deploy: eb952fa

_modules/easy_slurm/jobs.html

@@ -218,8 +218,9 @@ <h1>Source code for easy_slurm.jobs</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">re</span>
 <span class="kn">import</span> <span class="nn">stat</span>
 <span class="kn">import</span> <span class="nn">subprocess</span>
+<span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span>
 <span class="kn">from</span> <span class="nn">textwrap</span> <span class="kn">import</span> <span class="n">dedent</span><span class="p">,</span> <span class="n">indent</span>
-<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span>
+<span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Sequence</span>
 
 <span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">__version__</span>
 <span class="kn">from</span> <span class="nn">.format</span> <span class="kn">import</span> <span class="n">format_with_config</span>
@@ -241,8 +242,7 @@ <h1>Source code for easy_slurm.jobs</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="submit_job"><a class="viewcode-back" href="../../easy_slurm/jobs.html#easy_slurm.jobs.submit_job">[docs]</a><span class="k">def</span> <span class="nf">submit_job</span><span class="p">(</span>
  <span class="n">job_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
  <span class="o">*</span><span class="p">,</span>
- <span class="n">src</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
- <span class="n">assets</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
+ <span class="n">src</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="p">(),</span>
  <span class="n">on_run</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
  <span class="n">on_run_resume</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
  <span class="n">setup</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span><span class="p">,</span>
@@ -253,23 +253,20 @@ <h1>Source code for easy_slurm.jobs</h1><div class="highlight"><pre>
  <span class="n">submit</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
  <span class="n">interactive</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
  <span class="n">resubmit_limit</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">64</span><span class="p">,</span>
+ <span class="n">config</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="p">{},</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
 <span class="w"> </span><span class="sd">&quot;&quot;&quot;Submits job.</span>
 
-<span class="sd"> Creates job directory with frozen assets and submits job to slurm.</span>
+<span class="sd"> Creates job directory with frozen src and submits job to slurm.</span>
 
 <span class="sd"> Args:</span>
 <span class="sd"> job_dir (str):</span>
 <span class="sd"> Path to directory to keep all job files including</span>
-<span class="sd"> ``src.tar``, ``assets.tar``, and auto-generated ``job.sh``.</span>
-<span class="sd"> src (str):</span>
-<span class="sd"> Path to directory containing only source code.</span>
+<span class="sd"> ``src.tar`` and auto-generated ``job.sh``.</span>
+<span class="sd"> src (list[str]):</span>
+<span class="sd"> Path to directories containing only source code.</span>
 <span class="sd"> These will be archived in ``$JOB_DIR/src.tar`` and</span>
-<span class="sd"> extracted during job run into ``$SLURM_TMPDIR/src``.</span>
-<span class="sd"> assets (str):</span>
-<span class="sd"> Path to directory containing additional assets.</span>
-<span class="sd"> These will be archived in ``$JOB_DIR/assets.tar`` and</span>
-<span class="sd"> extracted during job run into ``$SLURM_TMPDIR/assets``.</span>
+<span class="sd"> extracted during job run into ``$SLURM_TMPDIR``.</span>
 <span class="sd"> on_run (str):</span>
 <span class="sd"> Bash code executed in &quot;on_run&quot; stage, but only for new jobs</span>
 <span class="sd"> that are running for the first time.</span>
@@ -307,13 +304,18 @@ <h1>Source code for easy_slurm.jobs</h1><div class="highlight"><pre>
 <span class="sd"> Maximum number of times to auto-submit a job for &quot;resume&quot;.</span>
 <span class="sd"> (Not entirely unlike submitting a resume for a job.)</span>
 <span class="sd"> Default is 64 resubmissions.</span>
+<span class="sd"> config (dict[str, Any]):</span>
+<span class="sd"> A dictionary of configuration values to use for formatting.</span>
 
 <span class="sd"> Returns:</span>
 <span class="sd"> Path to the newly created job directory.</span>
 <span class="sd"> &quot;&quot;&quot;</span>
  <span class="n">job_name</span> <span class="o">=</span> <span class="n">sbatch_options</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;job-name&quot;</span><span class="p">,</span> <span class="s2">&quot;untitled&quot;</span><span class="p">)</span>
- <span class="n">job_dir</span> <span class="o">=</span> <span class="n">_expand_path</span><span class="p">(</span><span class="n">format_with_config</span><span class="p">(</span><span class="n">job_dir</span><span class="p">,</span> <span class="p">{</span><span class="s2">&quot;job_name&quot;</span><span class="p">:</span> <span class="n">job_name</span><span class="p">}))</span>
- <span class="n">create_job_dir</span><span class="p">(</span><span class="n">job_dir</span><span class="p">,</span> <span class="n">src</span><span class="p">,</span> <span class="n">assets</span><span class="p">)</span>
+ <span class="n">job_name</span> <span class="o">=</span> <span class="n">format_with_config</span><span class="p">(</span><span class="n">job_name</span><span class="p">,</span> <span class="n">config</span><span class="p">)</span>
+ <span class="n">job_dir</span> <span class="o">=</span> <span class="n">_expand_path</span><span class="p">(</span>
+ <span class="n">format_with_config</span><span class="p">(</span><span class="n">job_dir</span><span class="p">,</span> <span class="p">{</span><span class="o">**</span><span class="n">config</span><span class="p">,</span> <span class="s2">&quot;job_name&quot;</span><span class="p">:</span> <span class="n">job_name</span><span class="p">})</span>
+ <span class="p">)</span>
+ <span class="n">create_job_dir</span><span class="p">(</span><span class="n">job_dir</span><span class="p">,</span> <span class="n">src</span><span class="p">)</span>
 
  <span class="n">_write_script</span><span class="p">(</span>
  <span class="n">filename</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">job_dir</span><span class="si">}</span><span class="s2">/job.sh&quot;</span><span class="p">,</span>
@@ -396,21 +398,13 @@ <h1>Source code for easy_slurm.jobs</h1><div class="highlight"><pre>
  <span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="create_job_dir"><a class="viewcode-back" href="../../easy_slurm/jobs.html#easy_slurm.jobs.create_job_dir">[docs]</a><span class="k">def</span> <span class="nf">create_job_dir</span><span class="p">(</span>
- <span class="n">job_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
- <span class="n">src</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
- <span class="n">assets</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
-<span class="p">):</span>
+<div class="viewcode-block" id="create_job_dir"><a class="viewcode-back" href="../../easy_slurm/jobs.html#easy_slurm.jobs.create_job_dir">[docs]</a><span class="k">def</span> <span class="nf">create_job_dir</span><span class="p">(</span><span class="n">job_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">src</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">str</span><span class="p">]):</span>
 <span class="w"> </span><span class="sd">&quot;&quot;&quot;Creates job directory and freezes all necessary files.&quot;&quot;&quot;</span>
  <span class="n">job_dir</span> <span class="o">=</span> <span class="n">_expand_path</span><span class="p">(</span><span class="n">job_dir</span><span class="p">)</span>
- <span class="n">src</span> <span class="o">=</span> <span class="n">_expand_path</span><span class="p">(</span><span class="n">src</span><span class="p">)</span>
- <span class="n">assets</span> <span class="o">=</span> <span class="n">_expand_path</span><span class="p">(</span><span class="n">assets</span><span class="p">)</span>
+ <span class="n">src</span> <span class="o">=</span> <span class="p">[</span><span class="n">_expand_path</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">src</span><span class="p">]</span>
 
  <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">job_dir</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">src</span> <span class="o">!=</span> <span class="s2">&quot;&quot;</span><span class="p">:</span>
- <span class="n">_create_tar_dir</span><span class="p">(</span><span class="n">src</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">job_dir</span><span class="si">}</span><span class="s2">/src.tar.gz&quot;</span><span class="p">,</span> <span class="s2">&quot;src&quot;</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">assets</span> <span class="o">!=</span> <span class="s2">&quot;&quot;</span><span class="p">:</span>
- <span class="n">_create_tar_dir</span><span class="p">(</span><span class="n">assets</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">job_dir</span><span class="si">}</span><span class="s2">/assets.tar.gz&quot;</span><span class="p">,</span> <span class="s2">&quot;assets&quot;</span><span class="p">)</span>
+ <span class="n">_create_tar_dir</span><span class="p">(</span><span class="n">src</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">job_dir</span><span class="si">}</span><span class="s2">/src.tar.gz&quot;</span><span class="p">)</span>
 
  <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">job_dir</span><span class="si">}</span><span class="s2">/status&quot;</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
  <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;status=new&quot;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">f</span><span class="p">)</span>
@@ -445,9 +439,18 @@ <h1>Source code for easy_slurm.jobs</h1><div class="highlight"><pre>
  <span class="k">return</span> <span class="s2">&quot;&quot;</span> <span class="k">if</span> <span class="n">path</span> <span class="o">==</span> <span class="s2">&quot;&quot;</span> <span class="k">else</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expandvars</span><span class="p">(</span><span class="n">path</span><span class="p">))</span>
 
 
-<span class="k">def</span> <span class="nf">_create_tar_dir</span><span class="p">(</span><span class="n">src</span><span class="p">,</span> <span class="n">dst</span><span class="p">,</span> <span class="n">root_name</span><span class="p">):</span>
- <span class="n">transform</span> <span class="o">=</span> <span class="sa">rf</span><span class="s2">&quot;s/^\./</span><span class="si">{</span><span class="n">root_name</span><span class="si">}</span><span class="s2">/&quot;</span>
- <span class="n">cmd</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;tar&quot;</span><span class="p">,</span> <span class="s2">&quot;czf&quot;</span><span class="p">,</span> <span class="n">dst</span><span class="p">,</span> <span class="s2">&quot;-C&quot;</span><span class="p">,</span> <span class="n">src</span><span class="p">,</span> <span class="s2">&quot;.&quot;</span><span class="p">,</span> <span class="s2">&quot;--transform&quot;</span><span class="p">,</span> <span class="n">transform</span><span class="p">]</span>
+<span class="k">def</span> <span class="nf">_create_tar_dir</span><span class="p">(</span><span class="n">src</span><span class="p">,</span> <span class="n">dst</span><span class="p">,</span> <span class="n">root_name</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">src</span><span class="p">:</span>
+ <span class="n">src_args</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;-T&quot;</span><span class="p">,</span> <span class="s2">&quot;/dev/null&quot;</span><span class="p">]</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">src_args</span> <span class="o">=</span> <span class="p">[</span>
+ <span class="n">arg</span>
+ <span class="k">for</span> <span class="n">srcdir</span> <span class="ow">in</span> <span class="n">src</span>
+ <span class="k">for</span> <span class="n">arg</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;-C&quot;</span><span class="p">,</span> <span class="n">Path</span><span class="p">(</span><span class="n">srcdir</span><span class="p">)</span><span class="o">.</span><span class="n">parent</span><span class="p">,</span> <span class="n">Path</span><span class="p">(</span><span class="n">srcdir</span><span class="p">)</span><span class="o">.</span><span class="n">name</span><span class="p">]</span>
+ <span class="p">]</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;tar&quot;</span><span class="p">,</span> <span class="s2">&quot;czf&quot;</span><span class="p">,</span> <span class="n">dst</span><span class="p">,</span> <span class="o">*</span><span class="n">src_args</span><span class="p">]</span>
+ <span class="k">if</span> <span class="n">root_name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+ <span class="n">cmd</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="s2">&quot;--transform&quot;</span><span class="p">,</span> <span class="sa">rf</span><span class="s2">&quot;s/^/</span><span class="si">{</span><span class="n">root_name</span><span class="si">}</span><span class="s2">\//&quot;</span><span class="p">])</span>
  <span class="n">subprocess</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">check</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 
 

_sources/index.rst.txt

@@ -10,7 +10,7 @@ Easy Slurm allows you to easily manage and submit robust jobs to Slurm using Pyt
 Features
 --------
 
-- **Freezes** source code and assets by copying to separate ``$JOB_DIR``.
+- **Freezes** source code by copying to separate ``$JOB_DIR``.
 - **Auto-submits** another job if current job times out.
 - **Exposes hooks** for custom bash code: ``setup``/``setup_resume``, ``on_run``/``on_run_resume``, and ``teardown``.
 - |Format job names|_ using parameters from config files.
@@ -40,8 +40,7 @@ To submit a job, simply fill in the various parameters shown in the example belo
 
  easy_slurm.submit_job(
  job_dir="$HOME/jobs/{date}-{job_name}",
- src="./src",
- assets="./assets",
+ src=["./src", "./assets"],
  setup="""
  virtualenv "$SLURM_TMPDIR/env"
  source "$SLURM_TMPDIR/env/bin/activate"
@@ -51,8 +50,8 @@ To submit a job, simply fill in the various parameters shown in the example belo
  # Runs only on subsequent runs. Call setup and do anything else needed.
  setup
  """,
- on_run="python main.py",
- on_run_resume="python main.py --resume",
+ on_run="cd src && python main.py",
+ on_run_resume="cd src && python main.py --resume",
  teardown="""
  # Do any cleanup tasks here.
  """,
@@ -65,7 +64,7 @@ To submit a job, simply fill in the various parameters shown in the example belo
  resubmit_limit=64, # Automatic resubmission limit.
  )
 
-All job files will be kept in the ``job_dir`` directory. Provide directory paths to ``src`` and ``assets`` -- these will be archived and copied to the ``job_dir`` directory. Also provide Bash code in the hooks, which will be run in the following order:
+All job files will be kept in the ``job_dir`` directory. Provide directory paths to ``src`` -- these will be archived and copied to the ``job_dir`` directory. Also provide Bash code in the hooks, which will be run in the following order:
 
 .. list-table:: Hooks order
  :widths: 50 50
@@ -95,17 +94,16 @@ Jobs can also be fully configured using YAML files. See `examples/simple_yaml`_.
 .. code-block:: yaml
 
  job_dir: "$HOME/jobs/{date}-{job_name}"
- src: "./src"
- assets: "./assets"
+ src: ["./src", "./assets"]
  setup: |
  virtualenv "$SLURM_TMPDIR/env"
  source "$SLURM_TMPDIR/env/bin/activate"
  pip install -r "$SLURM_TMPDIR/src/requirements.txt"
  setup_resume: |
  # Runs only on subsequent runs. Call setup and do anything else needed.
  setup
- on_run: "python main.py"
- on_run_resume: "python main.py --resume"
+ on_run: "cd src && python main.py"
+ on_run_resume: "cd src && python main.py --resume"
  teardown: |
  # Do any cleanup tasks here.
  sbatch_options: