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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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PBS Error allocating memory for add_verify_resources #229

Closed phil622 closed 3 years ago

phil622 commented 3 years ago

After i submit my scrips on the PBS, it tips that Error allocating memory for add_verify_resources. what can i do for that?

nchernia commented 3 years ago

I don't know what this function is so it's probably unique to the PBS system. You can change memory requirements within the script or talk to your cluster IT person.

On Fri, Jul 9, 2021 at 3:58 AM phil622 @.***> wrote:

After i submit my scrips on the PBS, it tips that Error allocating memory for add_verify_resources. what can i do for that?

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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

phil622 commented 3 years ago

I just use the 'juicer.sh' script and add some necessary parameters on PBS, but it till tip the same error.Do you mean that i have to change some things in the 'juicer.sh' script?

nchernia commented 3 years ago

Yes, you might have to change the memory requirements depending on your cluster set up. We set the parameters based on our (SLURM) system. You might have to use less memory, which will take more time. It's impossible for us to say without knowing your system, and moreover, the PBS branch is not tested by us since we do not have access to a PBS system.

On Fri, Jul 9, 2021 at 7:58 AM phil622 @.***> wrote:

I just use the 'juicer.sh' script and add some necessary parameters on PBS, but it till tip the same error.Do you mean that i have to change some things in the 'juicer.sh' script?

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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

phil622 commented 3 years ago

But i see the PBS version in the latest juicer package, and i think if it is specialized for the PBS system. Do you mean the PBS version in the juicer package is just a test version which is no be tested, so i have to change some things in this version depending on my cluster?

phil622 commented 3 years ago

well, now i just use the 'juicer.sh' script of the CPU version and put it in my own script about the PBS system.My script can be run now , but i am not sure if it can get a right result.

nchernia commented 3 years ago

We don’t have a PBS system. Someone else created the PBS script and we pulled it in but we have no way to debug or test.

CPU is fine.

On Sat, Jul 10, 2021 at 2:07 AM phil622 @.***> wrote:

well, now i just use the 'juicer.sh' script of the CPU version and put it in my own script about the PBS system.My script can be run now , but i am not sure if it can get a right result.

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/issues/229#issuecomment-877576163, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EW5YUF62QJG72MA37SDTW7PRJANCNFSM5ACICOAA .

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

phil622 commented 3 years ago

thank you