GenePattern Team Blog

Final Update to CentOS 5 Compute Node Availability for Broad-hosted Servers

Posted on Wednesday, July 18, 2018 at 03:01PM by Barbara Hill

On June 22, 2018, there was a fire at the main data center for the Broad Institute, resulting in an end of service for the last remaining CentOS 5 node, which enabled the running of the following legacy modules on our Broad-hosted servers:

  • ApplyGatingML
  • CopyNumberInferencePipeline (SNPFileCreator_SNP6, Birdseed, CopyNumberInference, CopyNumberNoise, RemoveCopyNumberOutliers, TangentNormalization, ParallelCBS, SegmentationCount)
  • ESPPredictor
  • FCMSinglePanelQC
  • FLAMEChooseOptimalClusterNumber
  • FLAMEMetacluster
  • FLAMEMixtureModel
  • FlowMeansCluster
  • FlowMergeCluster
  • GLAD
  • IlluminaDASLPipeline (IlluminaScanExtractor, IlluminaNormalizer, IlluminaConcatenate)
  • IlluminaNormalizer
  • ImmPortFCSConvLogicleTrans
  • ImmPort_FLOCK_CrossSample (ImmPortFCSConvLogicleTrans, ImmPortColSelection, ImmPortFLOCK, ImmPortCrossSample)
  • ImmPort_FLOCK_Individual_FCS (ImmPortFCSConvLogicleTrans, ImmPortColSelection, ImmPortFLOCK)
  • MultiplotPreprocess (and thus Multiplot)
  • RemoveCopyNumberOutliers
  • REVEALER
  • ...

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Updates to Job Runtime Settings for Public GenePattern server hosted at the Broad Institute

Posted on Tuesday, May 08, 2018 at 02:23PM by GenePattern Team

To help alleviate some of the heavy traffic we have seen in recent months on the public GenePattern server hosted at the Broad Institute, we have implemented a job.walltime limit of 36 hours

  • This means that, by default, jobs will be limited to running for 36 hours. After that, jobs will be terminated by the server. 

Feel free to contact us if you have any questions or comments about any of these updates.

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Updates to Compute Node Availability for Broad-hosted Public Server

Posted on Monday, May 07, 2018 at 12:57PM by GenePattern Team

 

Due to an end of service, we have just one CentOS 5 node for the running of legacy modules on the GenePattern server hosted at the Broad Institute:

  • This means that some of our legacy modules which depend on CentOS 5 may spend longer in the pending state.
    • This includes the following modules:
      • MultiplotPreprocess
        REVEALER
        ESPPredictor
        IlluminaNormalizer
        FLAMEMixtureModel
        FlowMeansCluster
        TangentNormalization
        RemoveCopyNumberOutliers
        FLAMEMetacluster
        FLAMEChooseOptimalClusterNumber
        ImmPortFCSConvLogicleTrans
        FCMSinglePanelQC
        SuggestNumberOfPopulationsFCS
        GLAD
        SamSPECTRALClusterFCS
        ApplyGatingML
        FlowMergeCluster

Feel free to contact us if you have any questions or comments about any of these updates.

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