[BUG] - tile of issue

[ghost]

Describe the bug PHOENIX is reporting a memory issue, but RAM was installed on computer to overcome this issue

Impact Unable to test local install of PHOENIX

To Reproduce Steps to reproduce the behavior:

• What environment you are running the pipeline in (i.e. HPC, local, cloud etc): Local
• What version of the pipeline you are using: v.2.0.0
• The command that was run to cause the error nextflow run cdcgov/phoenix -r v2.0.0 -profile docker,test -entry PHOENIX --kraken2db /mnt/p/Sequencing/k2_standard_08gb_20230605.tar.gz
• If you used a custom config file please provide it: None
• N/a
• The text of the error itself - screenshots are great for this!

Expected behavior PHOENIX test to run

Screenshots

[jvhagey]

@bdelavan I have removed screenshots as they contain your device information and file paths (I don't want the name of your computer showing). In the screenshot of the error block out your name in the Work Dir file path. Please block out this identifying information and reupload the screenshots.

Was there any other programs running while you were running PHX when you got this error? Its odd to see that you have the exact same amount of memory available as before you had more RAM installed. There must be some other memory restrain set other than what your computers RAM is since you theoretically have more than this. I might be how your docker is set-up/installed. I am not sure how you have docker installed so you might need to work with your system admin to figure out if docker has a memory limitation set on it. If you are using docker desktop then have a look at the memory configuration in the advanced settings so see if that has a lower limit set. This page has some screenshots.

In addition, to asking your system admin to have a look at docker try running phx with this additional parameter --max_memory 11.GB

[ghost]

Dr. Hagey.

Thank you for the advice...and removing screenshots. I forgot githib is open...appreciate that catch!

I'll work on my end to figure out what is going on...it will probably be later today or early next week.

If I don't hear from you before the end of the day, I hope you and yours have a great weekend

Brian

From: Jill V. Hagey, PhD @.> Sent: Friday, October 6, 2023 10:55 AM To: CDCgov/phoenix @.> Cc: Brian Delavan @.>; Mention @.> Subject: Re: [CDCgov/phoenix] [BUG] - tile of issue (Issue #124)

@bdelavanhttps://github.com/bdelavan I have removed screenshots as they contain your device information and file paths (I don't want the name of your computer showing). In the screenshot of the error block out your name in the Work Dir file path. Please block out this identifying information and reupload the screenshots.

Was there any other programs running while you were running PHX when you got this error? Its odd to see that you have the exact same amount of memory available as before you had more RAM installedhttps://github.com/CDCgov/phoenix/issues/121. There must be some other memory restrain set other than what your computers RAM is since you theoretically have more than this. I might be how your docker is set-up/installed. I am not sure how you have docker installed so you might need to work with your system admin to figure out if docker has a memory limitation set on it. If you are using docker desktop then have a look at the memory configuration in the advanced settings so see if that has a lower limit set. This pagehttps://forums.docker.com/t/how-to-increase-memory-size-that-is-available-for-a-docker-container/78483 has some screenshots.

In addition, to asking your system admin to have a look at docker try running phx with this additional parameter --max_memory 11.GB

- Reply to this email directly, view it on GitHubhttps://github.com/CDCgov/phoenix/issues/124#issuecomment-1750975483, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AV36PGULES5EK7XV7JOXRUTX6ASWXAVCNFSM6AAAAAA5V7EJG6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONJQHE3TKNBYGM. You are receiving this because you were mentioned.Message ID: @.**@.>>

[jvhagey]

Hi @bdelavan, just wanted to check in and see if this issue was resolved so I can close the issue?

[ghost]

Sorry...yes, you can close this

From: Jill V. Hagey, PhD @.> Sent: Tuesday, March 12, 2024 9:09 AM To: CDCgov/phoenix @.> Cc: Brian Delavan @.>; Mention @.> Subject: Re: [CDCgov/phoenix] [BUG] - tile of issue (Issue #124)

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Hi @bdelavanhttps://github.com/bdelavan, just wanted to check in and see if this issue was resolved so I can close the issue?

- Reply to this email directly, view it on GitHubhttps://github.com/CDCgov/phoenix/issues/124#issuecomment-1991738753, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AV36PGWRLSDKVP6MF5HBGBDYX4D6XAVCNFSM6AAAAAA5V7EJG6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJRG4ZTQNZVGM. You are receiving this because you were mentioned.Message ID: @.**@.>>