clutring stuck for long time

Dear FastPG team,

Thanks for this great tool. It is very fast and perform very well. However, I found the program sometime stuck for a long time. It happens randomly, and I have tested it on several servers. Could you help me check with this issue?

Thanks in advance!

Best, Mengwei

Thanks for your comment! Let's see if we can figure out what's going on. Can you give us a little info about the data set you are trying to cluster? How many features and how many samples? Have you watched your system monitor when it got stuck? @jefferys any thoughts on this?

Thanks for your prompt reply! I have run FastPG in tens of datasets (http://www.immunesinglecell.org/, all of data in this database are clustering by FastPG) and each dataset contains 0.5 million to 4 million cells. I used first 50 PCs as input. Normally, it works well and return the results in several minutes (100 threads). But the program occasionally gets stuck for a long time (several hours) without any error info and can be solved by just re-run it. So I can hardly find the debug information. This time, I run FastPG for 4.6M cells (50 PCs), it didn't return the result after 12 hours. And I try it several times in three servers. Does it normal for such big data? Our servers are equipped with two AMD EPYC 7552 cpu (196 threads and 2T memory). By the way, when I monitor the status of process, it still runs and take a lot of CPU.

Looking forward to your reply. Thank you for your help!

Best, Mengwei

I haven't seen it hang like that before. Stuart or Mahantesh, do you have any idea what's happening?

On Sat, Aug 28, 2021 at 8:36 PM Mengwei Lee @.***> wrote:

Thanks for your comment! Let's see if we can figure out what's going on. Can you give us a little info about the data set you are trying to cluster? How many features and how many samples? Have you watched your system monitor when it got stuck? @jefferys https://github.com/jefferys any thoughts on this?

Thanks for your prompt reply! I have run FastPG in tens of datasets ( http://www.immunesinglecell.org/, all of data in this database are clustering by FastPG) and each dataset contains 0.5 million to 4 million cells. I used first 50 PCs as input. Normally, it works well and return the results in several minutes (100 threads). But the program occasionally gets stuck for a long time (several hours) without any error info and can be solved by just re-run it. So I can hardly find the debug information. This time, I run FastPG for 4.6M cells (50 PCs), it didn't return the result after 12 hours. And I try it several times in three servers. Does it normal for such big data? Our servers are equipped with two AMD EPYC 7552 cpu (196 threads and 2T memory). By the way, when I monitor the status of process, it still runs and take a lot of CPU.

Looking forward to your reply. Thank you for your help!

Best, Mengwei

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sararselitsky/FastPG/issues/13#issuecomment-907708784, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQD6T5ZKYI7GK3S3HEIUYTT7F6ILANCNFSM5C6UWVAQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Sorry, I've never had it hang like that. Are you using your own install of FastPG or the Docker? Is this a live run or a submitted job? Are other people using the same machine at the same time?

Hi Sara,

One place Grappolo can hang is if the input is not correct. It usually prints something if that can be tracked. It might help to add some printouts after each step (if not already added).

If Mengwei can consistently make it hang with an input, we can try to replicate it. If not, I don’t know how to help. Stuart might be a better person to answer this one.

Regards, Mahantesh (he/him)

From: Sara Selitsky @.> Date: Sunday, August 29, 2021 at 9:37 AM To: sararselitsky/FastPG @.> Cc: sararselitsky/FastPG @.>, Subscribed @.>, "Jefferys, Stuart R" @.>, "Halappanavar, Mahantesh M" @.> Subject: Re: [sararselitsky/FastPG] clutring stuck for long time (#13)

Check twice before you click! This email originated from outside PNNL.

I haven't seen it hang like that before. Stuart or Mahantesh, do you have any idea what's happening?

On Sat, Aug 28, 2021 at 8:36 PM Mengwei Lee @.**@.>> wrote:

Thanks for your comment! Let's see if we can figure out what's going on. Can you give us a little info about the data set you are trying to cluster? How many features and how many samples? Have you watched your system monitor when it got stuck? @jefferyshttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjefferys&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752480071%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=nfKjQXdqaqFvQnvbxLw4xF6ztEKwI1nCAQmr%2B4v5FKY%3D&reserved=0 any thoughts on this?

Thanks for your prompt reply! I have run FastPG in tens of datasets (http://www.immunesinglecell.org/https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.immunesinglecell.org%2F&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752480071%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=98ZsAYFu8oSApOesRhJ1plS9thxSkQZSt68hoUtcE6E%3D&reserved=0, all of data in this database are clustering by FastPG) and each dataset contains 0.5 million to 4 million cells. I used first 50 PCs as input. Normally, it works well and return the results in several minutes (100 threads). But the program occasionally gets stuck for a long time (several hours) without any error info and can be solved by just re-run it. So I can hardly find the debug information. This time, I run FastPG for 4.6M cells (50 PCs), it didn't return the result after 12 hours. And I try it several times in three servers. Does it normal for such big data? Our servers are equipped with two AMD EPYC 7552 cpu (196 threads and 2T memory). By the way, when I monitor the status of process, it still runs and take a lot of CPU.

Looking forward to your reply. Thank you for your help!

Best, Mengwei

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsararselitsky%2FFastPG%2Fissues%2F13%23issuecomment-907708784&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752490016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eRwScoGOqMZtLXB8DKxjNEDxXdTZxXTrZ2cfXOMYHrE%3D&reserved=0, or unsubscribehttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACQD6T5ZKYI7GK3S3HEIUYTT7F6ILANCNFSM5C6UWVAQ&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752490016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2DpTmhIowdXPCpbR5LdwRB7PzKxlly57rjKpV3vmigM%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752490016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=NntCaJOBOhob3nbTALom9dJJPH6xbrFlXfbovGM0QPw%3D&reserved=0 or Androidhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752499979%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3A%2FoqGGyK%2Bn7CFGA9B3IIhU6bagbKo9EKZOAMK8fT0Q%3D&reserved=0.

Hi Sara, One place Grappolo can hang is if the input is not correct. It usually prints something if that can be tracked. It might help to add some printouts after each step (if not already added). If Mengwei can consistently make it hang with an input, we can try to replicate it. If not, I don’t know how to help. Stuart might be a better person to answer this one. Regards, Mahantesh (he/him) From: Sara Selitsky @.> Date: Sunday, August 29, 2021 at 9:37 AM To: sararselitsky/FastPG @.> Cc: sararselitsky/FastPG @.>, Subscribed @.>, "Jefferys, Stuart R" @.>, "Halappanavar, Mahantesh M" @.> Subject: Re: [sararselitsky/FastPG] clutring stuck for long time (#13) Check twice before you click! This email originated from outside PNNL. I haven't seen it hang like that before. Stuart or Mahantesh, do you have any idea what's happening? On Sat, Aug 28, 2021 at 8:36 PM Mengwei Lee @.**@.>> wrote: Thanks for your comment! Let's see if we can figure out what's going on. Can you give us a little info about the data set you are trying to cluster? How many features and how many samples? Have you watched your system monitor when it got stuck? @jefferyshttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjefferys&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752480071%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=nfKjQXdqaqFvQnvbxLw4xF6ztEKwI1nCAQmr%2B4v5FKY%3D&reserved=0 any thoughts on this? Thanks for your prompt reply! I have run FastPG in tens of datasets (http://www.immunesinglecell.org/https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.immunesinglecell.org%2F&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752480071%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=98ZsAYFu8oSApOesRhJ1plS9thxSkQZSt68hoUtcE6E%3D&reserved=0, all of data in this database are clustering by FastPG) and each dataset contains 0.5 million to 4 million cells. I used first 50 PCs as input. Normally, it works well and return the results in several minutes (100 threads). But the program occasionally gets stuck for a long time (several hours) without any error info and can be solved by just re-run it. So I can hardly find the debug information. This time, I run FastPG for 4.6M cells (50 PCs), it didn't return the result after 12 hours. And I try it several times in three servers. Does it normal for such big data? Our servers are equipped with two AMD EPYC 7552 cpu (196 threads and 2T memory). By the way, when I monitor the status of process, it still runs and take a lot of CPU. Looking forward to your reply. Thank you for your help! Best, Mengwei — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsararselitsky%2FFastPG%2Fissues%2F13%23issuecomment-907708784&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752490016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eRwScoGOqMZtLXB8DKxjNEDxXdTZxXTrZ2cfXOMYHrE%3D&reserved=0, or unsubscribehttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACQD6T5ZKYI7GK3S3HEIUYTT7F6ILANCNFSM5C6UWVAQ&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752490016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2DpTmhIowdXPCpbR5LdwRB7PzKxlly57rjKpV3vmigM%3D&reserved=0. 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Dear all,

Thanks for reply. Here is my input file (https://drive.google.com/file/d/1coKZrI636Usdp_9d9sUT0GYeGV0fDiIz/view?usp=sharing when use this as input, it always hangs). Could you help me to test on it? Thanks!

Best regards, Mengwei

Thanks for sending this! Stuart, do you have time to test this input? Thanks!

On Tue, Aug 31, 2021 at 8:37 AM Mengwei Lee @.***> wrote:

Hi Sara, One place Grappolo can hang is if the input is not correct. It usually prints something if that can be tracked. It might help to add some printouts after each step (if not already added). If Mengwei can consistently make it hang with an input, we can try to replicate it. If not, I don’t know how to help. Stuart might be a better person to answer this one. Regards, Mahantesh (he/him) From: Sara Selitsky @.> Date: Sunday, August 29, 2021 at 9:37 AM To: sararselitsky/FastPG @.> Cc: sararselitsky/FastPG @.>, Subscribed @.>, "Jefferys, Stuart R" @.>, "Halappanavar, Mahantesh M" @.> Subject: Re: [sararselitsky/FastPG] clutring stuck for long time (#13 https://github.com/sararselitsky/FastPG/issues/13) Check twice before you click! This email originated from outside PNNL. I haven't seen it hang like that before. Stuart or Mahantesh, do you have any idea what's happening? On Sat, Aug 28, 2021 at 8:36 PM Mengwei Lee *@@.****>> wrote: Thanks for your comment! Let's see if we can figure out what's going on. Can you give us a little info about the data set you are trying to cluster? How many features and how many samples? Have you watched your system monitor when it got stuck? @jefferys https://github.com/jefferys https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjefferys&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752480071%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=nfKjQXdqaqFvQnvbxLw4xF6ztEKwI1nCAQmr%2B4v5FKY%3D&reserved=0 any thoughts on this? Thanks for your prompt reply! I have run FastPG in tens of datasets (http://www.immunesinglecell.org/ https://gcc02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.immunesinglecell.org%2F&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752480071%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=98ZsAYFu8oSApOesRhJ1plS9thxSkQZSt68hoUtcE6E%3D&reserved=0, all of data in this database are clustering by FastPG) and each dataset contains 0.5 million to 4 million cells. I used first 50 PCs as input. Normally, it works well and return the results in several minutes (100 threads). But the program occasionally gets stuck for a long time (several hours) without any error info and can be solved by just re-run it. So I can hardly find the debug information. This time, I run FastPG for 4.6M cells (50 PCs), it didn't return the result after 12 hours. And I try it several times in three servers. Does it normal for such big data? Our servers are equipped with two AMD EPYC 7552 cpu (196 threads and 2T memory). By the way, when I monitor the status of process, it still runs and take a lot of CPU. Looking forward to your reply. Thank you for your help! Best, Mengwei — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsararselitsky%2FFastPG%2Fissues%2F13%23issuecomment-907708784&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752490016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eRwScoGOqMZtLXB8DKxjNEDxXdTZxXTrZ2cfXOMYHrE%3D&reserved=0, or unsubscribe https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACQD6T5ZKYI7GK3S3HEIUYTT7F6ILANCNFSM5C6UWVAQ&data=04%7C01%7CMahantesh.Halappanavar%40pnnl.gov%7Cca0b450479744b129a4208d96b0b571a%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C637658518752490016%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2DpTmhIowdXPCpbR5LdwRB7PzKxlly57rjKpV3vmigM%3D&reserved=0. 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Dear all,

Thanks for reply. Here is my input file ( https://drive.google.com/file/d/1coKZrI636Usdp_9d9sUT0GYeGV0fDiIz/view?usp=sharing when use this as input, it always hangs). Could you help me to test on it? Thanks!

Best regards, Mengwei

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/sararselitsky/FastPG/issues/13#issuecomment-909197540, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACQD6T5A5E6QO3UO5PPA6HDT7TEI3ANCNFSM5C6UWVAQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Checking. Its 4,615,568 observations with 50 features, as numeric values. No missing values. All values are close to 0. Is that expected? Min = -0.01083803; Max = 0.004925892.

The kNN and link generation steps appear to work (the separate steps of the analysis in the later part of the readme) and don't take all that long to run, although might hit a memory limit on an 8G machine. There were no errors. However, it does appear to be hanging in the louvain/grappolo portion. Sorry, but I don't have time to wait very long or to look into it in detail right now (e.g. to verify the output of the prior steps are reasonable). I'm on vacation this week.

The kNN and link generation steps appear to work (the separate steps of the analysis in the later part of the readme) and don't take all that long to run, although might hit a memory limit on an 8G machine. There were no errors. However, it does appear to be hanging in the louvain/grappolo portion. Sorry, but I don't have time to wait very long or to look into it in detail right now (e.g. to verify the output of the prior steps are reasonable). I'm on vacation this week.

Dear Stuart,

Thanks for your time! I'm not in a hurry. Stay safe and healthy!

Best regards, Mengwei

sararselitsky / FastPG

clutring stuck for long time #13