Hello, My pca test failed with the following error. The job is running on a Cloudera cluster using hail devel-7beaca7. I had to use the dev version as our VCF doesn’t have the PL field which was required for v.0.1 to load GT properly. What would you suggest I do? Where do I “boosting spark.yarn.exe…

Hi Jerry, The YARN defaults aren’t super great for a lot of the memory-intensive linear algebra routines we use. One way to make things a bit better is to increase the number of cores per executor from 1 to 4, so that all the overhead per JVM drops by a factor of 4. You can do this by setting spark…

@tpoterba I am having the same error as OP and I would like to increase the # of executor cores but I am using Hail in Terra. I know there is some collaboration between Hail and Terra with regards to a Terra Base Image (which I am currently using). Do you know if there is a custom image I can use …

You should be able to pass this parameter in hail initialization: import hail as hl hl.init(spark_conf={'spark.executor.cores': '4'})

Thanks @tpoterba . I later figured that out and was able to increase the # of executor cores but unfortunately I am still getting SparkExceptions on this PCA run. I have created a new line of inquiry at PCA job aborted from SparkException so as not to sidetrack this older thread. Do you think the i…

@tpoterba any updates about this?

Gosh! My apologies for not reading this thread as well as I should have! Thanks, Tim! :slight_smile:

Pca failed due to not enough executor memory

Help [0.1]

tpoterba July 16, 2020, 10:34am 7

we’re actively discussing here: PCA job aborted from SparkException

Topic		Replies	Views
Getting java heap error tried a bunch of things with the executor and memory settings Hail Batch & General Cloud	2	3570	October 5, 2022
Java Heap Space out of memory Hail Query & hailctl	5	3805	August 10, 2020
PCA job aborted from SparkException Hail Query & hailctl	46	3050	July 28, 2020
Ld_prune OutOfMemoryError: Java heap space Hail Query & hailctl	5	749	January 21, 2020
Error summary: OutOfMemoryError: Java heap space Hail Query & hailctl	15	2740	August 18, 2022

Pca failed due to not enough executor memory

Related topics