Giter VIP home page Giter VIP logo

Comments (6)

brianwalenz avatar brianwalenz commented on August 21, 2024

That should be the only change - just add the -R '...' to the end of the string. Or, pass this in through gridEngineMemoryOption="-M MEMORY -R '...'" on the canu command line (or specfile) and leave the code unmodified.

from canu.

aslett1 avatar aslett1 commented on August 21, 2024

Thanks! I'm giving the gridEngineMemoryOption a go. Got an error first
time up which may have been down to threaded jobs running on multiple
hosts (adding span [hosts=1] to the -R option).

As an aside, the link to the gzipped 25X subset FASTQ E. coli reads from
the readthedoces page throws a 404 error (using curl to get the unzipped
file works fine).

Best regards,

Martin

On Tue, 5 Jan 2016, brianwalenz wrote:

That should be the only change - just add the -R '...' to the end of the string. Or, pass this in through
gridEngineMemoryOption="-M MEMORY -R '...'" on the canu command line (or specfile) and leave the code unmodified.


Reply to this email directly or view it on GitHub.[AAwjN4XE4XmX0u6oaTSQe7MjDOXQQbn7ks5pW9aYgaJpZM4G-4xi.gif]

The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

from canu.

aslett1 avatar aslett1 commented on August 21, 2024

Hi again,

Setting gridEngineMemoryOption on the command line is working but my jobs are still failing. This time with a non-existent job array after the first job runs. It looks like the gridEngineHoldOption setting is causing problems. I've tried changing this on the command line but I'm not sure exactly what the format needs to be. I think the issue is that numended requires the job ID and the -w check is using job name?

I've attached the output file.

Thanks,

Martin

canu.01.out.txt

from canu.

skoren avatar skoren commented on August 21, 2024

Yep, now you're in the untested code based on LSF documentation since we don't have a system to test on. The LSF documentation claims that done, ended, etc take either job name or job id but it might be the case that numended doesn't follow this behavior. You can try modifying
src/pipelines/canu/Execution.pm, line 803 from:

        if (uc(getGlobal("gridEngine")) eq "PBS" || uc(getGlobal("gridEngine")) eq "SLURM"){

to

        if (uc(getGlobal("gridEngine")) eq "PBS" || uc(getGlobal("gridEngine")) eq "SLURM" || uc(getGlobal("gridEngine") eq "LSF"){

and see if that makes the holds valid. However, there would still be untested LSF code in terms of job restarts/resumes.

from canu.

txje avatar txje commented on August 21, 2024

This fix worked for me: #39

from canu.

brianwalenz avatar brianwalenz commented on August 21, 2024

And that was just merged in commit 7b16f2f. Thanks!

from canu.

Related Issues (20)

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.