Slow and unstable downloads from EBI upstreams increasing pipeline failures

[kltm]

Many downloads are slow to the point of a few megabytes taking hours. Figure out the source/reason and fix. More details to come.

• [x] reinstate go-ontology-dev
• [x] Get EBI downloads near their original speed

[kltm]

Going through the logs, we seem to have the following slow downloads:

• http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl => 13h, 6h
• https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz => 10hr

Trying locally, chebi.owl seems to be fine. goa_uniprot_all.gaf.gz is very very slow locally. Interestingly, for goa_uniprot_all.gaf.gz, switching to FTP gives me very fast (normal) speeds.

Looking through the logs, goa_uniprot_all.gaf.gz seems to have been getting worse since around the 14th; chebi.owl since the 25th.

[kltm]

Testing again, I can get good times for goa_uniprot_all.gaf.gz by switching to http or ftp, just not https. That would explain why we took a dive since https://github.com/geneontology/go-site/pull/1914/files .

@cmungall @balhoff Putting chebi being slow to the side for a moment, this seems to be a fundamental issue with EBI's https service (as opposed to http or ftp). If you're getting similar results (I've tried "locally" and at LBL), rather than waiting for an upstream resolution, I'd just as soon switch

https://github.com/geneontology/go-ontology/pull/24202/files https://github.com/geneontology/go-site/pull/1914/files etc.

over to http so we can get things ticking over again and revisit later.

[kltm]

Basically, for the same file, we'll get different download speeds depending on the schema. For example

https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl ~ 4.5KB/s http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl ~ 15.0MB/s ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl ~ 20.0MB/s

The difference between FTP and HTTP is not a lot and could probably be accounted for in a few different ways, the HTTPS download is remarkably slower.

[kltm]

@alexsign opened a ticket on our behalf and soon after the speed issue seems to have resolved for all the previously slow URLs that I've tested. Thank you!

[kltm]

@alexsign Unfortunately, after a short break, the very slow download speeds have started again.

[kltm]

@alexsign Doing some quick testing from a single site: https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl ~ 424KB/s (~26m) http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl ~ 422B/s (~27m) ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl ~ 9.0MB/s (~70s) It currently appears that http and https now have the same (slow) download speeds, while ftp is at least an order of magnitude faster.

[alexsign]

@kltm sorry for delay on this. The HTTPS download speed should improve now. Can you please test it and let me know.

[kltm]

@alexsign Cheers! It looks like we just missed the window with out current build; our next full build cycle will start tomorrow at midnight, so we'll get the results over the weekend. I've made a note to check in on them. Thank you for all of your help on this.

[kltm]

@alexsign Doing some testing locally and seeing the current load status, the numbers are completely consistent with https://github.com/geneontology/pipeline/issues/305#issuecomment-1303903774 ; basically, http and https still seem to be extremely slow and ftp is still relatively very very very fast.

[alexsign]

@kltm I sent your feedback to the EBI infrastructure team. Hopefully, they'll figure it out eventually.

[alexsign]

@kltm EBI infrastructure team made changes again. Please test when convenient.

[kltm]

@alexsign Previous runtime for downloads: 10h 33min; current runtime: 22min 59s. A huge improvement! Thank you for running this back and forth for us.

[kltm]

@alexsign I hate to do this; maybe there is a person I should be contacting directly? Since about the 25th or 26th of November, downloads are slow again.

[kltm]

Looks like things are "fast" again.

[kltm]

@alexsign Whoops--my bad. Checking in on this, it is still an ongoing issue, with downloads for our main pipeline runs taking more than ten (10) hours.

[kltm]

All EBI download resources

grep -r "ftp.ebi.ac.uk" ~/local/src/git/go-site/metadata/datasets/ | grep -oh "https:.*"

[kltm]

Getting all non-ontology EBI resources: grep -r "ftp.ebi.ac.uk" ~/local/src/git/go-site/metadata/datasets/ | grep -oh "https:.*" > /tmp/files.txt && sed -e 's/https/ftp/g' /tmp/files.txt > /tmp/files.txt.changed && wget -i /tmp/files.txt.changed

[pgaudet]

From @alexsign A proposal would be to download CHEBI only when there is a release (~ monthly)

[pgaudet]

Also, can you download the compressed file?

[alexsign]

@kltm I can suggest two things:

1. http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl.gz downloaded when needed it's ~ 46MB right now
2. For the next GOA release (in about 1 week time) I'll create MD5 file for https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz which is currently 16GB and updated every 2 month or so. The MD5 file should be downloaded first and used in check if new download needed or not.

[kltm]

Just some current stats:

file	thru	eta
http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl.gz	420KB/s	~100s
http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl	428KB/s	~1600s
ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl.gz	9.0MB/s	~6s
ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl	7.17MB/s	~90s
https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl.gz	432KB/s	~100s
https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl	432KB/s	~1600s

Noting current stats from local machine. I'm not sure about switching over generally to compressed ontology files--that might end up being a bit fiddly or take us to retool with catalogs (i.e. https://github.com/geneontology/pipeline/issues/27#issuecomment-499615634), but it's worth keeping in mind.

[alexsign]

@kltm I opened another ticket with EBI infrastructure team. Hopefully, it will be more successful than one before.

[kltm]

@alexsign No worries here--thank you for that :) The table above was just to be a note recent on the current state of play from here (not a poke in any way). We appreciate all of your help in mediating this!

[kltm]

@pgaudet We've had the second case in a week where either the EBI server or connection is unstable and we lose a run; like:

00:03:19  Download of https://ftp.ebi.ac.uk/pub/databases/GO/goa/CHICKEN/goa_chicken_isoform.gaf.gz failed: Unable to establish SSL connection.

I think I'm ready to implement a local cache/mirror to support our runs so that we can at least deal with late-stage errors. @cmungall Do you see any problems with this? For the moment it would be a GO-only resource.

[kltm]

Noting that grabbing all EBI files, using FTP, takes: mkdir -p /tmp/foo && cd /tmp/foo && grep -r "ftp.ebi.ac.uk" ~/local/src/git/go-site/metadata/datasets/ | grep -oh "https:.*" > /tmp/files.txt && sed -e 's/https/ftp/g' /tmp/files.txt > /tmp/files.txt.changed && time wget -i /tmp/files.txt.changed

Total wall clock time: 39m 53s
Downloaded: 83 files, 38G in 37m 32s (17.2 MB/s)

Which is a win over the 12+ hours we're currently at.

The upload from local was real 50m26.029s.

time s3cmd -c ~/SECRET_CRED --mime-type=text/plain put /tmp/foo/* s3://go-mirror

So let's say one and a half hours per mirror attempt. Pulling from our self-made mirror, we have:

Total wall clock time: 13m 29s
Downloaded: 83 files, 38G in 13m 12s (48.8 MB/s)

This means that we're doing 3x speed over the old EBI FTP and likely have better stability. I'd propose that we either 1) switch back to the old EBI FTP or 2) start the process of running off our own mirror. Tagging @cmungall @pgaudet .

[kltm]

I'd also note that we could front this with LBL Cloudflare for free, which might be a fun experiment :)

[kltm]

Currently looking at using pipeline branch goa-copy-to-mirror to interact with mirror.geneontology.io.

[kltm]

Currently running a full mirror build test.

[kltm]

@dustine32 I'm considering a non-breakign schema change for datasets.schema.yaml in the GO metadata, adding mirror_of. Essentially, I'd like to be able to refer to where we are directly getting the data for the pipeline (source) and how we are mirroring mirror_of in the same location. Any thoughts?

[dustine32]

@kltm Yeah, I think I'm a fan of mirror_of. Is this just an extra field initially for information only or does other code need to be changed to use it?

[kltm]

This would be an additional field. Only new code--namely my mirroring code--would need to "see" it, and even then only if they cared about mirrors. Everything else could safely ignore it.

[dustine32]

Ah, yeah, that sounds good to me!

[kltm]

Testing at https://build.geneontology.org/job/geneontology/job/pipeline/job/master/

[kltm]

Now testing on main pipeline branches.

[kltm]

Moving to clearing for testing.

[kltm]

Our download phase has gone from 11+h to 15+m. No oddities yet.