Added documentation on OMP_NUM_THREADS and MKL_NUM_THREADS to Germlin…

…eCNVCaller and DetermineGermlineContigPloidy. (#8223)
broadinstitute · Mar 16, 2023 · 2dbc025 · 2dbc025
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diff --git a/...in/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java b/...in/java/org/broadinstitute/hellbender/tools/copynumber/DetermineGermlineContigPloidy.java
@@ -64,6 +64,9 @@
  * the python environment is already set up. Otherwise, the environment must be created and activated as described in the
  * main GATK README.md file.</p>
  *
+ * <p>OpenMP and MKL parallelism can be controlled by setting the <code>OMP_NUM_THREADS</code> and <code>MKL_NUM_THREADS</code>
+ * environment variables, respectively.</p>
+ *
  * <p>Advanced users may wish to set the <code>THEANO_FLAGS</code> environment variable to override the GATK theano
  * configuration. For example, by running
  * <code>THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk DetermineGermlineContigPloidy ...</code>, users can specify

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java
@@ -89,6 +89,9 @@
  * the python environment is already set up. Otherwise, the environment must be created and activated as described in the
  * main GATK README.md file.</p>
  *
+ * <p>OpenMP and MKL parallelism can be controlled by setting the <code>OMP_NUM_THREADS</code> and <code>MKL_NUM_THREADS</code>
+ * environment variables, respectively.</p>
+ *
  * <p>Advanced users may wish to set the <code>THEANO_FLAGS</code> environment variable to override the GATK theano
  * configuration. For example, by running
  * <code>THEANO_FLAGS="base_compiledir=PATH/TO/BASE_COMPILEDIR" gatk GermlineCNVCaller ...</code>, users can specify