget 'https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.0.tar.gz'
   

2. uncompress it the download dependencies:

    tar xzf openmpi-3.1.0.tar.gz
    cd openmpi-3.1.0
   

3. build the source code and install

    mkdir build && cd build/
    ../configure --prefix=/dir/to/install/openmpi-3.1.0
    make -j 16 && make install
   

4. Update the environmental

    export PATH=$PATH:/dir/to/install/openmpi-3.1.0/bin
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/dir/to/install/openmpi-3.1.0/lib
    # check installation
    mpic++ --showme:version