Difficulty getting started

[arnavm]

Hi,

I'm having some trouble getting RS-FISH-Spark working locally. One issue I've been able to troubleshoot, the other one is a little bit harder to debug:

1. Installation (on MacOS 12.7)

> mvn clean package
[INFO] Scanning for projects...
[INFO]
[INFO] --------------------< net.preibisch:RS-FISH-Spark >---------------------
[INFO] Building RS-FISH Spark 0.0.1-SNAPSHOT
[INFO]   from pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- clean:3.1.0:clean (default-clean) @ RS-FISH-Spark ---
[INFO]
[INFO] --- enforcer:3.0.0-M3:enforce (enforce-rules) @ RS-FISH-Spark ---
[INFO] Adding ignore: module-info
[INFO] Adding ignore: META-INF/versions/*/module-info
[INFO] Adding ignore: com.esotericsoftware.kryo.*
[INFO] Adding ignore: com.esotericsoftware.minlog.*
[INFO] Adding ignore: com.esotericsoftware.reflectasm.*
[INFO] Adding ignore: com.google.inject.*
[INFO] Adding ignore: jnr.ffi.*
[INFO] Adding ignore: org.apache.hadoop.yarn.*.package-info
[INFO] Adding ignore: org.apache.spark.unused.UnusedStubClass
[INFO] Adding ignore: org.hibernate.stat.ConcurrentStatisticsImpl
[INFO] Adding ignore: org.jetbrains.kotlin.daemon.common.*
[INFO] Adding ignore: org.junit.runner.Runner
[INFO] Adding ignore: module-info
[INFO] Adding ignore: module-info
[INFO]
[INFO] --- build-helper:3.0.0:regex-property (sanitize-version) @ RS-FISH-Spark ---
[INFO]
[INFO] --- build-helper:3.0.0:regex-property (guess-package) @ RS-FISH-Spark ---
[INFO]
[INFO] --- buildnumber:1.4:create (default) @ RS-FISH-Spark ---
[INFO] Executing: /bin/sh -c cd '/Users/arnav/Downloads/RS-FISH-Spark-main' && 'git' 'rev-parse' '--verify' 'HEAD'
[INFO] Working directory: /Users/arnav/Downloads/RS-FISH-Spark-main
[INFO] Storing buildNumber: UNKNOWN at timestamp: 1696003952159
[WARNING] Cannot get the branch information from the git repository:
Detecting the current branch failed: fatal: not a git repository (or any of the parent directories): .git

[INFO] Executing: /bin/sh -c cd '/Users/arnav/Downloads/RS-FISH-Spark-main' && 'git' 'rev-parse' '--verify' 'HEAD'
[INFO] Working directory: /Users/arnav/Downloads/RS-FISH-Spark-main
[INFO] Storing buildScmBranch: UNKNOWN_BRANCH
[INFO]
[INFO] --- scijava:2.0.0:set-rootdir (set-rootdir) @ RS-FISH-Spark ---
[INFO] Setting rootdir: /Users/arnav/Downloads/RS-FISH-Spark-main
[INFO]
[INFO] --- jacoco:0.8.6:prepare-agent (jacoco-initialize) @ RS-FISH-Spark ---
[INFO] argLine set to -javaagent:/Users/arnav/.m2/repository/org/jacoco/org.jacoco.agent/0.8.6/org.jacoco.agent-0.8.6-runtime.jar=destfile=/Users/arnav/Downloads/RS-FISH-Spark-main/target/jacoco.exec
[INFO]
[INFO] --- resources:3.1.0:resources (default-resources) @ RS-FISH-Spark ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 98 resources
[INFO]
[INFO] --- compiler:3.8.1:compile (default-compile) @ RS-FISH-Spark ---
[INFO] Compiling 20 source files to /Users/arnav/Downloads/RS-FISH-Spark-main/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  13.339 s
[INFO] Finished at: 2023-09-29T09:12:33-07:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.1:compile (default-compile) on project RS-FISH-Spark: Fatal error compiling: error: release version 1.8 not supported -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

This I was able to fix by un-commenting line 91 in pom.xml. The package builds successfully.

2. Execution (using the supplied test.n5 image)

> java -cp target/RS-Fish-jar-with-dependencies.jar -Xmx12G "-Dspark.master=local[4]" net.preibisch.rsfish.spark.SparkRSFISH --image=src/main/resources/test.n5 --dataset=/N2-702-ch0/c0/s0 --minIntensity=0 --maxIntensity=4096 --anisotropy=0.7 --output=points.csv
--image=src/main/resources/test.n5 --dataset=/N2-702-ch0/c0/s0 --minIntensity=0 --maxIntensity=4096 --anisotropy=0.7 --output=points.csv
N5/HDF5/ZARR dataset dimensionality: 3
N5/HDF5/ZARR dataset size: (334, 454, 81)
Processing interval: [0, 0, 0] -> [333, 453, 80], dimensions (334, 454, 81)
Processing blocksize: (128, 128, 64)
09:18:24.887 [main] INFO org.apache.spark.SparkContext - Running Spark version 2.4.7
log4j:WARN No appenders could be found for logger (org.apache.hadoop.metrics2.lib.MutableMetricsFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
09:18:25.087 [main] DEBUG org.apache.hadoop.security.authentication.util.KerberosName - Kerberos krb5 configuration not found, setting default realm to empty
09:18:25.097 [main] DEBUG org.apache.hadoop.util.PerformanceAdvisory - Falling back to shell based
Exception in thread "main" java.lang.ExceptionInInitializerError
	at org.apache.hadoop.util.StringUtils.<clinit>(StringUtils.java:79)
	at org.apache.hadoop.security.Groups.parseStaticMapping(Groups.java:116)
	at org.apache.hadoop.security.Groups.<init>(Groups.java:93)
	at org.apache.hadoop.security.Groups.<init>(Groups.java:73)
	at org.apache.hadoop.security.Groups.getUserToGroupsMappingService(Groups.java:293)
	at org.apache.hadoop.security.UserGroupInformation.initialize(UserGroupInformation.java:283)
	at org.apache.hadoop.security.UserGroupInformation.ensureInitialized(UserGroupInformation.java:260)
	at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:789)
	at org.apache.hadoop.security.UserGroupInformation.getLoginUser(UserGroupInformation.java:774)
	at org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:647)
	at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2422)
	at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2422)
	at scala.Option.getOrElse(Option.scala:121)
	at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2422)
	at org.apache.spark.SparkContext.<init>(SparkContext.scala:293)
	at org.apache.spark.api.java.JavaSparkContext.<init>(JavaSparkContext.scala:58)
	at net.preibisch.rsfish.spark.SparkRSFISH.call(SparkRSFISH.java:211)
	at net.preibisch.rsfish.spark.SparkRSFISH.call(SparkRSFISH.java:32)
	at picocli.CommandLine.executeUserObject(CommandLine.java:1853)
	at picocli.CommandLine.access$1100(CommandLine.java:145)
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2255)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2249)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2213)
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2080)
	at picocli.CommandLine.execute(CommandLine.java:1978)
	at net.preibisch.rsfish.spark.SparkRSFISH.main(SparkRSFISH.java:338)
Caused by: java.lang.StringIndexOutOfBoundsException: Range [0, 3) out of bounds for length 2
	at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:55)
	at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:52)
	at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:213)
	at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:210)
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:98)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckFromToIndex(Preconditions.java:112)
	at java.base/jdk.internal.util.Preconditions.checkFromToIndex(Preconditions.java:349)
	at java.base/java.lang.String.checkBoundsBeginEnd(String.java:4861)
	at java.base/java.lang.String.substring(String.java:2830)
	at org.apache.hadoop.util.Shell.<clinit>(Shell.java:50)
	... 26 more

I'm not sure where this out of bounds exception is coming from, nor how best to proceed. Any suggestions would helpful. Thanks!