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GeneMANIA data processing pipeline
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Precomputing weights hangs at memory cache miss #30

Open jlaw9 opened 6 years ago

jlaw9 commented 6 years ago

I'm trying to import my own data to weight a couple networks I have. The pipeline runs until Job 2: NetworkPrecombiner. It spits out a bunch of "memory cache miss" warnings, and then just sits and does nothing.

java -cp lib/genemania.jar -Xmx4G org.genemania.engine.apps.NetworkPrecombiner         -indexDir "result/lucene_index" -cachedir "result/network_cache"         -log "workogs/NetworkPrecombiner.log"
Jan31@11:17:27 DEBUG MemObjectCache:87->memory cache miss for /CORE/19/KtK_BASIC.KtK
Jan31@11:17:27 DEBUG MemObjectCache:87->memory cache miss for /CORE/19/BP.KtT
Jan31@11:17:27 DEBUG MemObjectCache:87->memory cache miss for /CORE/19/KtK_Features
Jan31@11:17:27 DEBUG MemObjectCache:87->memory cache miss for /CORE/19/DatasetInfo
Jan31@11:17:27 DEBUG Solver:76->applying regularization with constant 1.0
Jan31@11:17:27 DEBUG Solver:92->solving for weights
Jan31@11:17:27 DEBUG Solver:164->normalizing network weights to add to 1
Jan31@11:17:27  INFO Solver:168->number of weights : 2
Jan31@11:17:27 DEBUG MemObjectCache:87->memory cache miss for /CORE/19/nodeIds
Jan31@11:17:27 DEBUG MemObjectCache:87->memory cache miss for /CORE/19/2
Jan31@11:17:27 DEBUG MemObjectCache:87->memory cache miss for /CORE/19/1

Do you have an idea of how I can fix this and get my networks weighted?

I'm running the pipeline on Ubuntu 16 with java 1.8. Thanks!