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MSKCC cBio cluster documentation
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R failed to start on some Hal nodes #420

Closed jiayuwen closed 8 years ago

jiayuwen commented 8 years ago

Hello,

I am running Rscript on Hal. Some jobs worked, but for many of my failed jobs, I got the below error:

-bash: /var/spool/torque/mom_priv/jobs/7292190-146.hal-sched1.local.SC: /usr/bin/Rscript: bad interpreter: No such file or directory

Could you please help to check. Thanks.

Also, the current R version on Hal is R version 3.0.1 (2013-05-16) -- "Good Sport". Some commonly used R packages such as dplyr and tidyr requires a later R version. I am wondering whether you will be able to install it centrally.

Thanks.

juanperin commented 8 years ago

Jiayuwen

Please forward this email to hpc-support@cbio.mskcc.org

We’ll have more sys-admins available to help you through that email. R is available in many versions on Hal. I’m not sure what’s causing your error, but we will take a look.

Juan

On May 26, 2016, at 6:09 PM, jiayuwen notifications@github.com wrote:

Hello,

I am running Rscript on Hal. Some jobs worked, but for many of my failed jobs, I got the below error:

-bash: /var/spool/torque/mom_priv/jobs/7292190-146.hal-sched1.local.SC: /usr/bin/Rscript: bad interpreter: No such file or directory

Could you please help to check. Thanks.

Also, the current R version on Hal is R version 3.0.1 (2013-05-16) -- "Good Sport". Some commonly used R packages such as dplyr and tidyr requires a later R version. I am wondering whether you will be able to install it centrally.

Thanks.

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/cBio/cbio-cluster/issues/420

jiayuwen commented 8 years ago

Thank you for your quick reply. I forwarded it to hpc-support@cbio.mskcc.org. Looking forward to your reply.

tatarsky commented 8 years ago

This was resolved via that method. module system contains newer R versions.