From 8422fc059fc72a1f6842b0d8f97b2d27b8e456d9 Mon Sep 17 00:00:00 2001 From: Greg Caporaso Date: Thu, 22 Aug 2024 17:21:23 -0700 Subject: [PATCH] squash --- book/_config.yml | 6 +++--- book/plugins/tutorials/add-parallel-pipeline.md | 8 +++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/book/_config.yml b/book/_config.yml index 3d4fb31d..eacb423c 100644 --- a/book/_config.yml +++ b/book/_config.yml @@ -92,9 +92,9 @@ parse: dwq2_add_2nd_transformer_commit_url: "{{dwq2_gh_commit_url.format(dwq2_add_2nd_transformer_commit)}}" dwq2_add_pipeline_commit: "1e601c41b86d98b22f4e16685e868f1c5710f3bf" dwq2_add_pipeline_commit_url: "{{dwq2_gh_commit_url.format(dwq2_add_pipeline_commit)}}" - dwq2_add_parallel_pipeline_commit_1: "a45f6fb85315843078c0777326031dbce9564802" + dwq2_add_parallel_pipeline_commit_1: "d0d5f38ca6d2e8cdc647660db8d1923b048f8e1e" dwq2_add_parallel_pipeline_commit_1_url: "{{dwq2_gh_commit_url.format(dwq2_add_parallel_pipeline_commit_1)}}" - dwq2_add_parallel_pipeline_commit_2: "fd36ec2ec8cf463ee568074a2ba25823e4f02352" + dwq2_add_parallel_pipeline_commit_2: "4ed7e01a6da9a10e7ddf1956877cf494740e35cd" dwq2_add_parallel_pipeline_commit_2_url: "{{dwq2_gh_commit_url.format(dwq2_add_parallel_pipeline_commit_2)}}" - dwq2_add_parallel_pipeline_commit_3: "f978c064a7e941081c7b2e697087be32a7db0e97" + dwq2_add_parallel_pipeline_commit_3: "590263ee9bb8c48df09fe62c0e966acfa99f9aff" dwq2_add_parallel_pipeline_commit_3_url: "{{dwq2_gh_commit_url.format(dwq2_add_parallel_pipeline_commit_3)}}" diff --git a/book/plugins/tutorials/add-parallel-pipeline.md b/book/plugins/tutorials/add-parallel-pipeline.md index 20013cf6..55fe9297 100644 --- a/book/plugins/tutorials/add-parallel-pipeline.md +++ b/book/plugins/tutorials/add-parallel-pipeline.md @@ -7,9 +7,10 @@ This will enable your users to utilize multi-processor computers or multi-node h ```{admonition} tl;dr :class: tip -The complete code that I wrote to add the second `Pipeline` to my plugin can be found here: {{ dwq2_add_parallel_pipeline_commit_1_url }}. The code that I developed to add parallel computing support to the new `Pipeline` can be found here: {{ dwq2_add_parallel_pipeline_commit_2_url }}. -I also included a usage example at the end which you can use to compare the performance of serial and parallel runs of the new Pipeline here: {{ dwq2_add_parallel_pipeline_commit_3_url }}. -That third commit does increase the runtime of the unit tests considerably (from about 30 seconds to about 6 minutes, on the computer that I'm developing on). +1. The complete code that I wrote to add the second `Pipeline` to my plugin can be found here: {{ dwq2_add_parallel_pipeline_commit_1_url }}. +2. The code that I developed to add parallel computing support to the new `Pipeline` can be found here: {{ dwq2_add_parallel_pipeline_commit_2_url }}. +3. Finally, I added a usage example that can be used to compare the performance of serial and parallel runs of the new Pipeline here: {{ dwq2_add_parallel_pipeline_commit_3_url }}. +Because the third commit includes (a small amount) of real data, as opposed to the toy-sized data we've been using in unit tests, it increases the runtime of the test suite considerably (from about 30 seconds to about 6 minutes, on the M3 MacBook Pro that that I'm developing on). ``` ## Add a local alignment search `Pipeline` @@ -396,6 +397,7 @@ After making all of the changes described here to your `_pipelines.py` and `test If all tests pass, you should be good to go. If not, compare your code to mine ({{ dwq2_add_parallel_pipeline_commit_2_url }}) to see what's different. +(serial-parallel-runtime)= ## Compare the serial versus parallel run times of the `search-and-summarize` Now that we've added parallel computing support to our `search-and-summarize` Pipeline, we can try it out to see how it impacts run time.