# Using --fork on VEP?

**URL:** <https://discuss.hail.is/t/using-fork-on-vep/1283>\
**Category:** Hail Query & hailctl\
**Created:** [February 11, 2020, 1:48am UTC](https://discuss.hail.is/t/using-fork-on-vep/1283 "2020-02-11T01:48:55Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![nicklecompteBCH](https://avatars.discourse-cdn.com/v4/letter/n/e47c2d/32.png) [@nicklecompteBCH](https://discuss.hail.is/u/nicklecompteBCH)\
**Post date:** [February 11, 2020, 1:48am UTC](https://discuss.hail.is/t/using-fork-on-vep/1283/1 "2020-02-11T01:48:55Z")

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Hello,

I am using Hail 0.2 to run VEP, and have added `"--fork", "6",` to my vep config .json. I have not done a lot of testing with VEP by itself but my understanding is that the fork option is generally recommended on modern processors. I could not even tell you if running VEP through Hail is actually faster with --fork - it seems like it is? It doesn’t crash too often, at least 🙂 But I have not had a lot of time/resources for performance tuning.

I am wondering if anyone here has experience doing this. It does not seem to be used very widely in the Hail community (based on the other VEP configs I’ve seen) but I haven’t checked extensively. Unfortunately I am not being very careful about executor CPU count vs. VEP CPU count - is this something I should be more concerned about?

It is also a bit opaque to me how this affects memory considerations. I am using yarn, and have had to twiddle quite a few settings to get --fork 6 to reliably work on larger datasets (oddly --fork 6 works reliably out-of-the-box on a single-sample VCF with a small cluster). Specifically I had to manually override the `spark.executor.memoryOverhead` default of 10% of executor memory so that yarn doesn’t shut down the container during VEP execution. I **think** VEP (considered by the JVM to be native) runs exclusively in that memoryOverhead, so if VEP is being multithreaded within a container then increasing the limit makes sense. 25% seems to work but maybe that’s too much.

Anyway, is there any general guidance about this?

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [February 11, 2020, 1:41pm UTC](https://discuss.hail.is/t/using-fork-on-vep/1283/2 "2020-02-11T13:41:19Z")

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I would expect this to slightly degrade performance, actually – Hail runs VEP in parallel already, launching VEP processes on each worker CPU. Since it’s already parallelized (and all CPUs are already busy), there’s little benefit to using additional threads.

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [February 11, 2020, 1:42pm UTC](https://discuss.hail.is/t/using-fork-on-vep/1283/3 "2020-02-11T13:42:06Z")

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Also, I hear you about the memory management pain. It’s not easy to configure this stuff.

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<div class="post-metadata">

**Author:** ![nicklecompteBCH](https://avatars.discourse-cdn.com/v4/letter/n/e47c2d/32.png) [@nicklecompteBCH](https://discuss.hail.is/u/nicklecompteBCH)\
**Post date:** [February 11, 2020, 2:18pm UTC](https://discuss.hail.is/t/using-fork-on-vep/1283/4 "2020-02-11T14:18:06Z")

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Thanks! That makes sense - I thought maybe Hail was running one VEP process per executor but good to know that’s not the case. I will leave the option off by default.