# LD pruning error

**URL:** <https://discuss.hail.is/t/ld-pruning-error/2577>\
**Category:** Hail Query & hailctl\
**Created:** [April 4, 2022, 10:38am UTC](https://discuss.hail.is/t/ld-pruning-error/2577 "2022-04-04T10:38:57Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![sk4919](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/sk4919/32/1244_2.png) [@sk4919](https://discuss.hail.is/u/sk4919)\
**Post date:** [April 4, 2022, 10:38am UTC](https://discuss.hail.is/t/ld-pruning-error/2577/1 "2022-04-04T10:38:57Z")

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Hello

I’m running LD-prune step on a (344031, 37702) matrix, on a cluster with 10 n1-highmem-8 worker nodes. I get an error: _Executor heartbeat timed out after 137902 ms._  
The following parameters are set in my spark-defaults conf file:  
spark.executor.memory=10117m  
spark.executor.memoryOverhead=15175m

I was able to run a smaller dataset (~90k, 20k) individuals, which took about an hour to run. Although the command succeeded in the spark UI I could see jobs failing with the same error message

What would I need to do here?

Thank you very much

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**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\
**Post date:** [April 4, 2022, 1:19pm UTC](https://discuss.hail.is/t/ld-pruning-error/2577/2 "2022-04-04T13:19:13Z")

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Hey @sk4919 !

Can you try adding `block_size=2048` to your call to `ld_prune`?

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<div class="post-metadata">

**Author:** ![sk4919](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/sk4919/32/1244_2.png) [@sk4919](https://discuss.hail.is/u/sk4919)\
**Post date:** [April 4, 2022, 3:51pm UTC](https://discuss.hail.is/t/ld-pruning-error/2577/3 "2022-04-04T15:51:12Z")

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Thank you, it’s working now.

What does block size do exactly, and which functions is it relevant to?

Thanks