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JinmiaoChenLab / Batch-effect-removal-benchmarking

A benchmark of batch-effect correction methods for single-cell RNA sequencing data
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How to record memory usage #11

Closed sldyns closed 3 years ago

sldyns commented 3 years ago

Hello,

I was hoping to evaluate the performance of my algorithm, but confused on how to record memory usage. I didn't find a description of the tool for recording memory usage in your article. Could you please tell me what tools are?

Thanks!

jinmiaochen commented 3 years ago

Hi Kun,

Thanks for your question. Here I forward your question to xiaomeng who did memory assessment for our paper.

Thanks xiaomeng!

Best, Jinmiao

From: Kun Qian @.> Sent: Monday, August 30, 2021 8:05 PM To: JinmiaoChenLab/Batch-effect-removal-benchmarking @.> Cc: Subscribed @.***> Subject: [JinmiaoChenLab/Batch-effect-removal-benchmarking] How to record memory usage (#11)

Hello,

I was hoping to evaluate the performance of my algorithm, but confused on how to record memory usage. I didn't find a description of the tool for recording memory usage in your article. Could you please tell me what tools are?

Thanks!

- You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/JinmiaoChenLab/Batch-effect-removal-benchmarking/issues/11, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACD33WQBSFZP6ET74DLXMZ3T7NXX7ANCNFSM5DBXFP4A. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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sldyns commented 3 years ago

Hello Prof. Jinmiao,

Sorry to bother you again. I'm really in a bit of a hurry lately and need to know how to log runtime memory. Could you please advise on this as soon as possible. Your help is greatly appreciated!

Thanks!

jinmiaochen commented 3 years ago

Hi Mengwei,

Could we help Kun Qian on how to log runtime and memory in R? Many thanks.

Best, Jinmiao

From: Kun Qian @.> Sent: Saturday, September 4, 2021 12:27 AM To: JinmiaoChenLab/Batch-effect-removal-benchmarking @.> Cc: Chen Jinmiao @.>; Comment @.> Subject: Re: [JinmiaoChenLab/Batch-effect-removal-benchmarking] How to record memory usage (#11)

Hello Prof. Jinmiao,

Sorry to bother you again. I'm really in a bit of a hurry lately and need to know how to log runtime memory. Could you please advise on this as soon as possible. Your help is greatly appreciated!

Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/JinmiaoChenLab/Batch-effect-removal-benchmarking/issues/11#issuecomment-912662014, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACD33WTSUUGMPYQVWFMRWCDUADZLVANCNFSM5DBXFP4A. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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jinmiaochen commented 3 years ago

Hi, Kun Qian,

You can use rbenchmark (https://www.rdocumentation.org/packages/rbenchmark/versions/1.0.0) package in R script or use sysbench (https://linuxconfig.org/how-to-benchmark-your-linux-system) in shell script.

Hope it can help you. Thanks!

Best regards, Mengwei Li

Mengwei Li Research Fellow (postdoctoral)

Single-cell & AI for precision immunology Singapore Immunology Network (SIgN) Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove IMMUNOS bldg, Level 3, SINGAPORE 138648

From: Chen Jinmiao @.> Sent: Saturday, September 4, 2021 11:33 To: JinmiaoChenLab/Batch-effect-removal-benchmarking @.>; JinmiaoChenLab/Batch-effect-removal-benchmarking @.> Cc: Comment @.>; Li Mengwei @.***> Subject: RE: [JinmiaoChenLab/Batch-effect-removal-benchmarking] How to record memory usage (#11)

Hi Mengwei,

Could we help Kun Qian on how to log runtime and memory in R? Many thanks.

Best,

Jinmiao

From: Kun Qian @.> Sent: Saturday, September 4, 2021 12:27 AM To: JinmiaoChenLab/Batch-effect-removal-benchmarking @.> Cc: Chen Jinmiao @.>; Comment @.> Subject: Re: [JinmiaoChenLab/Batch-effect-removal-benchmarking] How to record memory usage (#11)

Hello Prof. Jinmiao,

Sorry to bother you again. I'm really in a bit of a hurry lately and need to know how to log runtime memory. Could you please advise on this as soon as possible. Your help is greatly appreciated!

Thanks!

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/JinmiaoChenLab/Batch-effect-removal-benchmarking/issues/11#issuecomment-912662014, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACD33WTSUUGMPYQVWFMRWCDUADZLVANCNFSM5DBXFP4A. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person. This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person.

sldyns commented 3 years ago

Hello Prof. Jinmiao and Mengwei,

Your suggestions have been very helpful in my research, thank you very much!

Best, Kun