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- Committer: Chris Bunch
- Date: 2012-02-26 03:20:57 UTC
- Revision ID: cgb@cs.ucsb.edu-20120226032057-ad0cy0zgx4we4exc
adding in repo over app engine support, and tests for most of datastore repo on appscale and s3
added
removed
AppController/coverage/-home-cgb-clients-main-main-cgb-research-Neptune-ssa_helper_rb.html
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<td class="left_align"><a href="-home-cgb-clients-main-main-cgb-research-Neptune-ssa_helper_rb.html">/home/cgb/clients/main/main-cgb-research/Neptune/ssa_helper.rb</a></td>
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<td class='right_align'><tt>274</tt></td>
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<td class='right_align'><tt>195</tt></td>
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<td class="left_align"><div class="percent_graph_legend"><tt class=''>13.50%</tt></div>
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<td class='right_align'><tt>282</tt></td>
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<td class='right_align'><tt>198</tt></td>
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<td class="left_align"><div class="percent_graph_legend"><tt class=''>16.31%</tt></div>
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</div></td>
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<td class="left_align"><div class="percent_graph_legend"><tt class=''>9.23%</tt></div>
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<td class="left_align"><div class="percent_graph_legend"><tt class=''>10.61%</tt></div>
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<div class="covered" style="width:9px"></div>
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<td><pre><a name="line3">3</a> # baz</pre></td>
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<td><pre><a name="line3">3</a> </pre></td>
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<td><pre><a name="line5">5</a> require 'djinn'</pre></td>
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<td><pre><a name="line6">6</a> </pre></td>
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<td><pre><a name="line7">7</a> MULTICORE = true</pre></td>
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<td><pre><a name="line8">8</a> SSA_HOME = "/usr/local/StochKit2.0/"</pre></td>
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<td><pre><a name="line9">9</a> </pre></td>
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<td><pre><a name="line10">10</a> IS_FILE = true</pre></td>
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<td><pre><a name="line11">11</a> NOT_A_FILE = false</pre></td>
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<td><pre><a name="line5">5</a> $:.unshift File.join(File.dirname(__FILE__), "..", "AppController")</pre></td>
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<td><pre><a name="line6">6</a> require 'djinn'</pre></td>
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<td><pre><a name="line7">7</a> </pre></td>
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<td><pre><a name="line8">8</a> </pre></td>
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<td><pre><a name="line9">9</a> $:.unshift File.join(File.dirname(__FILE__), "..", "AppController", "lib")</pre></td>
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<td><pre><a name="line10">10</a> require 'datastore_factory'</pre></td>
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<td><pre><a name="line11">11</a> </pre></td>
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<td><pre><a name="line13">13</a> public </pre></td>
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<td><pre><a name="line14">14</a> </pre></td>
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<td><pre><a name="line15">15</a> def neptune_ssa_run_job(nodes, job_data, secret)</pre></td>
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<td><pre><a name="line16">16</a> return BAD_SECRET_MSG unless valid_secret?(secret)</pre></td>
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<td><pre><a name="line17">17</a> Djinn.log_debug("ssa - run")</pre></td>
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<td><pre><a name="line18">18</a> </pre></td>
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<td><pre><a name="line19">19</a> Thread.new {</pre></td>
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<td><pre><a name="line20">20</a> start_time = Time.now</pre></td>
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<td><pre><a name="line21">21</a> total_compute_time = 0</pre></td>
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<td><pre><a name="line22">22</a> total_storage_time = 0</pre></td>
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<td><pre><a name="line23">23</a> total_slowest_path = 0</pre></td>
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<td><pre><a name="line24">24</a> c_times = []</pre></td>
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<td><pre><a name="line25">25</a> s_times = []</pre></td>
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<td><pre><a name="line26">26</a> </pre></td>
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<td><pre><a name="line27">27</a> Djinn.log_debug("job data is #{job_data.inspect}")</pre></td>
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<td><pre><a name="line28">28</a> keyname = @creds['keyname']</pre></td>
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<td><pre><a name="line29">29</a> </pre></td>
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<td><pre><a name="line30">30</a> nodes = Djinn.convert_location_array_to_class(nodes, keyname)</pre></td>
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<td><pre><a name="line31">31</a> </pre></td>
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<td><pre><a name="line32">32</a> sims = neptune_get_ssa_num_simulations(nodes, job_data)</pre></td>
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<td><pre><a name="line33">33</a> </pre></td>
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<td><pre><a name="line34">34</a> working_dir = "/tmp/ssa-#{rand(10000)}"</pre></td>
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<td><pre><a name="line35">35</a> FileUtils.mkdir_p(working_dir)</pre></td>
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<td><pre><a name="line36">36</a> </pre></td>
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<td><pre><a name="line37">37</a> tar = working_dir + "/" + File.basename(job_data['@tar'])</pre></td>
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<td><pre><a name="line13">13</a> MULTICORE = true</pre></td>
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<td><pre><a name="line14">14</a> SSA_HOME = "/usr/local/StochKit2.0/"</pre></td>
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<td><pre><a name="line15">15</a> </pre></td>
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<td><pre><a name="line16">16</a> </pre></td>
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<td><pre><a name="line17">17</a> IS_FILE = true</pre></td>
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<td><pre><a name="line18">18</a> NOT_A_FILE = false</pre></td>
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<td><pre><a name="line19">19</a> </pre></td>
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<td><pre><a name="line20">20</a> </pre></td>
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<td><pre><a name="line21">21</a> public </pre></td>
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<td><pre><a name="line22">22</a> </pre></td>
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<td><pre><a name="line23">23</a> </pre></td>
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<td><pre><a name="line24">24</a> def neptune_ssa_run_job(nodes, job_data, secret)</pre></td>
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<td><pre><a name="line25">25</a> return BAD_SECRET_MSG unless valid_secret?(secret)</pre></td>
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<td><pre><a name="line26">26</a> Djinn.log_debug("ssa - run")</pre></td>
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<td><pre><a name="line27">27</a> </pre></td>
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<td><pre><a name="line28">28</a> Thread.new {</pre></td>
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<td><pre><a name="line29">29</a> start_time = Time.now</pre></td>
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<td><pre><a name="line30">30</a> total_compute_time = 0</pre></td>
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<td><pre><a name="line31">31</a> total_storage_time = 0</pre></td>
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<td><pre><a name="line32">32</a> total_slowest_path = 0</pre></td>
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<td><pre><a name="line33">33</a> c_times = []</pre></td>
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<td><pre><a name="line34">34</a> s_times = []</pre></td>
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<td><pre><a name="line35">35</a> </pre></td>
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<td><pre><a name="line36">36</a> Djinn.log_debug("job data is #{job_data.inspect}")</pre></td>
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<td><pre><a name="line37">37</a> keyname = @creds['keyname']</pre></td>
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<td><pre><a name="line39">39</a> Djinn.log_debug("tar is #{job_data['@tar']}")</pre></td>
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<td><pre><a name="line40">40</a> Djinn.log_debug("working dir is #{working_dir}")</pre></td>
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<td><pre><a name="line41">41</a> </pre></td>
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<td><pre><a name="line42">42</a> remote = job_data['@tar']</pre></td>
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<td><pre><a name="line43">43</a> storage = job_data['@storage']</pre></td>
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<td><pre><a name="line44">44</a> creds = Djinn.neptune_parse_creds(storage, job_data)</pre></td>
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<td><pre><a name="line39">39</a> nodes = Djinn.convert_location_array_to_class(nodes, keyname)</pre></td>
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<td><pre><a name="line40">40</a> </pre></td>
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<td><pre><a name="line41">41</a> sims = neptune_get_ssa_num_simulations(nodes, job_data)</pre></td>
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<td><pre><a name="line42">42</a> </pre></td>
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<td><pre><a name="line43">43</a> working_dir = "/tmp/ssa-#{rand(10000)}"</pre></td>
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<td><pre><a name="line44">44</a> FileUtils.mkdir_p(working_dir)</pre></td>
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<td><pre><a name="line46">46</a> Repo.get_output(remote, storage, creds, tar)</pre></td>
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<td><pre><a name="line47">47</a> neptune_uncompress_file(tar)</pre></td>
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<td><pre><a name="line48">48</a> </pre></td>
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<td><pre><a name="line49">49</a> num_sims = job_data["@trajectories"] || job_data["@simulations"]</pre></td>
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<td><pre><a name="line50">50</a> #seeds = neptune_get_ssa_seed_vals(num_sims)</pre></td>
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<td><pre><a name="line51">51</a> #Djinn.log_debug("seeds are #{seeds.join(', ')}")</pre></td>
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<td><pre><a name="line52">52</a> </pre></td>
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<td><pre><a name="line53">53</a> param_num = job_data['@param_num']</pre></td>
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<td><pre><a name="line55">55</a> threads = []</pre></td>
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<td><pre><a name="line56">56</a> node_times = []</pre></td>
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<td><pre><a name="line57">57</a> at = 0 </pre></td>
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<td><pre><a name="line58">58</a> nodes.each_with_index { |node, i|</pre></td>
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<td><pre><a name="line59">59</a> threads << Thread.new {</pre></td>
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<td><pre><a name="line60">60</a> node_times[i] = 0</pre></td>
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<td><pre><a name="line61">61</a> </pre></td>
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<td><pre><a name="line62">62</a> ip = node.private_ip</pre></td>
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<td><pre><a name="line63">63</a> ssh_key = node.ssh_key</pre></td>
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<td><pre><a name="line64">64</a> start = at</pre></td>
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<td><pre><a name="line65">65</a> fin = at + sims[i]</pre></td>
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<td><pre><a name="line66">66</a> at = fin</pre></td>
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<td><pre><a name="line67">67</a> fin -= 1 </pre></td>
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<td><pre><a name="line68">68</a> Djinn.log_debug("This node will run trajectories #{start} to #{fin}")</pre></td>
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<td><pre><a name="line46">46</a> tar = working_dir + "/" + File.basename(job_data['@tar'])</pre></td>
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<td><pre><a name="line47">47</a> </pre></td>
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<td><pre><a name="line48">48</a> Djinn.log_debug("tar is #{job_data['@tar']}")</pre></td>
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<td><pre><a name="line49">49</a> Djinn.log_debug("working dir is #{working_dir}")</pre></td>
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<td><pre><a name="line50">50</a> </pre></td>
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<td><pre><a name="line51">51</a> remote = job_data['@tar']</pre></td>
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<td><pre><a name="line52">52</a> storage = job_data['@storage']</pre></td>
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<td><pre><a name="line53">53</a> </pre></td>
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<td><pre><a name="line54">54</a> datastore = DatastoreFactory.get_datastore(storage, job_data)</pre></td>
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<td><pre><a name="line55">55</a> datastore.get_output_and_save_to_fs(remote, tar)</pre></td>
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<td><pre><a name="line56">56</a> </pre></td>
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<td><pre><a name="line57">57</a> neptune_uncompress_file(tar)</pre></td>
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<td><pre><a name="line58">58</a> </pre></td>
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<td><pre><a name="line59">59</a> num_sims = job_data["@trajectories"] || job_data["@simulations"]</pre></td>
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<td><pre><a name="line60">60</a> </pre></td>
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<td><pre><a name="line61">61</a> param_num = job_data['@param_num']</pre></td>
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<td><pre><a name="line62">62</a> </pre></td>
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<td><pre><a name="line63">63</a> threads = []</pre></td>
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<tr class="uncovered">
438
<td><pre><a name="line64">64</a> node_times = []</pre></td>
439
</tr>
440
441
442
443
<tr class="uncovered">
444
<td><pre><a name="line65">65</a> at = 0 </pre></td>
445
</tr>
446
447
448
449
<tr class="uncovered">
450
<td><pre><a name="line66">66</a> nodes.each_with_index { |node, i|</pre></td>
451
</tr>
452
453
454
455
<tr class="uncovered">
456
<td><pre><a name="line67">67</a> threads << Thread.new {</pre></td>
457
</tr>
458
459
460
461
<tr class="uncovered">
462
<td><pre><a name="line68">68</a> node_times[i] = 0</pre></td>
463
463
</tr>
464
464
465
465
471
471
472
472
473
473
<tr class="uncovered">
474
<td><pre><a name="line70">70</a> code_path = "#{working_dir}/code/run.sh"</pre></td>
475
</tr>
476
477
478
479
<tr class="uncovered">
480
<td><pre><a name="line71">71</a> Djinn.log_run("chmod +x #{code_path}")</pre></td>
481
</tr>
482
483
484
485
<tr class="uncovered">
486
<td><pre><a name="line72">72</a> exec = "bash #{code_path}"</pre></td>
487
</tr>
488
489
490
491
<tr class="uncovered">
492
<td><pre><a name="line73">73</a> </pre></td>
493
</tr>
494
495
496
497
<tr class="uncovered">
498
<td><pre><a name="line74">74</a> input = "#{working_dir}/code/#{job_data['@input']}"</pre></td>
499
</tr>
500
501
502
503
<tr class="uncovered">
504
<td><pre><a name="line75">75</a> </pre></td>
505
</tr>
506
507
508
509
<tr class="uncovered">
510
<td><pre><a name="line76">76</a> unless ip == HelperFunctions.local_ip</pre></td>
511
</tr>
512
513
514
515
<tr class="uncovered">
516
<td><pre><a name="line77">77</a> Djinn.log_run("scp -r -i #{ssh_key} -o StrictHostkeyChecking=no #{working_dir} root@#{ip}:#{working_dir}")</pre></td>
517
</tr>
518
519
520
521
<tr class="uncovered">
522
<td><pre><a name="line78">78</a> end</pre></td>
523
</tr>
524
525
526
527
<tr class="uncovered">
528
<td><pre><a name="line79">79</a> </pre></td>
529
</tr>
530
531
532
533
<tr class="uncovered">
534
<td><pre><a name="line80">80</a> trajectories = fin - start + 1 </pre></td>
474
<td><pre><a name="line70">70</a> ip = node.private_ip</pre></td>
475
</tr>
476
477
478
479
<tr class="uncovered">
480
<td><pre><a name="line71">71</a> ssh_key = node.ssh_key</pre></td>
481
</tr>
482
483
484
485
<tr class="uncovered">
486
<td><pre><a name="line72">72</a> start = at</pre></td>
487
</tr>
488
489
490
491
<tr class="uncovered">
492
<td><pre><a name="line73">73</a> fin = at + sims[i]</pre></td>
493
</tr>
494
495
496
497
<tr class="uncovered">
498
<td><pre><a name="line74">74</a> at = fin</pre></td>
499
</tr>
500
501
502
503
<tr class="uncovered">
504
<td><pre><a name="line75">75</a> fin -= 1 </pre></td>
505
</tr>
506
507
508
509
<tr class="uncovered">
510
<td><pre><a name="line76">76</a> Djinn.log_debug("This node will run trajectories #{start} to #{fin}")</pre></td>
511
</tr>
512
513
514
515
<tr class="uncovered">
516
<td><pre><a name="line77">77</a> </pre></td>
517
</tr>
518
519
520
521
<tr class="uncovered">
522
<td><pre><a name="line78">78</a> code_path = "#{working_dir}/code/run.sh"</pre></td>
523
</tr>
524
525
526
527
<tr class="uncovered">
528
<td><pre><a name="line79">79</a> Djinn.log_run("chmod +x #{code_path}")</pre></td>
529
</tr>
530
531
532
533
<tr class="uncovered">
534
<td><pre><a name="line80">80</a> exec = "bash #{code_path}"</pre></td>
535
535
</tr>
536
536
537
537
543
543
544
544
545
545
<tr class="uncovered">
546
<td><pre><a name="line82">82</a> if MULTICORE</pre></td>
547
</tr>
548
549
550
551
<tr class="uncovered">
552
<td><pre><a name="line83">83</a> cores = HelperFunctions.get_num_cpus()</pre></td>
553
</tr>
554
555
556
557
<tr class="uncovered">
558
<td><pre><a name="line84">84</a> else</pre></td>
559
</tr>
560
561
562
563
<tr class="uncovered">
564
<td><pre><a name="line85">85</a> cores = 1</pre></td>
546
<td><pre><a name="line82">82</a> input = "#{working_dir}/code/#{job_data['@input']}"</pre></td>
547
</tr>
548
549
550
551
<tr class="uncovered">
552
<td><pre><a name="line83">83</a> </pre></td>
553
</tr>
554
555
556
557
<tr class="uncovered">
558
<td><pre><a name="line84">84</a> unless ip == HelperFunctions.local_ip</pre></td>
559
</tr>
560
561
562
563
<tr class="uncovered">
564
<td><pre><a name="line85">85</a> Djinn.log_run("scp -r -i #{ssh_key} -o StrictHostkeyChecking=no #{working_dir} root@#{ip}:#{working_dir}")</pre></td>
565
565
</tr>
566
566
567
567
579
579
580
580
581
581
<tr class="uncovered">
582
<td><pre><a name="line88">88</a> done = 0</pre></td>
583
</tr>
584
585
586
587
<tr class="uncovered">
588
<td><pre><a name="line89">89</a> loop {</pre></td>
589
</tr>
590
591
592
593
<tr class="uncovered">
594
<td><pre><a name="line90">90</a> trajectories_left = trajectories - done</pre></td>
595
</tr>
596
597
598
599
<tr class="uncovered">
600
<td><pre><a name="line91">91</a> Djinn.log_debug("Need to run #{trajectories_left} more trajectories on #{cores} cores")</pre></td>
601
</tr>
602
603
604
605
<tr class="uncovered">
606
<td><pre><a name="line92">92</a> break if trajectories_left.zero?</pre></td>
607
</tr>
608
609
610
611
<tr class="uncovered">
612
<td><pre><a name="line93">93</a> need_to_run = [trajectories_left, cores].min</pre></td>
613
</tr>
614
615
616
617
<tr class="uncovered">
618
<td><pre><a name="line94">94</a> </pre></td>
619
</tr>
620
621
622
623
<tr class="uncovered">
624
<td><pre><a name="line95">95</a> Djinn.log_debug("Running #{need_to_run} trajectories")</pre></td>
625
</tr>
626
627
628
629
<tr class="uncovered">
630
<td><pre><a name="line96">96</a> core_threads = []</pre></td>
631
</tr>
632
633
634
635
<tr class="uncovered">
636
<td><pre><a name="line97">97</a> current_times = []</pre></td>
637
</tr>
638
639
640
641
<tr class="uncovered">
642
<td><pre><a name="line98">98</a> need_to_run.times { |j|</pre></td>
643
</tr>
644
645
646
647
<tr class="uncovered">
648
<td><pre><a name="line99">99</a> core_threads << Thread.new {</pre></td>
649
</tr>
650
651
652
653
<tr class="uncovered">
654
<td><pre><a name="line100">100</a> my_trajectory = start+done+j</pre></td>
655
</tr>
656
657
658
659
<tr class="uncovered">
660
<td><pre><a name="line101">101</a> Djinn.log_debug("Thread #{j} is running trajectory #{my_trajectory}")</pre></td>
661
</tr>
662
663
664
665
<tr class="uncovered">
666
<td><pre><a name="line102">102</a> output = File.expand_path("#{working_dir}/output-#{my_trajectory}")</pre></td>
667
</tr>
668
669
670
671
<tr class="uncovered">
672
<td><pre><a name="line103">103</a> </pre></td>
673
</tr>
674
675
676
677
<tr class="uncovered">
678
<td><pre><a name="line104">104</a> # run the computation, remembering to place StochKit in the user's PATH</pre></td>
679
</tr>
680
681
682
683
<tr class="uncovered">
684
<td><pre><a name="line105">105</a> path = "PATH=$PATH:#{SSA_HOME}"</pre></td>
685
</tr>
686
687
688
689
<tr class="uncovered">
690
<td><pre><a name="line106">106</a> run_command = "#{path} #{exec} #{input} #{output} #{my_trajectory} #{param_num}"</pre></td>
691
</tr>
692
693
694
695
<tr class="uncovered">
696
<td><pre><a name="line107">107</a> </pre></td>
697
</tr>
698
699
700
701
<tr class="uncovered">
702
<td><pre><a name="line108">108</a> start_compute = Time.now</pre></td>
703
</tr>
704
705
706
707
<tr class="uncovered">
708
<td><pre><a name="line109">109</a> Djinn.log_run("ssh -i #{ssh_key} -o StrictHostkeyChecking=no root@#{ip} '#{run_command}'")</pre></td>
709
</tr>
710
711
712
713
<tr class="uncovered">
714
<td><pre><a name="line110">110</a> end_compute = Time.now</pre></td>
715
</tr>
716
717
718
719
<tr class="uncovered">
720
<td><pre><a name="line111">111</a> c_time = end_compute - start_compute</pre></td>
721
</tr>
722
723
724
725
<tr class="uncovered">
726
<td><pre><a name="line112">112</a> total_compute_time += c_time</pre></td>
727
</tr>
728
729
730
731
<tr class="uncovered">
732
<td><pre><a name="line113">113</a> c_times << c_time</pre></td>
733
</tr>
734
735
736
737
<tr class="uncovered">
738
<td><pre><a name="line114">114</a> </pre></td>
739
</tr>
740
741
742
743
<tr class="uncovered">
744
<td><pre><a name="line115">115</a> # copy the output back to this box - in the future we can do merges here</pre></td>
745
</tr>
746
747
748
749
<tr class="uncovered">
750
<td><pre><a name="line116">116</a> # or in the future we can just have the node upload to s3</pre></td>
751
</tr>
752
753
754
755
<tr class="uncovered">
756
<td><pre><a name="line117">117</a> start_storage = Time.now</pre></td>
757
</tr>
758
759
760
761
<tr class="uncovered">
762
<td><pre><a name="line118">118</a> unless HelperFunctions.local_ip == ip</pre></td>
763
</tr>
764
765
766
767
<tr class="uncovered">
768
<td><pre><a name="line119">119</a> remote_cp_command = "scp -r -i #{ssh_key} -o StrictHostkeyChecking=no root@#{ip}:#{output} #{output}"</pre></td>
769
</tr>
770
771
772
773
<tr class="uncovered">
774
<td><pre><a name="line120">120</a> Djinn.log_run(remote_cp_command)</pre></td>
775
</tr>
776
777
778
779
<tr class="uncovered">
780
<td><pre><a name="line121">121</a> </pre></td>
781
</tr>
782
783
784
785
<tr class="uncovered">
786
<td><pre><a name="line122">122</a> end</pre></td>
787
</tr>
788
789
790
791
<tr class="uncovered">
792
<td><pre><a name="line123">123</a> </pre></td>
793
</tr>
794
795
796
797
<tr class="uncovered">
798
<td><pre><a name="line124">124</a> remote_location = "#{job_data['@output']}/output-#{my_trajectory}"</pre></td>
799
</tr>
800
801
802
803
<tr class="uncovered">
804
<td><pre><a name="line125">125</a> Repo.set_output(remote_location, output, storage, creds, IS_FILE)</pre></td>
805
</tr>
806
807
808
809
<tr class="uncovered">
810
<td><pre><a name="line126">126</a> end_storage = Time.now</pre></td>
811
</tr>
812
813
814
815
<tr class="uncovered">
816
<td><pre><a name="line127">127</a> s_time = end_storage - start_storage</pre></td>
817
</tr>
818
819
820
821
<tr class="uncovered">
822
<td><pre><a name="line128">128</a> total_storage_time += s_time</pre></td>
823
</tr>
824
825
826
827
<tr class="uncovered">
828
<td><pre><a name="line129">129</a> s_times << s_time</pre></td>
829
</tr>
830
831
832
833
<tr class="uncovered">
834
<td><pre><a name="line130">130</a> </pre></td>
835
</tr>
836
837
838
839
<tr class="uncovered">
840
<td><pre><a name="line131">131</a> node_times[i] += (c_time + s_time)</pre></td>
841
</tr>
842
843
844
845
<tr class="uncovered">
846
<td><pre><a name="line132">132</a> </pre></td>
847
</tr>
848
849
850
851
<tr class="uncovered">
852
<td><pre><a name="line133">133</a> # remove our output - we can't want the disk to fill up</pre></td>
853
</tr>
854
855
856
857
<tr class="uncovered">
858
<td><pre><a name="line134">134</a> remove_cmd = "rm -rf #{output}"</pre></td>
859
</tr>
860
861
862
863
<tr class="uncovered">
864
<td><pre><a name="line135">135</a> Djinn.log_run("ssh -i #{ssh_key} -o StrictHostkeyChecking=no root@#{ip} '#{remove_cmd}'")</pre></td>
865
</tr>
866
867
868
869
<tr class="uncovered">
870
<td><pre><a name="line136">136</a> Djinn.log_run(remove_cmd)</pre></td>
871
</tr>
872
873
874
875
<tr class="uncovered">
876
<td><pre><a name="line137">137</a> }</pre></td>
877
</tr>
878
879
880
881
<tr class="uncovered">
882
<td><pre><a name="line138">138</a> }</pre></td>
883
</tr>
884
885
886
887
<tr class="uncovered">
888
<td><pre><a name="line139">139</a> </pre></td>
889
</tr>
890
891
892
893
<tr class="uncovered">
894
<td><pre><a name="line140">140</a> core_threads.each { |c| c.join }</pre></td>
895
</tr>
896
897
898
899
<tr class="uncovered">
900
<td><pre><a name="line141">141</a> </pre></td>
901
</tr>
902
903
904
905
<tr class="uncovered">
906
<td><pre><a name="line142">142</a> done += need_to_run</pre></td>
907
</tr>
908
909
910
911
<tr class="uncovered">
912
<td><pre><a name="line143">143</a> Djinn.log_debug("Done running #{need_to_run} trajectories, #{trajectories - done} to go")</pre></td>
913
</tr>
914
915
916
917
<tr class="uncovered">
918
<td><pre><a name="line144">144</a> }</pre></td>
919
</tr>
920
921
922
923
<tr class="uncovered">
924
<td><pre><a name="line145">145</a> }</pre></td>
925
</tr>
926
927
928
929
<tr class="uncovered">
930
<td><pre><a name="line146">146</a> }</pre></td>
582
<td><pre><a name="line88">88</a> trajectories = fin - start + 1 </pre></td>
583
</tr>
584
585
586
587
<tr class="uncovered">
588
<td><pre><a name="line89">89</a> </pre></td>
589
</tr>
590
591
592
593
<tr class="uncovered">
594
<td><pre><a name="line90">90</a> if MULTICORE</pre></td>
595
</tr>
596
597
598
599
<tr class="uncovered">
600
<td><pre><a name="line91">91</a> cores = HelperFunctions.get_num_cpus()</pre></td>
601
</tr>
602
603
604
605
<tr class="uncovered">
606
<td><pre><a name="line92">92</a> else</pre></td>
607
</tr>
608
609
610
611
<tr class="uncovered">
612
<td><pre><a name="line93">93</a> cores = 1</pre></td>
613
</tr>
614
615
616
617
<tr class="uncovered">
618
<td><pre><a name="line94">94</a> end</pre></td>
619
</tr>
620
621
622
623
<tr class="uncovered">
624
<td><pre><a name="line95">95</a> </pre></td>
625
</tr>
626
627
628
629
<tr class="uncovered">
630
<td><pre><a name="line96">96</a> done = 0</pre></td>
631
</tr>
632
633
634
635
<tr class="uncovered">
636
<td><pre><a name="line97">97</a> loop {</pre></td>
637
</tr>
638
639
640
641
<tr class="uncovered">
642
<td><pre><a name="line98">98</a> trajectories_left = trajectories - done</pre></td>
643
</tr>
644
645
646
647
<tr class="uncovered">
648
<td><pre><a name="line99">99</a> Djinn.log_debug("Need to run #{trajectories_left} more trajectories on #{cores} cores")</pre></td>
649
</tr>
650
651
652
653
<tr class="uncovered">
654
<td><pre><a name="line100">100</a> break if trajectories_left.zero?</pre></td>
655
</tr>
656
657
658
659
<tr class="uncovered">
660
<td><pre><a name="line101">101</a> need_to_run = [trajectories_left, cores].min</pre></td>
661
</tr>
662
663
664
665
<tr class="uncovered">
666
<td><pre><a name="line102">102</a> </pre></td>
667
</tr>
668
669
670
671
<tr class="uncovered">
672
<td><pre><a name="line103">103</a> Djinn.log_debug("Running #{need_to_run} trajectories")</pre></td>
673
</tr>
674
675
676
677
<tr class="uncovered">
678
<td><pre><a name="line104">104</a> core_threads = []</pre></td>
679
</tr>
680
681
682
683
<tr class="uncovered">
684
<td><pre><a name="line105">105</a> current_times = []</pre></td>
685
</tr>
686
687
688
689
<tr class="uncovered">
690
<td><pre><a name="line106">106</a> need_to_run.times { |j|</pre></td>
691
</tr>
692
693
694
695
<tr class="uncovered">
696
<td><pre><a name="line107">107</a> core_threads << Thread.new {</pre></td>
697
</tr>
698
699
700
701
<tr class="uncovered">
702
<td><pre><a name="line108">108</a> my_trajectory = start+done+j</pre></td>
703
</tr>
704
705
706
707
<tr class="uncovered">
708
<td><pre><a name="line109">109</a> Djinn.log_debug("Thread #{j} is running trajectory #{my_trajectory}")</pre></td>
709
</tr>
710
711
712
713
<tr class="uncovered">
714
<td><pre><a name="line110">110</a> output = File.expand_path("#{working_dir}/output-#{my_trajectory}")</pre></td>
715
</tr>
716
717
718
719
<tr class="uncovered">
720
<td><pre><a name="line111">111</a> </pre></td>
721
</tr>
722
723
724
725
<tr class="uncovered">
726
<td><pre><a name="line112">112</a> # run the computation, remembering to place StochKit in the user's PATH</pre></td>
727
</tr>
728
729
730
731
<tr class="uncovered">
732
<td><pre><a name="line113">113</a> path = "PATH=$PATH:#{SSA_HOME}"</pre></td>
733
</tr>
734
735
736
737
<tr class="uncovered">
738
<td><pre><a name="line114">114</a> run_command = "#{path} #{exec} #{input} #{output} #{my_trajectory} #{param_num}"</pre></td>
739
</tr>
740
741
742
743
<tr class="uncovered">
744
<td><pre><a name="line115">115</a> </pre></td>
745
</tr>
746
747
748
749
<tr class="uncovered">
750
<td><pre><a name="line116">116</a> start_compute = Time.now</pre></td>
751
</tr>
752
753
754
755
<tr class="uncovered">
756
<td><pre><a name="line117">117</a> Djinn.log_run("ssh -i #{ssh_key} -o StrictHostkeyChecking=no root@#{ip} '#{run_command}'")</pre></td>
757
</tr>
758
759
760
761
<tr class="uncovered">
762
<td><pre><a name="line118">118</a> end_compute = Time.now</pre></td>
763
</tr>
764
765
766
767
<tr class="uncovered">
768
<td><pre><a name="line119">119</a> c_time = end_compute - start_compute</pre></td>
769
</tr>
770
771
772
773
<tr class="uncovered">
774
<td><pre><a name="line120">120</a> total_compute_time += c_time</pre></td>
775
</tr>
776
777
778
779
<tr class="uncovered">
780
<td><pre><a name="line121">121</a> c_times << c_time</pre></td>
781
</tr>
782
783
784
785
<tr class="uncovered">
786
<td><pre><a name="line122">122</a> </pre></td>
787
</tr>
788
789
790
791
<tr class="uncovered">
792
<td><pre><a name="line123">123</a> # copy the output back to this box - in the future we can do merges here</pre></td>
793
</tr>
794
795
796
797
<tr class="uncovered">
798
<td><pre><a name="line124">124</a> # or in the future we can just have the node upload to s3</pre></td>
799
</tr>
800
801
802
803
<tr class="uncovered">
804
<td><pre><a name="line125">125</a> start_storage = Time.now</pre></td>
805
</tr>
806
807
808
809
<tr class="uncovered">
810
<td><pre><a name="line126">126</a> unless HelperFunctions.local_ip == ip</pre></td>
811
</tr>
812
813
814
815
<tr class="uncovered">
816
<td><pre><a name="line127">127</a> remote_cp_command = "scp -r -i #{ssh_key} -o StrictHostkeyChecking=no root@#{ip}:#{output} #{output}"</pre></td>
817
</tr>
818
819
820
821
<tr class="uncovered">
822
<td><pre><a name="line128">128</a> Djinn.log_run(remote_cp_command)</pre></td>
823
</tr>
824
825
826
827
<tr class="uncovered">
828
<td><pre><a name="line129">129</a> </pre></td>
829
</tr>
830
831
832
833
<tr class="uncovered">
834
<td><pre><a name="line130">130</a> end</pre></td>
835
</tr>
836
837
838
839
<tr class="uncovered">
840
<td><pre><a name="line131">131</a> </pre></td>
841
</tr>
842
843
844
845
<tr class="uncovered">
846
<td><pre><a name="line132">132</a> remote_location = "#{job_data['@output']}/output-#{my_trajectory}"</pre></td>
847
</tr>
848
849
850
851
<tr class="uncovered">
852
<td><pre><a name="line133">133</a> datastore.write_remote_file_from_local_file(remote_location, output)</pre></td>
853
</tr>
854
855
856
857
<tr class="uncovered">
858
<td><pre><a name="line134">134</a> end_storage = Time.now</pre></td>
859
</tr>
860
861
862
863
<tr class="uncovered">
864
<td><pre><a name="line135">135</a> s_time = end_storage - start_storage</pre></td>
865
</tr>
866
867
868
869
<tr class="uncovered">
870
<td><pre><a name="line136">136</a> total_storage_time += s_time</pre></td>
871
</tr>
872
873
874
875
<tr class="uncovered">
876
<td><pre><a name="line137">137</a> s_times << s_time</pre></td>
877
</tr>
878
879
880
881
<tr class="uncovered">
882
<td><pre><a name="line138">138</a> </pre></td>
883
</tr>
884
885
886
887
<tr class="uncovered">
888
<td><pre><a name="line139">139</a> node_times[i] += (c_time + s_time)</pre></td>
889
</tr>
890
891
892
893
<tr class="uncovered">
894
<td><pre><a name="line140">140</a> </pre></td>
895
</tr>
896
897
898
899
<tr class="uncovered">
900
<td><pre><a name="line141">141</a> # remove our output - we can't want the disk to fill up</pre></td>
901
</tr>
902
903
904
905
<tr class="uncovered">
906
<td><pre><a name="line142">142</a> remove_cmd = "rm -rf #{output}"</pre></td>
907
</tr>
908
909
910
911
<tr class="uncovered">
912
<td><pre><a name="line143">143</a> Djinn.log_run("ssh -i #{ssh_key} -o StrictHostkeyChecking=no root@#{ip} '#{remove_cmd}'")</pre></td>
913
</tr>
914
915
916
917
<tr class="uncovered">
918
<td><pre><a name="line144">144</a> Djinn.log_run(remove_cmd)</pre></td>
919
</tr>
920
921
922
923
<tr class="uncovered">
924
<td><pre><a name="line145">145</a> }</pre></td>
925
</tr>
926
927
928
929
<tr class="uncovered">
930
<td><pre><a name="line146">146</a> }</pre></td>
931
931
</tr>
932
932
933
933
939
939
940
940
941
941
<tr class="uncovered">
942
<td><pre><a name="line148">148</a> Djinn.log_debug("ssa - joining threads")</pre></td>
942
<td><pre><a name="line148">148</a> core_threads.each { |c| c.join }</pre></td>
943
943
</tr>
944
944
945
945
951
951
952
952
953
953
<tr class="uncovered">
954
<td><pre><a name="line150">150</a> threads.each { |t| t.join }</pre></td>
955
</tr>
956
957
958
959
<tr class="uncovered">
960
<td><pre><a name="line151">151</a> </pre></td>
961
</tr>
962
963
964
965
<tr class="uncovered">
966
<td><pre><a name="line152">152</a> # clean up after ourselves</pre></td>
967
</tr>
968
969
970
971
<tr class="uncovered">
972
<td><pre><a name="line153">153</a> Djinn.log_run("rm -rf #{working_dir}")</pre></td>
973
</tr>
974
975
976
977
<tr class="uncovered">
978
<td><pre><a name="line154">154</a> </pre></td>
979
</tr>
980
981
982
983
<tr class="uncovered">
984
<td><pre><a name="line155">155</a> fin_time = Time.now</pre></td>
985
</tr>
986
987
988
989
<tr class="uncovered">
990
<td><pre><a name="line156">156</a> total = fin_time - start_time</pre></td>
991
</tr>
992
993
994
995
<tr class="uncovered">
996
<td><pre><a name="line157">157</a> total_slowest_path = node_times.max</pre></td>
997
</tr>
998
999
1000
1001
<tr class="uncovered">
1002
<td><pre><a name="line158">158</a> total_overhead_time = total - total_slowest_path</pre></td>
954
<td><pre><a name="line150">150</a> done += need_to_run</pre></td>
955
</tr>
956
957
958
959
<tr class="uncovered">
960
<td><pre><a name="line151">151</a> Djinn.log_debug("Done running #{need_to_run} trajectories, #{trajectories - done} to go")</pre></td>
961
</tr>
962
963
964
965
<tr class="uncovered">
966
<td><pre><a name="line152">152</a> }</pre></td>
967
</tr>
968
969
970
971
<tr class="uncovered">
972
<td><pre><a name="line153">153</a> }</pre></td>
973
</tr>
974
975
976
977
<tr class="uncovered">
978
<td><pre><a name="line154">154</a> }</pre></td>
979
</tr>
980
981
982
983
<tr class="uncovered">
984
<td><pre><a name="line155">155</a> </pre></td>
985
</tr>
986
987
988
989
<tr class="uncovered">
990
<td><pre><a name="line156">156</a> Djinn.log_debug("ssa - joining threads")</pre></td>
991
</tr>
992
993
994
995
<tr class="uncovered">
996
<td><pre><a name="line157">157</a> </pre></td>
997
</tr>
998
999
1000
1001
<tr class="uncovered">
1002
<td><pre><a name="line158">158</a> threads.each { |t| t.join }</pre></td>
1003
1003
</tr>
1004
1004
1005
1005
1011
1011
1012
1012
1013
1013
<tr class="uncovered">
1014
<td><pre><a name="line160">160</a> timing_info = <<BAZ</pre></td>
1015
</tr>
1016
1017
1018
1019
<tr class="uncovered">
1020
<td><pre><a name="line161">161</a> TIMING: total execution time is #{total} seconds.</pre></td>
1021
</tr>
1022
1023
1024
1025
<tr class="uncovered">
1026
<td><pre><a name="line162">162</a> TIMING: total compute time is #{total_compute_time} seconds.</pre></td>
1027
</tr>
1028
1029
1030
1031
<tr class="uncovered">
1032
<td><pre><a name="line163">163</a> TIMING: total storage time is #{total_storage_time} seconds.</pre></td>
1033
</tr>
1034
1035
1036
1037
<tr class="uncovered">
1038
<td><pre><a name="line164">164</a> TIMING: slowest path time is #{total_slowest_path} seconds.</pre></td>
1039
</tr>
1040
1041
1042
1043
<tr class="uncovered">
1044
<td><pre><a name="line165">165</a> TIMING: overhead time is #{total_overhead_time} seconds.</pre></td>
1045
</tr>
1046
1047
1048
1049
<tr class="uncovered">
1050
<td><pre><a name="line166">166</a> TIMING: average compute time is #{average(c_times)} seconds.</pre></td>
1051
</tr>
1052
1053
1054
1055
<tr class="uncovered">
1056
<td><pre><a name="line167">167</a> TIMING: stddev compute time is #{standard_deviation(c_times)} seconds.</pre></td>
1057
</tr>
1058
1059
1060
1061
<tr class="uncovered">
1062
<td><pre><a name="line168">168</a> TIMING: average storage time is #{average(s_times)} seconds.</pre></td>
1063
</tr>
1064
1065
1066
1067
<tr class="uncovered">
1068
<td><pre><a name="line169">169</a> TIMING: stddev storage time is #{standard_deviation(s_times)} seconds.</pre></td>
1069
</tr>
1070
1071
1072
1073
<tr class="uncovered">
1074
<td><pre><a name="line170">170</a> RAW_DATA: node times are: [#{node_times.join(', ')}]</pre></td>
1075
</tr>
1076
1077
1078
1079
<tr class="uncovered">
1080
<td><pre><a name="line171">171</a> RAW_DATA: compute times are: [#{c_times.join(', ')}]</pre></td>
1081
</tr>
1082
1083
1084
1085
<tr class="uncovered">
1086
<td><pre><a name="line172">172</a> RAW_DATA: storage times are: [#{s_times.join(', ')}]</pre></td>
1087
</tr>
1088
1089
1090
1091
<tr class="uncovered">
1092
<td><pre><a name="line173">173</a> BAZ</pre></td>
1093
</tr>
1094
1095
1096
1097
<tr class="uncovered">
1098
<td><pre><a name="line174">174</a> </pre></td>
1099
</tr>
1100
1101
1102
1103
<tr class="uncovered">
1104
<td><pre><a name="line175">175</a> Djinn.log_debug(timing_info)</pre></td>
1105
</tr>
1106
1107
1108
1109
<tr class="uncovered">
1110
<td><pre><a name="line176">176</a> </pre></td>
1111
</tr>
1112
1113
1114
1115
<tr class="uncovered">
1116
<td><pre><a name="line177">177</a> remote_location = "#{job_data['@output']}/timing_info.txt"</pre></td>
1117
</tr>
1118
1119
1120
1121
<tr class="uncovered">
1122
<td><pre><a name="line178">178</a> Repo.set_output(remote_location, timing_info, storage, creds, NOT_A_FILE)</pre></td>
1123
</tr>
1124
1125
1126
1127
<tr class="uncovered">
1128
<td><pre><a name="line179">179</a> </pre></td>
1129
</tr>
1130
1131
1132
1133
<tr class="uncovered">
1134
<td><pre><a name="line180">180</a> remove_lock_file(job_data)</pre></td>
1135
</tr>
1136
1137
1138
1139
<tr class="uncovered">
1140
<td><pre><a name="line181">181</a> }</pre></td>
1014
<td><pre><a name="line160">160</a> # clean up after ourselves</pre></td>
1015
</tr>
1016
1017
1018
1019
<tr class="uncovered">
1020
<td><pre><a name="line161">161</a> Djinn.log_run("rm -rf #{working_dir}")</pre></td>
1021
</tr>
1022
1023
1024
1025
<tr class="uncovered">
1026
<td><pre><a name="line162">162</a> </pre></td>
1027
</tr>
1028
1029
1030
1031
<tr class="uncovered">
1032
<td><pre><a name="line163">163</a> fin_time = Time.now</pre></td>
1033
</tr>
1034
1035
1036
1037
<tr class="uncovered">
1038
<td><pre><a name="line164">164</a> total = fin_time - start_time</pre></td>
1039
</tr>
1040
1041
1042
1043
<tr class="uncovered">
1044
<td><pre><a name="line165">165</a> total_slowest_path = node_times.max</pre></td>
1045
</tr>
1046
1047
1048
1049
<tr class="uncovered">
1050
<td><pre><a name="line166">166</a> total_overhead_time = total - total_slowest_path</pre></td>
1051
</tr>
1052
1053
1054
1055
<tr class="uncovered">
1056
<td><pre><a name="line167">167</a> </pre></td>
1057
</tr>
1058
1059
1060
1061
<tr class="uncovered">
1062
<td><pre><a name="line168">168</a> timing_info = <<BAZ</pre></td>
1063
</tr>
1064
1065
1066
1067
<tr class="uncovered">
1068
<td><pre><a name="line169">169</a> TIMING: total execution time is #{total} seconds.</pre></td>
1069
</tr>
1070
1071
1072
1073
<tr class="uncovered">
1074
<td><pre><a name="line170">170</a> TIMING: total compute time is #{total_compute_time} seconds.</pre></td>
1075
</tr>
1076
1077
1078
1079
<tr class="uncovered">
1080
<td><pre><a name="line171">171</a> TIMING: total storage time is #{total_storage_time} seconds.</pre></td>
1081
</tr>
1082
1083
1084
1085
<tr class="uncovered">
1086
<td><pre><a name="line172">172</a> TIMING: slowest path time is #{total_slowest_path} seconds.</pre></td>
1087
</tr>
1088
1089
1090
1091
<tr class="uncovered">
1092
<td><pre><a name="line173">173</a> TIMING: overhead time is #{total_overhead_time} seconds.</pre></td>
1093
</tr>
1094
1095
1096
1097
<tr class="uncovered">
1098
<td><pre><a name="line174">174</a> TIMING: average compute time is #{average(c_times)} seconds.</pre></td>
1099
</tr>
1100
1101
1102
1103
<tr class="uncovered">
1104
<td><pre><a name="line175">175</a> TIMING: stddev compute time is #{standard_deviation(c_times)} seconds.</pre></td>
1105
</tr>
1106
1107
1108
1109
<tr class="uncovered">
1110
<td><pre><a name="line176">176</a> TIMING: average storage time is #{average(s_times)} seconds.</pre></td>
1111
</tr>
1112
1113
1114
1115
<tr class="uncovered">
1116
<td><pre><a name="line177">177</a> TIMING: stddev storage time is #{standard_deviation(s_times)} seconds.</pre></td>
1117
</tr>
1118
1119
1120
1121
<tr class="uncovered">
1122
<td><pre><a name="line178">178</a> RAW_DATA: node times are: [#{node_times.join(', ')}]</pre></td>
1123
</tr>
1124
1125
1126
1127
<tr class="uncovered">
1128
<td><pre><a name="line179">179</a> RAW_DATA: compute times are: [#{c_times.join(', ')}]</pre></td>
1129
</tr>
1130
1131
1132
1133
<tr class="uncovered">
1134
<td><pre><a name="line180">180</a> RAW_DATA: storage times are: [#{s_times.join(', ')}]</pre></td>
1135
</tr>
1136
1137
1138
1139
<tr class="uncovered">
1140
<td><pre><a name="line181">181</a> BAZ</pre></td>
1141
1141
</tr>
1142
1142
1143
1143
1149
1149
1150
1150
1151
1151
<tr class="uncovered">
1152
<td><pre><a name="line183">183</a> return "OK"</pre></td>
1153
</tr>
1154
1155
1156
1157
<tr class="uncovered">
1158
<td><pre><a name="line184">184</a> end</pre></td>
1159
</tr>
1160
1161
1162
1163
<tr class="inferred">
1164
<td><pre><a name="line185">185</a> </pre></td>
1165
</tr>
1166
1167
1168
1169
<tr class="marked">
1170
<td><pre><a name="line186">186</a> private</pre></td>
1171
</tr>
1172
1173
1174
1175
<tr class="inferred">
1152
<td><pre><a name="line183">183</a> Djinn.log_debug(timing_info)</pre></td>
1153
</tr>
1154
1155
1156
1157
<tr class="uncovered">
1158
<td><pre><a name="line184">184</a> </pre></td>
1159
</tr>
1160
1161
1162
1163
<tr class="uncovered">
1164
<td><pre><a name="line185">185</a> remote_location = "#{job_data['@output']}/timing_info.txt"</pre></td>
1165
</tr>
1166
1167
1168
1169
<tr class="uncovered">
1170
<td><pre><a name="line186">186</a> datastore.write_remote_file_from_string(remote_location, timing_info)</pre></td>
1171
</tr>
1172
1173
1174
1175
<tr class="uncovered">
1176
1176
<td><pre><a name="line187">187</a> </pre></td>
1177
1177
</tr>
1178
1178
1179
1179
1180
1180
1181
<tr class="marked">
1182
<td><pre><a name="line188">188</a> def neptune_ssa_get_output(job_data)</pre></td>
1183
</tr>
1184
1185
1186
1187
<tr class="uncovered">
1188
<td><pre><a name="line189">189</a> return SSA_HOME</pre></td>
1189
</tr>
1190
1191
1192
1193
<tr class="uncovered">
1194
<td><pre><a name="line190">190</a> end</pre></td>
1181
<tr class="uncovered">
1182
<td><pre><a name="line188">188</a> remove_lock_file(job_data)</pre></td>
1183
</tr>
1184
1185
1186
1187
<tr class="uncovered">
1188
<td><pre><a name="line189">189</a> }</pre></td>
1189
</tr>
1190
1191
1192
1193
<tr class="uncovered">
1194
<td><pre><a name="line190">190</a> </pre></td>
1195
</tr>
1196
1197
1198
1199
<tr class="uncovered">
1200
<td><pre><a name="line191">191</a> return "OK"</pre></td>
1201
</tr>
1202
1203
1204
1205
<tr class="uncovered">
1206
<td><pre><a name="line192">192</a> end</pre></td>
1195
1207
</tr>
1196
1208
1197
1209
1198
1210
1199
1211
<tr class="inferred">
1200
<td><pre><a name="line191">191</a> </pre></td>
1212
<td><pre><a name="line193">193</a> </pre></td>
1201
1213
</tr>
1202
1214
1203
1215
1204
1216
1205
1217
<tr class="marked">
1206
<td><pre><a name="line192">192</a> def start_ssa_master()</pre></td>
1207
</tr>
1208
1209
1210
1211
<tr class="uncovered">
1212
<td><pre><a name="line193">193</a> Djinn.log_debug("#{my_node.private_ip} is starting ssa master")</pre></td>
1213
</tr>
1214
1215
1216
1217
<tr class="uncovered">
1218
<td><pre><a name="line194">194</a> end</pre></td>
1218
<td><pre><a name="line194">194</a> private</pre></td>
1219
1219
</tr>
1220
1220
1221
1221
1227
1227
1228
1228
1229
1229
<tr class="marked">
1230
<td><pre><a name="line196">196</a> def start_ssa_slave()</pre></td>
1230
<td><pre><a name="line196">196</a> def neptune_ssa_get_output(job_data)</pre></td>
1231
1231
</tr>
1232
1232
1233
1233
1234
1234
1235
1235
<tr class="uncovered">
1236
<td><pre><a name="line197">197</a> Djinn.log_debug("#{my_node.private_ip} is starting ssa slave")</pre></td>
1236
<td><pre><a name="line197">197</a> return SSA_HOME</pre></td>
1237
1237
</tr>
1238
1238
1239
1239
1251
1251
1252
1252
1253
1253
<tr class="marked">
1254
<td><pre><a name="line200">200</a> def stop_ssa_master()</pre></td>
1254
<td><pre><a name="line200">200</a> def start_ssa_master()</pre></td>
1255
1255
</tr>
1256
1256
1257
1257
1258
1258
1259
1259
<tr class="uncovered">
1260
<td><pre><a name="line201">201</a> Djinn.log_debug("#{my_node.private_ip} is stopping ssa master")</pre></td>
1260
<td><pre><a name="line201">201</a> Djinn.log_debug("#{my_node.private_ip} is starting ssa master")</pre></td>
1261
1261
</tr>
1262
1262
1263
1263
1275
1275
1276
1276
1277
1277
<tr class="marked">
1278
<td><pre><a name="line204">204</a> def stop_ssa_slave()</pre></td>
1278
<td><pre><a name="line204">204</a> def start_ssa_slave()</pre></td>
1279
1279
</tr>
1280
1280
1281
1281
1282
1282
1283
1283
<tr class="uncovered">
1284
<td><pre><a name="line205">205</a> Djinn.log_debug("#{my_node.private_ip} is stopping ssa slave")</pre></td>
1284
<td><pre><a name="line205">205</a> Djinn.log_debug("#{my_node.private_ip} is starting ssa slave")</pre></td>
1285
1285
</tr>
1286
1286
1287
1287
1299
1299
1300
1300
1301
1301
<tr class="marked">
1302
<td><pre><a name="line208">208</a> def neptune_get_ssa_seed_vals(num_vals)</pre></td>
1303
</tr>
1304
1305
1306
1307
<tr class="uncovered">
1308
<td><pre><a name="line209">209</a> random_numbers = []</pre></td>
1309
</tr>
1310
1311
1312
1313
<tr class="uncovered">
1314
<td><pre><a name="line210">210</a> loop {</pre></td>
1315
</tr>
1316
1317
1318
1319
<tr class="uncovered">
1320
<td><pre><a name="line211">211</a> possible_rand = rand(32000)</pre></td>
1321
</tr>
1322
1323
1324
1325
<tr class="uncovered">
1326
<td><pre><a name="line212">212</a> unless random_numbers.include?(possible_rand)</pre></td>
1327
</tr>
1328
1329
1330
1331
<tr class="uncovered">
1332
<td><pre><a name="line213">213</a> random_numbers << possible_rand</pre></td>
1333
</tr>
1334
1335
1336
1337
<tr class="uncovered">
1338
<td><pre><a name="line214">214</a> end</pre></td>
1339
</tr>
1340
1341
1342
1343
<tr class="uncovered">
1344
<td><pre><a name="line215">215</a> break if num_vals == random_numbers.length</pre></td>
1345
</tr>
1346
1347
1348
1349
<tr class="uncovered">
1350
<td><pre><a name="line216">216</a> }</pre></td>
1351
</tr>
1352
1353
1354
1355
<tr class="uncovered">
1356
<td><pre><a name="line217">217</a> </pre></td>
1357
</tr>
1358
1359
1360
1361
<tr class="uncovered">
1362
<td><pre><a name="line218">218</a> return random_numbers</pre></td>
1363
</tr>
1364
1365
1366
1367
<tr class="uncovered">
1368
<td><pre><a name="line219">219</a> end</pre></td>
1369
</tr>
1370
1371
1372
1373
<tr class="inferred">
1374
<td><pre><a name="line220">220</a> </pre></td>
1375
</tr>
1376
1377
1378
1379
<tr class="marked">
1380
<td><pre><a name="line221">221</a> def neptune_get_ssa_num_simulations(nodes, job_data)</pre></td>
1381
</tr>
1382
1383
1384
1385
<tr class="uncovered">
1386
<td><pre><a name="line222">222</a> num_nodes = nodes.length</pre></td>
1387
</tr>
1388
1389
1390
1391
<tr class="uncovered">
1392
<td><pre><a name="line223">223</a> num_sims = job_data["@trajectories"] || job_data["@simulations"]</pre></td>
1393
</tr>
1394
1395
1396
1397
<tr class="uncovered">
1398
<td><pre><a name="line224">224</a> sims_per_node = num_sims / num_nodes</pre></td>
1302
<td><pre><a name="line208">208</a> def stop_ssa_master()</pre></td>
1303
</tr>
1304
1305
1306
1307
<tr class="uncovered">
1308
<td><pre><a name="line209">209</a> Djinn.log_debug("#{my_node.private_ip} is stopping ssa master")</pre></td>
1309
</tr>
1310
1311
1312
1313
<tr class="uncovered">
1314
<td><pre><a name="line210">210</a> end</pre></td>
1315
</tr>
1316
1317
1318
1319
<tr class="inferred">
1320
<td><pre><a name="line211">211</a> </pre></td>
1321
</tr>
1322
1323
1324
1325
<tr class="marked">
1326
<td><pre><a name="line212">212</a> def stop_ssa_slave()</pre></td>
1327
</tr>
1328
1329
1330
1331
<tr class="uncovered">
1332
<td><pre><a name="line213">213</a> Djinn.log_debug("#{my_node.private_ip} is stopping ssa slave")</pre></td>
1333
</tr>
1334
1335
1336
1337
<tr class="uncovered">
1338
<td><pre><a name="line214">214</a> end</pre></td>
1339
</tr>
1340
1341
1342
1343
<tr class="inferred">
1344
<td><pre><a name="line215">215</a> </pre></td>
1345
</tr>
1346
1347
1348
1349
<tr class="marked">
1350
<td><pre><a name="line216">216</a> def neptune_get_ssa_seed_vals(num_vals)</pre></td>
1351
</tr>
1352
1353
1354
1355
<tr class="uncovered">
1356
<td><pre><a name="line217">217</a> random_numbers = []</pre></td>
1357
</tr>
1358
1359
1360
1361
<tr class="uncovered">
1362
<td><pre><a name="line218">218</a> loop {</pre></td>
1363
</tr>
1364
1365
1366
1367
<tr class="uncovered">
1368
<td><pre><a name="line219">219</a> possible_rand = rand(32000)</pre></td>
1369
</tr>
1370
1371
1372
1373
<tr class="uncovered">
1374
<td><pre><a name="line220">220</a> unless random_numbers.include?(possible_rand)</pre></td>
1375
</tr>
1376
1377
1378
1379
<tr class="uncovered">
1380
<td><pre><a name="line221">221</a> random_numbers << possible_rand</pre></td>
1381
</tr>
1382
1383
1384
1385
<tr class="uncovered">
1386
<td><pre><a name="line222">222</a> end</pre></td>
1387
</tr>
1388
1389
1390
1391
<tr class="uncovered">
1392
<td><pre><a name="line223">223</a> break if num_vals == random_numbers.length</pre></td>
1393
</tr>
1394
1395
1396
1397
<tr class="uncovered">
1398
<td><pre><a name="line224">224</a> }</pre></td>
1399
1399
</tr>
1400
1400
1401
1401
1407
1407
1408
1408
1409
1409
<tr class="uncovered">
1410
<td><pre><a name="line226">226</a> Djinn.log_debug("num nodes = #{num_nodes}")</pre></td>
1411
</tr>
1412
1413
1414
1415
<tr class="uncovered">
1416
<td><pre><a name="line227">227</a> Djinn.log_debug("num_sims = #{num_sims}")</pre></td>
1417
</tr>
1418
1419
1420
1421
<tr class="uncovered">
1422
<td><pre><a name="line228">228</a> Djinn.log_debug("sims_per_node = #{sims_per_node}")</pre></td>
1423
</tr>
1424
1425
1426
1427
<tr class="uncovered">
1428
<td><pre><a name="line229">229</a> </pre></td>
1429
</tr>
1430
1431
1432
1433
<tr class="uncovered">
1434
<td><pre><a name="line230">230</a> # set up how many simulations each node</pre></td>
1435
</tr>
1436
1437
1438
1439
<tr class="uncovered">
1440
<td><pre><a name="line231">231</a> # should run by divying it up equally</pre></td>
1441
</tr>
1442
1443
1444
1445
<tr class="uncovered">
1446
<td><pre><a name="line232">232</a> # any remainder can be assigned to an</pre></td>
1447
</tr>
1448
1449
1450
1451
<tr class="uncovered">
1452
<td><pre><a name="line233">233</a> # arbitrary node</pre></td>
1453
</tr>
1454
1455
1456
1457
<tr class="uncovered">
1458
<td><pre><a name="line234">234</a> </pre></td>
1459
</tr>
1460
1461
1462
1463
<tr class="uncovered">
1464
<td><pre><a name="line235">235</a> sims = [sims_per_node] * num_nodes</pre></td>
1465
</tr>
1466
1467
1468
1469
<tr class="uncovered">
1470
<td><pre><a name="line236">236</a> remainder = num_sims % num_nodes</pre></td>
1471
</tr>
1472
1473
1474
1475
<tr class="uncovered">
1476
<td><pre><a name="line237">237</a> sims[-1] += remainder</pre></td>
1477
</tr>
1478
1479
1480
1481
<tr class="uncovered">
1482
<td><pre><a name="line238">238</a> </pre></td>
1483
</tr>
1484
1485
1486
1487
<tr class="uncovered">
1488
<td><pre><a name="line239">239</a> Djinn.log_debug("sims = #{sims.join(', ')}")</pre></td>
1489
</tr>
1490
1491
1492
1493
<tr class="uncovered">
1494
<td><pre><a name="line240">240</a> Djinn.log_debug("remainder = #{remainder}")</pre></td>
1495
</tr>
1496
1497
1498
1499
<tr class="uncovered">
1500
<td><pre><a name="line241">241</a> </pre></td>
1501
</tr>
1502
1503
1504
1505
<tr class="uncovered">
1506
<td><pre><a name="line242">242</a> return sims</pre></td>
1507
</tr>
1508
1509
1510
1511
<tr class="uncovered">
1512
<td><pre><a name="line243">243</a> end</pre></td>
1513
</tr>
1514
1515
1516
1517
<tr class="inferred">
1518
<td><pre><a name="line244">244</a> </pre></td>
1519
</tr>
1520
1521
1522
1523
<tr class="marked">
1524
<td><pre><a name="line245">245</a> def average(population)</pre></td>
1525
</tr>
1526
1527
1528
1529
<tr class="uncovered">
1530
<td><pre><a name="line246">246</a> total = 0.0</pre></td>
1531
</tr>
1532
1533
1534
1535
<tr class="uncovered">
1536
<td><pre><a name="line247">247</a> n = 0</pre></td>
1537
</tr>
1538
1539
1540
1541
<tr class="uncovered">
1542
<td><pre><a name="line248">248</a> </pre></td>
1543
</tr>
1544
1545
1546
1547
<tr class="uncovered">
1548
<td><pre><a name="line249">249</a> population.each { |val|</pre></td>
1549
</tr>
1550
1551
1552
1553
<tr class="uncovered">
1554
<td><pre><a name="line250">250</a> total += val</pre></td>
1555
</tr>
1556
1557
1558
1559
<tr class="uncovered">
1560
<td><pre><a name="line251">251</a> n += 1</pre></td>
1561
</tr>
1562
1563
1564
1565
<tr class="uncovered">
1566
<td><pre><a name="line252">252</a> }</pre></td>
1567
</tr>
1568
1569
1570
1571
<tr class="uncovered">
1572
<td><pre><a name="line253">253</a> </pre></td>
1573
</tr>
1574
1575
1576
1577
<tr class="uncovered">
1578
<td><pre><a name="line254">254</a> return total / n</pre></td>
1579
</tr>
1580
1581
1582
1583
<tr class="uncovered">
1584
<td><pre><a name="line255">255</a> end</pre></td>
1585
</tr>
1586
1587
1588
1589
<tr class="inferred">
1410
<td><pre><a name="line226">226</a> return random_numbers</pre></td>
1411
</tr>
1412
1413
1414
1415
<tr class="uncovered">
1416
<td><pre><a name="line227">227</a> end</pre></td>
1417
</tr>
1418
1419
1420
1421
<tr class="inferred">
1422
<td><pre><a name="line228">228</a> </pre></td>
1423
</tr>
1424
1425
1426
1427
<tr class="marked">
1428
<td><pre><a name="line229">229</a> def neptune_get_ssa_num_simulations(nodes, job_data)</pre></td>
1429
</tr>
1430
1431
1432
1433
<tr class="uncovered">
1434
<td><pre><a name="line230">230</a> num_nodes = nodes.length</pre></td>
1435
</tr>
1436
1437
1438
1439
<tr class="uncovered">
1440
<td><pre><a name="line231">231</a> num_sims = job_data["@trajectories"] || job_data["@simulations"]</pre></td>
1441
</tr>
1442
1443
1444
1445
<tr class="uncovered">
1446
<td><pre><a name="line232">232</a> sims_per_node = num_sims / num_nodes</pre></td>
1447
</tr>
1448
1449
1450
1451
<tr class="uncovered">
1452
<td><pre><a name="line233">233</a> </pre></td>
1453
</tr>
1454
1455
1456
1457
<tr class="uncovered">
1458
<td><pre><a name="line234">234</a> Djinn.log_debug("num nodes = #{num_nodes}")</pre></td>
1459
</tr>
1460
1461
1462
1463
<tr class="uncovered">
1464
<td><pre><a name="line235">235</a> Djinn.log_debug("num_sims = #{num_sims}")</pre></td>
1465
</tr>
1466
1467
1468
1469
<tr class="uncovered">
1470
<td><pre><a name="line236">236</a> Djinn.log_debug("sims_per_node = #{sims_per_node}")</pre></td>
1471
</tr>
1472
1473
1474
1475
<tr class="uncovered">
1476
<td><pre><a name="line237">237</a> </pre></td>
1477
</tr>
1478
1479
1480
1481
<tr class="uncovered">
1482
<td><pre><a name="line238">238</a> # set up how many simulations each node</pre></td>
1483
</tr>
1484
1485
1486
1487
<tr class="uncovered">
1488
<td><pre><a name="line239">239</a> # should run by divying it up equally</pre></td>
1489
</tr>
1490
1491
1492
1493
<tr class="uncovered">
1494
<td><pre><a name="line240">240</a> # any remainder can be assigned to an</pre></td>
1495
</tr>
1496
1497
1498
1499
<tr class="uncovered">
1500
<td><pre><a name="line241">241</a> # arbitrary node</pre></td>
1501
</tr>
1502
1503
1504
1505
<tr class="uncovered">
1506
<td><pre><a name="line242">242</a> </pre></td>
1507
</tr>
1508
1509
1510
1511
<tr class="uncovered">
1512
<td><pre><a name="line243">243</a> sims = [sims_per_node] * num_nodes</pre></td>
1513
</tr>
1514
1515
1516
1517
<tr class="uncovered">
1518
<td><pre><a name="line244">244</a> remainder = num_sims % num_nodes</pre></td>
1519
</tr>
1520
1521
1522
1523
<tr class="uncovered">
1524
<td><pre><a name="line245">245</a> sims[-1] += remainder</pre></td>
1525
</tr>
1526
1527
1528
1529
<tr class="uncovered">
1530
<td><pre><a name="line246">246</a> </pre></td>
1531
</tr>
1532
1533
1534
1535
<tr class="uncovered">
1536
<td><pre><a name="line247">247</a> Djinn.log_debug("sims = #{sims.join(', ')}")</pre></td>
1537
</tr>
1538
1539
1540
1541
<tr class="uncovered">
1542
<td><pre><a name="line248">248</a> Djinn.log_debug("remainder = #{remainder}")</pre></td>
1543
</tr>
1544
1545
1546
1547
<tr class="uncovered">
1548
<td><pre><a name="line249">249</a> </pre></td>
1549
</tr>
1550
1551
1552
1553
<tr class="uncovered">
1554
<td><pre><a name="line250">250</a> return sims</pre></td>
1555
</tr>
1556
1557
1558
1559
<tr class="uncovered">
1560
<td><pre><a name="line251">251</a> end</pre></td>
1561
</tr>
1562
1563
1564
1565
<tr class="inferred">
1566
<td><pre><a name="line252">252</a> </pre></td>
1567
</tr>
1568
1569
1570
1571
<tr class="marked">
1572
<td><pre><a name="line253">253</a> def average(population)</pre></td>
1573
</tr>
1574
1575
1576
1577
<tr class="uncovered">
1578
<td><pre><a name="line254">254</a> total = 0.0</pre></td>
1579
</tr>
1580
1581
1582
1583
<tr class="uncovered">
1584
<td><pre><a name="line255">255</a> n = 0</pre></td>
1585
</tr>
1586
1587
1588
1589
<tr class="uncovered">
1590
1590
<td><pre><a name="line256">256</a> </pre></td>
1591
1591
</tr>
1592
1592
1593
1593
1594
1594
1595
<tr class="uncovered">
1596
<td><pre><a name="line257">257</a> population.each { |val|</pre></td>
1597
</tr>
1598
1599
1600
1601
<tr class="uncovered">
1602
<td><pre><a name="line258">258</a> total += val</pre></td>
1603
</tr>
1604
1605
1606
1607
<tr class="uncovered">
1608
<td><pre><a name="line259">259</a> n += 1</pre></td>
1609
</tr>
1610
1611
1612
1613
<tr class="uncovered">
1614
<td><pre><a name="line260">260</a> }</pre></td>
1615
</tr>
1616
1617
1618
1619
<tr class="uncovered">
1620
<td><pre><a name="line261">261</a> </pre></td>
1621
</tr>
1622
1623
1624
1625
<tr class="uncovered">
1626
<td><pre><a name="line262">262</a> return total / n</pre></td>
1627
</tr>
1628
1629
1630
1631
<tr class="uncovered">
1632
<td><pre><a name="line263">263</a> end</pre></td>
1633
</tr>
1634
1635
1636
1637
<tr class="inferred">
1638
<td><pre><a name="line264">264</a> </pre></td>
1639
</tr>
1640
1641
1642
1595
1643
<tr class="marked">
1596
<td><pre><a name="line257">257</a> def variance(population)</pre></td>
1597
</tr>
1598
1599
1600
1601
<tr class="uncovered">
1602
<td><pre><a name="line258">258</a> n = 0</pre></td>
1603
</tr>
1604
1605
1606
1607
<tr class="uncovered">
1608
<td><pre><a name="line259">259</a> mean = 0.0</pre></td>
1609
</tr>
1610
1611
1612
1613
<tr class="uncovered">
1614
<td><pre><a name="line260">260</a> </pre></td>
1615
</tr>
1616
1617
1618
1619
<tr class="uncovered">
1620
<td><pre><a name="line261">261</a> sum = population.reduce(0.0) do |sum, x|</pre></td>
1621
</tr>
1622
1623
1624
1625
<tr class="uncovered">
1626
<td><pre><a name="line262">262</a> n += 1</pre></td>
1627
</tr>
1628
1629
1630
1631
<tr class="uncovered">
1632
<td><pre><a name="line263">263</a> delta = x - mean</pre></td>
1633
</tr>
1634
1635
1636
1637
<tr class="uncovered">
1638
<td><pre><a name="line264">264</a> mean += delta / n</pre></td>
1639
</tr>
1640
1641
1642
1643
<tr class="uncovered">
1644
<td><pre><a name="line265">265</a> </pre></td>
1645
</tr>
1646
1647
1648
1649
<tr class="uncovered">
1650
<td><pre><a name="line266">266</a> sum + delta * (x - mean)</pre></td>
1651
</tr>
1652
1653
1654
1655
<tr class="uncovered">
1656
<td><pre><a name="line267">267</a> end</pre></td>
1644
<td><pre><a name="line265">265</a> def variance(population)</pre></td>
1645
</tr>
1646
1647
1648
1649
<tr class="uncovered">
1650
<td><pre><a name="line266">266</a> n = 0</pre></td>
1651
</tr>
1652
1653
1654
1655
<tr class="uncovered">
1656
<td><pre><a name="line267">267</a> mean = 0.0</pre></td>
1657
1657
</tr>
1658
1658
1659
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<tr class="uncovered">
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<td><pre><a name="line269">269</a> sum / n</pre></td>
1669
</tr>
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<tr class="uncovered">
1674
<td><pre><a name="line270">270</a> end</pre></td>
1668
<td><pre><a name="line269">269</a> sum = population.reduce(0.0) do |sum, x|</pre></td>
1669
</tr>
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<tr class="uncovered">
1674
<td><pre><a name="line270">270</a> n += 1</pre></td>
1675
</tr>
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1678
1679
<tr class="uncovered">
1680
<td><pre><a name="line271">271</a> delta = x - mean</pre></td>
1681
</tr>
1682
1683
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1685
<tr class="uncovered">
1686
<td><pre><a name="line272">272</a> mean += delta / n</pre></td>
1687
</tr>
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<tr class="uncovered">
1692
<td><pre><a name="line273">273</a> </pre></td>
1693
</tr>
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<tr class="uncovered">
1698
<td><pre><a name="line274">274</a> sum + delta * (x - mean)</pre></td>
1699
</tr>
1700
1701
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1703
<tr class="uncovered">
1704
<td><pre><a name="line275">275</a> end</pre></td>
1705
</tr>
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1707
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1709
<tr class="uncovered">
1710
<td><pre><a name="line276">276</a> </pre></td>
1711
</tr>
1712
1713
1714
1715
<tr class="uncovered">
1716
<td><pre><a name="line277">277</a> sum / n</pre></td>
1717
</tr>
1718
1719
1720
1721
<tr class="uncovered">
1722
<td><pre><a name="line278">278</a> end</pre></td>
1675
1723
</tr>
1676
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1725
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1726
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1727
<tr class="inferred">
1680
<td><pre><a name="line271">271</a> </pre></td>
1728
<td><pre><a name="line279">279</a> </pre></td>
1681
1729
</tr>
1682
1730
1683
1731
1684
1732
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1733
<tr class="marked">
1686
<td><pre><a name="line272">272</a> def standard_deviation(population)</pre></td>
1687
</tr>
1688
1689
1690
1691
<tr class="uncovered">
1692
<td><pre><a name="line273">273</a> Math.sqrt(variance(population))</pre></td>
1693
</tr>
1694
1695
1696
1697
<tr class="uncovered">
1698
<td><pre><a name="line274">274</a> end</pre></td>
1734
<td><pre><a name="line280">280</a> def standard_deviation(population)</pre></td>
1735
</tr>
1736
1737
1738
1739
<tr class="uncovered">
1740
<td><pre><a name="line281">281</a> Math.sqrt(variance(population))</pre></td>
1741
</tr>
1742
1743
1744
1745
<tr class="uncovered">
1746
<td><pre><a name="line282">282</a> end</pre></td>
1699
1747
</tr>
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1749
</tbody>
1702
1750
</table>
1703
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1704
<p>Generated on Mon Feb 20 14:30:58 -0800 2012 with <a href="http://github.com/relevance/rcov">rcov 0.9.8</a></p>
1752
<p>Generated on Sat Feb 25 19:19:09 -0800 2012 with <a href="http://github.com/relevance/rcov">rcov 0.9.8</a></p>
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</body>
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</html>
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