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Odyssey in computer science

Pytorch

  • torch.cuda.is_available() check cuda
  • tensorboard --logdir=/home/jing/python_code/DeepRT/torch/runs use tensorboard web graph

Conda

  • conda --version check version
  • conda env list exsisted environments
  • conda install python==3.6 install specific python
  • conda create -n name python=3.9 create a conda env
  • conda create -n newenv --clone oldenv copy a conda env
  • conda remove -n envname --all delete a conda env
  • conda activate envname activate a conda env
  • conda deactivate close a conda env
  • export to another machone
    • conda env export > envname.yaml
    • conda env create -f envname.yaml

Python

  • print(sys.version) print python version
  • print(glob.glob("path/*.mhd")) print files names
  • files = os.listdir(path); files.sort() sort the files names
  • for x, y in zip(directory_image, directory_label): double loop
  • print(f'text {variable:.3f}') print in specific format

Terminal

  • hostname -I ip address
  • ps or top show running programs
  • sudo vi /etc/hostname change hostname, remember to reboot
  • ps -ef | grep ssh check ssh
  • python --version check python version
  • nvidia-smi check GPU info
  • nvidia-smi -L check available GPU
  • htop check memory
  • touch test.py create a new file
  • vi test.py edit a file
  • cd ~ come to home
  • bash xxx.sh run .sh file
  • sudo vim /home/jing/.bashrc modigy environment variables
  • export PATH=path1:path2: ...... :$PATH add multiple variables
  • source ~/.bashrc make it into effect
  • unset PYTORCH_CUDA_ALLOC_CONF cancel the previous command
  • sudo apt-get update update software
  • pip install opengate -U update lib
  • sudo apt-get remove --auto-remove qtcreator uninstall software
  • scp -r /datapath/* username@ip address:/savepath/ upload data to cluster
  • scp -r username@ip address:'/remotepath/file_{367..497}.root' savepath batch download files to local
  • scp -r phantom*_atn_1.bin username@ip address:remotepath/ upload specific type files
  • ls -l . | egrep -c '^-' check file numbers
  • ls -lh path/file_name check file size
  • ffmpeg -i input.mp3 -ss 00:01:00 -to 00:05:23.27 -c copy output.mp3 edit audio length
  • su root, change to root user
  • su jing, change to other user
  • sudo passwd root, change password of root
  • passwd, change password
  • watch -n 10 squeue -u jzhang, watch slurm jobs every 10 seconds
  • df -h /, check disk space
  • du -sh /home2/jzhang/, check total data used of certain path
  • du /home2/jzhang/, check detail data used of certain path
  • tree -L 1, show tree structure in 1 level
  • tree -d, show directory only
  • tree -L 2 > structure.txt export tree structure to file
  • tree /A in Windows, show tree structure with directory only
  • tree in Windows, similar as above
  • tree /F in Windows, show all information

WSL=Windows subsystom linux

  • A good subsitute for vmware virtual machine.
  • version wsl -l -v
  • sudo apt-get install x11-apps to support visualization, xeyes for testing.
  • in CMD, ubuntu config --default-user jing or root, change user or root user.
  • in CMD, wsl --shutdown, shutdown the wsl system.
  • in CMD, wsl -l, print info of OS.

Hybrid programming between python and C/C++

  • Essence: python calls dynamic link libraries compiled by C/C++. e.g. convert the data types in python to those in c/c++, pass them to the compiled functions, and then convert returned parameters to the data types in python.
  • C/C++ --> dynamic link library (Pybind11) <-- Python

LaTeX

adjust blank:

\setlength{\abovedisplayskip}{3pt}
\setlength{\belowdisplayskip}{3pt}
adjust the space between title and fig \setlength{\abovecaptionskip}{-0.2cm}
adjust the distance between title and the below context \setlength{\belowcaptionskip}{-1cm} 

\begin{equation}
\setlength{\abovedisplayskip}{3pt}
\setlength{\belowdisplayskip}{3pt}
y(t)=a(t)-b(t).
\end{equation}

table:
tabular* can automatically adjust the width to fit the text.
{\textwidth} width of column{@{\extracolsep{\fill}} ll} column setting

\begin{table}[htbp]
\caption{Dataset}
\begin{tabular*}{\textwidth}{@{\extracolsep{\fill}} ll}
\toprule
data 1 & data 2 \\
\midrule
 1 &  2 \\
 3 &  4 \\
\bottomrule
\end{tabular*}
\end{table}

split a cell into two rows

\begin{tabular}[c]{@{}c@{}} part A \\ part B \end{tabular}