forked from negrinho/deep_architect
-
Notifications
You must be signed in to change notification settings - Fork 0
/
utils.sh
258 lines (228 loc) · 10.9 KB
/
utils.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
# 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;
}