The feature to address this issue has been merged into the master branch (https://github.com/Alluxio/alluxio/pull/3089). It introduces a configuration parameter 'alluxio.user.file.cache.partially.read.block' that you can set to true for your applications. Then, it will cache partially read blocks into Alluxio. You can try out the feature in the master branch, and see if that can resolve your issues.
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