utils.sh

# useful functions to work with the repo.

ut_random_run_script_name(){ python -c 'import uuid; print("run_%s.sh" % uuid.uuid4())'; }
ut_convert_md_to_rst(){ pandoc "$1" -f markdown -t rst -o "$2"; }
ut_convert_rst_to_md(){ pandoc "$1" -f rst -t markdown -o "$2"; }

ut_extract_python_code_from_docs() {
    out_fp=`echo "${1%.*}"`".py" &&
    python docs/main_get_code_from_docs.py \
        --in_filepath "$1" \
        --out_filepath "$out_fp";
}

# NOTE: this updates code in the documentation in place.
# check that changes are as expected after using.
ut_update_python_code_in_docs() {
    code_fp=`echo "${1%.*}"`".py" &&
    python docs/main_update_code_in_docs.py \
        --in_doc_filepath "$1" \
        --in_code_filepath "$code_fp" \
        --out_filepath "$1";
}

ut_build_documentation(){
    export LC_ALL=C && \
    ut_convert_md_to_rst README.md docs/source/readme.rst && \
    ut_convert_md_to_rst CONTRIBUTING.md docs/source/contributing.rst && \
    cd docs && \
    make clean && \
    make html && \
    cd -;
}

ut_spellcheck_file(){ aspell check "$1"; }

# ut_build_py27_cpu_docker_container(){}
# ut_build_py27_gpu_docker_container(){}
ut_build_py27_cpu_singularity_container(){
    python containers/main.py && \
    ./containers/singularity/deep_architect-py27-cpu/build.sh;
}
# ut_build_py27_gpu_singularity_container(){}
# ut_build_py36_cpu_docker_container(){}
# ut_build_py36_gpu_docker_container(){}
# ut_build_py36_cpu_singularity_container(){}
# ut_build_py36_gpu_singularity_container(){}
# ut_run_in_py27_cpu_docker_container(){}
# ut_run_in_py27_gpu_docker_container(){}
ut_run_in_py27_cpu_singularity_container(){
    echo "$1" > "run.sh" && singularity exec containers/singularity/deep_architect-py27-cpu/deep_architect.img bash run.sh;
}
ut_bash_in_py27_cpu_singularity_container(){
    singularity exec containers/singularity/deep_architect-py27-cpu/deep_architect.img bash run.sh;
}
# ut_run_in_py27_gpu_singularity_container(){}
# ut_run_in_py36_cpu_docker_container(){}
# ut_run_in_py36_gpu_docker_container(){}
ut_run_in_py36_cpu_singularity_container(){
    echo "$1" > "run.sh" && singularity exec containers/singularity/deep_architect-py36-cpu/deep_architect.img bash run.sh;
}
# ut_run_in_py36_gpu_singularity_container(){}
# ut_run_fast_tests(){}
ut_run_all_tests(){
    set -x && ut_preappend_to_pythonpath "." &&
    python examples/mnist/main.py &&
    python examples/mnist_with_logging/main.py --config_filepath examples/mnist_with_logging/configs/debug.json &&
    # python examples/benchmarks/main.py --config_filepath examples/benchmarks/configs/debug.json;
    # ./examples/simplest_multiworker/run.sh debug 2 \
    # ./tutorials/full_search/launch_file_based_search.sh 2 \
    # ./tutorials/full_search/launch_mpi_based_search.sh 2 \
    python examples/framework_starters/main_keras.py &&
    python examples/framework_starters/main_tensorflow.py &&
    python examples/framework_starters/main_pytorch.py;
}

ut_extract_all_doc_code(){
    ut_extract_python_code_from_docs README.md &&
    ut_extract_python_code_from_docs docs/source/tutorials/search_space_constructs.rst &&
    ut_extract_python_code_from_docs docs/source/tutorials/new_frameworks.rst &&
    ut_extract_python_code_from_docs docs/source/tutorials/new_modules.rst &&
    ut_extract_python_code_from_docs docs/source/tutorials/new_searchers.rst &&
    ut_extract_python_code_from_docs docs/source/tutorials/logging_and_visualization.rst;
}

ut_update_all_doc_code(){
    ut_update_python_code_in_docs README.md &&
    ut_update_python_code_in_docs docs/source/tutorials/search_space_constructs.rst &&
    ut_update_python_code_in_docs docs/source/tutorials/new_frameworks.rst &&
    ut_update_python_code_in_docs docs/source/tutorials/new_modules.rst &&
    ut_update_python_code_in_docs docs/source/tutorials/new_searchers.rst &&
    ut_update_python_code_in_docs docs/source/tutorials/logging_and_visualization.rst;
}

# NOTE: this is for testing.
ut_run_all_doc_code(){
    set +x &&
    python README.py &&
    python docs/source/tutorials/search_space_constructs.py &&
    python docs/source/tutorials/new_frameworks.py &&
    python docs/source/tutorials/new_modules.py &&
    python docs/source/tutorials/new_searchers.py &&
    python docs/source/tutorials/logging_and_visualization.py;
}

# A large fraction of this code was pulled from research_toolbox
# https://github.com/negrinho/research_toolbox

UT_RSYNC_FLAGS="--archive --update --recursive --verbose"
ut_sync_folder_to_server() { rsync $UT_RSYNC_FLAGS "$1/" "$2/"; }
ut_sync_folder_from_server() { rsync $UT_RSYNC_FLAGS "$1/" "$2/"; }

# command, job name, folder, num cpus, memory in mbs, time in minutes
# limits: 4GB per cpu, 48 hours,
# NOTE: read https://www.psc.edu/bridges/user-guide/running-jobs for more details.
ut_submit_bridges_cpu_job_with_resources() {
    script='#!/bin/bash'"
#SBATCH --nodes=1
#SBATCH --partition=RM-shared
#SBATCH --cpus-per-task=$4
#SBATCH --mem=$5MB
#SBATCH --time=$6
#SBATCH --job-name=\"$2\"
$1" && ut_run_command_on_bridges "cd \"./$3\" && echo \"$script\" > _run.sh && chmod +x _run.sh && sbatch _run.sh && rm _run.sh";
}

# 1: command, 2: job name, 3: folder, 4: num cpus, 5: num_gpus, 6: memory in mbs, 7: time in minutes
# limits: 7GB per gpu, 48 hours, 16 cores per gpu,
# NOTE: read https://www.psc.edu/bridges/user-guide/running-jobs for more details.
ut_submit_bridges_gpu_job_with_resources() {
    script='#!/bin/bash'"
#SBATCH --nodes=1
#SBATCH --partition=GPU-shared
#SBATCH --gres=gpu:k80:$5
#SBATCH --cpus-per-task=$4
#SBATCH --mem=$6MB
#SBATCH --time=$7
#SBATCH --job-name=\"$2\"
$1" && ut_run_command_on_bridges "cd \"./$3\" && echo \"$script\" > _run.sh && chmod +x _run.sh && sbatch _run.sh && rm _run.sh";
}

ut_show_cpu_info() { lscpu; }
ut_show_gpu_info() { nvidia-smi; }
ut_show_memory_info() { free -m; }
ut_show_hardware_info() { lshw; }

ut_up1() { cd ..; }
ut_up2() { cd ../..; }
ut_up3() { cd ../../..; }
ut_get_last_process_id() { echo "$!"; }
ut_get_last_process_exit_code() { echo "$?"; }
ut_wait_on_process_id() { wait "$1"; }

ut_get_containing_folderpath() { echo "$(dirname "$1")"; }
ut_get_filename_from_filepath() { echo "$(basename "$1")"; }
ut_get_foldername_from_folderpath() { echo "$(basename "$1")"; }
ut_get_absolute_path_from_relative_path() { realpath "$1"; }

ut_find_files() { find "$1" -name "$2"; }
ut_find_folders() { find "$1" -type d -name "$2"; }
ut_create_folder() { mkdir -p "$1"; }
ut_copy_folder() { ut_create_folder "$2" && cp -r "$1"/* "$2"; }
ut_rename() { mv "$1" "$2"; }
ut_delete_folder() { rm -rf "$1"; }
ut_delete_folder_interactively() { rm -rfi "$1"; }
ut_get_folder_size() { du -sh $1; }
ut_rename_file_in_place(){ folderpath="$(dirname "$1")" && mv "$1" "$(dirname "$1")/$2"; }
ut_rename_folder_in_place(){ folderpath="$(dirname "$1")" && mv "$1" "$(dirname "$1")/$2"; }
ut_compress_folder(){ foldername=`ut_get_foldername_from_folderpath $1` && tar -zcf "$foldername.tar.gz" "$1"; }
ut_uncompress_folder(){ tar -zxf "$1"; }

ut_send_mail_message_with_subject_to_address() { echo "$1" | mail "--subject=$2" "$3"; }
ut_send_mail_message_with_subject_and_attachment_to_address() { echo "$1" | mail "--subject=$2" "--attach=$3" "$4"; }

ut_run_headless_command() { nohup $1; }
ut_run_command_on_server() { ssh "$2" -t "$1"; }
ut_run_command_on_server_on_folder() { ssh "$2" -t "cd \"$3\" && $1"; }
ut_run_bash_on_server_on_folder() { ssh "$1" -t "cd \"$2\" && bash"; }
ut_run_python_command() { python -c "$1" >&2; }
ut_profile_python_with_cprofile() { python -m cProfile -s cumtime $"$1"; }

ut_get_git_head_sha() { git rev-parse HEAD; }
ut_show_git_commits_for_file(){ git log --follow -- "$1"; }
ut_show_oneline_git_log(){ git log --pretty=oneline; }
ut_show_files_ever_tracked_by_git() { git log --pretty=format: --name-only --diff-filter=A | sort - | sed '/^$/d'; }
ut_show_files_currently_tracked_by_git_on_branch() { git ls-tree -r "$1" --name-only; }
ut_discard_git_uncommited_changes_for_file() { git checkout -- "$1"; }
ut_discard_all_git_uncommitted_changes() { git checkout -- .; }

ut_grep_history() { history | grep "$1"; }
ut_show_known_hosts() { cat ~/.ssh/config; }
ut_register_ssh_key_on_server() { ssh-copy-id "$1"; }

ut_show_environment_variables() { printenv; }
ut_preappend_to_pythonpath() { export PYTHONPATH="$1:$PYTHONPATH"; }

ut_run_command_on_server() { ssh "$2" -t "$1"; }
ut_run_command_on_server_on_folder() { ssh "$2" -t "cd \"$3\" && $1"; }
ut_run_bash_on_server_on_folder() { ssh "$1" -t "cd \"$2\" && bash"; }

# both are slurm managed clusters. hosts defined in ~/.ssh/config
ut_run_command_on_bridges() { ut_run_command_on_server "$1" bridges; }
ut_run_command_on_bridges_on_folder() { ut_run_command_on_server_on_folder "$1" bridges "$2"; }
ut_run_bash_on_bridges_on_folder() { ut_run_bash_on_server_on_folder bridges "$1"; }

ut_run_command_on_matrix() { ut_run_command_on_server "$1" matrix; }
ut_run_command_on_matrix_on_folder() { ut_run_command_on_server_on_folder "$1" matrix "$2"; }
ut_run_bash_on_matrix_on_folder() { ut_run_bash_on_server_on_folder matrix "$1"; }

ut_create_conda_environment() { conda create --name "$1"; }
ut_create_conda_py27_environment() { conda create --name "$1" python=2.7; }
ut_create_conda_py36_environment() { conda create --name "$1" python=3.6; }
ut_show_conda_environments() { conda info --envs; }
ut_show_installed_conda_packages() { conda list; }
ut_delete_conda_environment() { conda env remove --name "$1"; }
ut_activate_conda_environment() { conda activate "$1"; }
ut_deactivate_conda_environment() { conda deactivate; }

# command, job name, folder, num cpus, memory in mbs, time in minutes
# limits: 4GB per cpu, 48 hours,
# NOTE: read https://www.psc.edu/bridges/user-guide/running-jobs for more details.
ut_submit_bridges_cpu_job_with_resources() {
    script='#!/bin/bash'"
#SBATCH --nodes=1
#SBATCH --partition=RM-shared
#SBATCH --cpus-per-task=$4
#SBATCH --mem=$5MB
#SBATCH --time=$6
#SBATCH --job-name=\"$2\"
$1" && ut_run_command_on_bridges "cd \"./$3\" && echo \"$script\" > _run.sh && chmod +x _run.sh && sbatch _run.sh && rm _run.sh";
}

# 1: command, 2: job name, 3: folder, 4: num cpus, 5: num_gpus, 6: memory in mbs, 7: time in minutes
# limits: 7GB per gpu, 48 hours, 16 cores per gpu,
# NOTE: read https://www.psc.edu/bridges/user-guide/running-jobs for more details.
ut_submit_bridges_gpu_job_with_resources() {
    script='#!/bin/bash'"
#SBATCH --nodes=1
#SBATCH --partition=GPU-shared
#SBATCH --gres=gpu:k80:$5
#SBATCH --cpus-per-task=$4
#SBATCH --mem=$6MB
#SBATCH --time=$7
#SBATCH --job-name=\"$2\"
$1" && ut_run_command_on_bridges "cd \"./$3\" && echo \"$script\" > _run.sh && chmod +x _run.sh && sbatch _run.sh && rm _run.sh";
}

ut_show_bridges_queue() { ut_run_command_on_bridges "squeue"; }
ut_show_my_jobs_on_bridges() { ut_run_command_on_bridges "squeue -u rpereira"; }
ut_cancel_job_on_bridges() { ut_run_command_on_bridges "scancel -n \"$1\""; }
ut_cancel_all_my_jobs_on_bridges() { ut_run_command_on_bridges "scancel -u rpereira"; }

# TODO: this needs to be adapted.
ut_install_packages() {
    sudo apt-get install \
        singularity \
        mailutils \
        tree;
}