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broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
BSD 3-Clause "New" or "Revised" License
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Use Nd4j workspaces for better memory management #1059

Closed mbabadi closed 7 years ago

mbabadi commented 7 years ago

We have to learn the upcoming Nd4j workspaces and use it to reduce the memory footprint of gCNV. It is already merged but the latest Nd4j release (0.8.0) doesn't have it yet.

API: https://github.com/deeplearning4j/nd4j/blob/master/nd4j-buffer/src/main/java/org/nd4j/linalg/api/memory/conf/WorkspaceConfiguration.java https://github.com/deeplearning4j/nd4j/blob/master/nd4j-buffer/src/main/java/org/nd4j/linalg/api/memory/MemoryWorkspaceManager.java https://github.com/deeplearning4j/nd4j/blob/master/nd4j-backends/nd4j-api-parent/nd4j-api/src/main/java/org/nd4j/linalg/memory/abstracts/Nd4jWorkspace.java https://github.com/deeplearning4j/nd4j/blob/master/nd4j-buffer/src/main/java/org/nd4j/linalg/api/memory/MemoryWorkspace.java

Tests: https://github.com/deeplearning4j/nd4j/blob/master/nd4j-backends/nd4j-tests/src/test/java/org/nd4j/linalg/workspace/BasicWorkspaceTests.java https://github.com/deeplearning4j/nd4j/blob/master/nd4j-backends/nd4j-tests/src/test/java/org/nd4j/linalg/workspace/EndlessWorkspaceTests.java https://github.com/deeplearning4j/nd4j/blob/master/nd4j-backends/nd4j-tests/src/test/java/org/nd4j/linalg/workspace/SpecialWorkspaceTests.java

droazen commented 7 years ago

Issue moved to broadinstitute/gatk #2996 via ZenHub