[23.2] Use python-isal for fast zip deflate compression in rocrate export #17342
Conversation
mvdbeek
force-pushed
the
isal_celery_export
branch
from
5c08f00
to
7e9c02b
Compare
mvdbeek
force-pushed
the
isal_celery_export
branch
from
8ee3b56
to
a4b14be
Compare
| @@ -2753,7 +2753,7 @@ def _finalize(self) -> None: | |||
| out_file = out_file_name[: -len(".zip")] | |||
| else: | |||
| out_file = out_file_name | |||
| rval = shutil.make_archive(out_file, "zip", self.export_directory) | |||
| rval = shutil.make_archive(out_file, "fastzip", self.export_directory) | |||
There was a problem hiding this comment.
I think this works only because this files also imports from galaxy.util.compression_utils import CompressedFile. Should we re-export shutil (maybe as gx_shutil) in lib/galaxy/util/compression_utils.py and import it in this file from there?
There was a problem hiding this comment.
I think this works only because this files also imports
from galaxy.util.compression_utils import CompressedFile
yes
Should we re-export
shutil(maybe asgx_shutil) inlib/galaxy/util/compression_utils.pyand import it in this file from there?
makes sense, sure
| @@ -34,6 +34,7 @@ include_package_data = True | |||
| install_requires = | |||
| galaxy-util | |||
| fs | |||
| isal | |||
There was a problem hiding this comment.
@mvdbeek Do you remember why you added the isal dependency here as well?
I don't think it's currently used?
There was a problem hiding this comment.
It's used in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/compression_utils.py#L361-L372 or am I missing something ?
There was a problem hiding this comment.
Ah, why it's used in the files package ? I don't know, it should be enough to just have it be a dependency of data I thuok ?
There was a problem hiding this comment.
Yep, exactly. I'll drop it in #18449 .
We're currently archiving a lot of old and unused histories to tape by exporting histories to RO-crates, and CPU utilization appears to be the bottleneck.
I've switched out the default zlib DEFLATE compression with the more efficient DEFLATE implementation provided by https://github.com/intel/isa-l via https://pypi.org/project/isal/. I've also tried zlib-ng (https://github.com/zlib-ng/zlib-ng) but that was only marginally faster.
This is about 3 times faster on 8GB sampled from /dev/urandom (~160 MB/s vs ~56 MB/s), both locally and on galaxy07 under heavy load.
How to test the changes?
(Select all options that apply)
License