GenePattern Team Blog

Change in GenePattern Data Storage Policy

Posted on Monday, September 22, 2014 at 03:26PM by Barbara Hill Meyers

On October 6, 2014, we will be making some changes to the way that data is stored for your account on genepattern.broadinstitute.org:

  • Your account will have a storage quota of 30GB. To accommodate the increased use of the Broad's GenePattern server, each user account will have 30GB to store files in the Files tab.
  • Data in inactive accounts will be removed. If you haven't logged into your GenePattern account in the past 6 months, we will clear the data that is associated with your account.
We will send you messages in advance of the dates if you will be affected by either of these policies. Please feel free to contact us at gp-help@broadinstitute.org if you have any extenuating circumstances, questions, or concerns.
 
Additional information
 
What data is subject to the quota? Quotas apply only to files stored in the Files Tab and do not apply to job results, which remain on the server for 7 days.

How can I tell how...

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Changes to Startup Env Impact R Modules on Broad Hosted Servers

Posted on Thursday, September 18, 2014 at 04:52PM by Peter Carr

As a result of the software update on August 14, we modified the startup environment for the server. This was necessary because the server now requires Java 7. It was previously using Java 6. Surprisingly, this necessitated a change to the R configuration. You may notice slight changes to the behavior of your R modules. For example, the ATLANTISInputs module failed with this error message:

/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_3.0.2/lib64/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

The workaround is to change the command line for your R modules to use the preferred command line substitution parameter. For example, for an R 3.0 module use <R3.0_Rscript>. For an R 2.15 module use <R2.15_Rscript>.

Please contact us for further assistance. Thanks! Originally posted on gpbroad at 4pm on Monday Aug 25

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Upcoming GenePattern Downtime

Posted on Wednesday, July 23, 2014 at 12:56PM by GenePattern Team

GenePattern downtime 7/25 - 7/28: Because of systems maintenance at the Broad, the following job queue interruptions will take place between 5 PM on Friday, July 25 and 10 AM Monday, July 28.

Timeline:

  • 5 PM Friday, July 25 - The job queue will be suspended. All new job submissions will remain PENDING until after the system maintenance period. This should allow most running jobs to complete before the system shutdown on Monday
  • 8 AM Monday, July 28 - All running jobs will be terminated, unceremoniously.
  • 8 AM Monday, July 28 - The GenePattern server will be shut down for system maintenance.
  • approximately 10 AM Monday, July 28 - The GenePattern server will resume normal operations.

Please feel free to contact us if you have any questions or concerns

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