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run_test.sh
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run_test.sh
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#SPARK_DRIVER_MEMORY=60g /cluster/spark/spark-1.5.1-bin-hadoop2.4/bin/spark-submit --executor-memory 48g --class cs.ucla.edu.bwaspark.BWAMEMSpark --total-executor-cores 150 --master spark://10.0.1.2:7077 --driver-java-options "-XX:+PrintFlagsFinal" --conf spark.driver.host=10.0.1.2 --conf spark.driver.cores=20 --conf spark.driver.maxResultSize=40g --conf spark.storage.memoryFraction=0.7 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir="hdfs://cdsc0:9000/user/ytchen/eventLogs" --conf spark.akka.threads=20 --conf spark.akka.frameSize=1024 /home/ytchen/cs-bwamem/master/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.2-assembly.jar cs-bwamem -bfn 4 -bPSW 1 -sbatch 10 -bPSWJNI 1 -jniPath /curr/ytchen0323/shared_lib/jniNative.so -oChoice 2 -oPath hdfs://cdsc0:9000/user/ytchen0323/data/SC_data/HCC1954_100Mreads_tinyPart.adam -localRef 1 -R "@RG ID:HCC1954 LB:HCC1954 SM:HCC1954" -isSWExtBatched 1 -bSWExtSize 32768 -FPGAAccSWExt 0 -FPGASWExtThreshold 64 -jniSWExtendLibPath "/curr/genomics_spark/shared_lib/jniSWExtend.so" 1 /space/scratch/ReferenceMetadata/human_g1k_v37.fasta hdfs://cdsc0:9000/user/ytchen0323/data/SC_data/HCC1954_100Mreads_tinyPart.fq
#SPARK_DRIVER_MEMORY=60g /cluster/spark/spark-1.5.1-bin-hadoop2.4/bin/spark-submit --executor-memory 48g --class cs.ucla.edu.bwaspark.BWAMEMSpark --total-executor-cores 48 --master spark://10.0.1.2:7077 --driver-java-options "-XX:+PrintFlagsFinal" --conf spark.driver.host=10.0.1.2 --conf spark.driver.cores=20 --conf spark.driver.maxResultSize=40g --conf spark.storage.memoryFraction=0.7 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir="hdfs://cdsc0:9000/user/ytchen/eventLogs" --conf spark.akka.threads=20 --conf spark.akka.frameSize=1024 /home/ytchen/cs-bwamem/master/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.2-assembly.jar cs-bwamem -bfn 1 -bPSW 1 -sbatch 10 -bPSWJNI 1 -jniPath /curr/ytchen0323/shared_lib/jniNative.so -oChoice 2 -oPath hdfs://cdsc0:9000/user/ytchen0323/data/SC_data/HCC1954_100Mreads_tinyPart_1folder.adam -localRef 1 -R "@RG ID:HCC1954 LB:HCC1954 SM:HCC1954" -isSWExtBatched 1 -bSWExtSize 32768 -FPGAAccSWExt 1 -FPGASWExtThreshold 64 -jniSWExtendLibPath "/curr/genomics_spark/shared_lib/jniSWExtend.so" 1 /space/scratch/ReferenceMetadata/human_g1k_v37.fasta hdfs://cdsc0:9000/user/ytchen0323/data/SC_data/HCC1954_100Mreads_tinyPart_1folder.fq
#SPARK_DRIVER_MEMORY=60g /cluster/spark/spark-1.5.1-bin-hadoop2.4/bin/spark-submit --executor-memory 48g --class cs.ucla.edu.bwaspark.BWAMEMSpark --total-executor-cores 48 --master spark://10.0.1.2:7077 --driver-java-options "-XX:+PrintFlagsFinal" --conf spark.driver.host=10.0.1.2 --conf spark.driver.cores=20 --conf spark.driver.maxResultSize=40g --conf spark.storage.memoryFraction=0.7 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir="hdfs://cdsc0:9000/user/ytchen/eventLogs" --conf spark.akka.threads=20 --conf spark.akka.frameSize=1024 /home/ytchen/cs-bwamem/master/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.2-assembly.jar cs-bwamem -bfn 1 -bPSW 1 -sbatch 10 -bPSWJNI 1 -jniPath /curr/ytchen0323/shared_lib/jniNative.so -oChoice 2 -oPath hdfs://cdsc0:9000/user/ytchen0323/data/SC_data/HCC1954_100Mreads_tinyPart_1folder.adam -localRef 1 -R "@RG ID:HCC1954 LB:HCC1954 SM:HCC1954" -isSWExtBatched 1 -bSWExtSize 32768 -FPGAAccSWExt 0 -FPGASWExtThreshold 64 -jniSWExtendLibPath "/curr/genomics_spark/shared_lib/jniSWExtend.so" 1 /space/scratch/ReferenceMetadata/human_g1k_v37.fasta hdfs://cdsc0:9000/user/ytchen0323/data/SC_data/HCC1954_100Mreads_tinyPart_1folder.fq
SPARK_DRIVER_MEMORY=60g /cluster/spark/spark-1.5.1-bin-hadoop2.4/bin/spark-submit --executor-memory 48g --class cs.ucla.edu.bwaspark.BWAMEMSpark --total-executor-cores 20 --master local[20] --driver-java-options "-XX:+PrintFlagsFinal" --conf spark.driver.host=10.0.1.2 --conf spark.driver.cores=20 --conf spark.driver.maxResultSize=40g --conf spark.storage.memoryFraction=0.7 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir="hdfs://cdsc0:9000/user/ytchen/eventLogs" --conf spark.akka.threads=20 --conf spark.akka.frameSize=1024 /home/ytchen/cs-bwamem/master/cloud-scale-bwamem/target/cloud-scale-bwamem-0.2.2-assembly.jar cs-bwamem -bfn 1 -bPSW 1 -sbatch 10 -bPSWJNI 1 -jniPath /curr/ytchen0323/shared_lib/jniNative.so -oChoice 2 -oPath hdfs://cdsc0:9000/user/ytchen0323/data/SC_data/HCC1954_100Mreads_tinyPart_1folder.adam -localRef 1 -R "@RG ID:HCC1954 LB:HCC1954 SM:HCC1954" -isSWExtBatched 1 -bSWExtSize 32768 -FPGAAccSWExt 0 -FPGASWExtThreshold 64 -jniSWExtendLibPath "/curr/genomics_spark/shared_lib/jniSWExtend.so" 1 /space/scratch/ReferenceMetadata/human_g1k_v37.fasta hdfs://cdsc0:9000/user/ytchen0323/data/SC_data/HCC1954_100Mreads_tinyPart_1folder.fq