Gradlew build fails for nativeLib


#1

Hi,

I’m trying to compile the latest version of Hail, but it fails. Any idea?

16:46:56.835 [DEBUG] [org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter] Executing actions for task ‘:nativeLib’.
16:46:56.835 [INFO] [org.gradle.process.internal.DefaultExecHandle] Starting process ‘command ‘make’’. Working directory: /home/ubuntu/hail/hail/src/main/c Command: make
16:46:56.835 [DEBUG] [org.gradle.process.internal.DefaultExecHandle] Environment for process ‘command ‘make’’: {PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games, LESSCLOSE=/usr/bin/lesspipe %s %s, LESSOPEN=| /usr/bin/lesspipe %s, SHELL=/bin/bash, OLDPWD=/home/ubuntu/hail/hail, TERM=xterm, USER=root, LANG=en_US.UTF-8, SUDO_COMMAND=/bin/su, SUDO_USER=ubuntu, SUDO_GID=1000, MAIL=/var/mail/root, LC_ALL=POSIX, USERNAME=root, LOGNAME=root, LC_CTYPE=POSIX, PWD=/home/ubuntu/hail/hail, SUDO_UID=1000, LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.jpg=01;35:.jpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36:, SHLVL=1, HOME=/root}
16:46:56.835 [DEBUG] [org.gradle.process.internal.DefaultExecHandle] Changing state to: STARTING
16:46:56.835 [DEBUG] [org.gradle.process.internal.DefaultExecHandle] Waiting until process started: command ‘make’.
16:46:56.837 [DEBUG] [org.gradle.process.internal.DefaultExecHandle] Changing state to: STARTED
16:46:56.837 [DEBUG] [org.gradle.process.internal.ExecHandleRunner] waiting until streams are handled…
16:46:56.837 [INFO] [org.gradle.process.internal.DefaultExecHandle] Successfully started process ‘command ‘make’’
16:46:56.938 [QUIET] [system.out] tar -xzf libsimdpp-2.1.tar.gz
16:46:57.002 [QUIET] [system.out] g++ -o build/Encoder.o -march=sandybridge -O3 -std=c++11 -Ilibsimdpp-2.1 -Wall -Werror -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux -c Encoder.cpp
16:46:57.009 [ERROR] [system.err] In file included from Encoder.cpp:1:0:
16:46:57.009 [ERROR] [system.err] …/resources/include/hail/Encoder.h:3:17: fatal error: lz4.h: No such file or directory
16:46:57.009 [ERROR] [system.err] compilation terminated.
16:46:57.014 [ERROR] [system.err] make: *** [build/Encoder.o] Error 1
16:46:57.014 [QUIET] [system.out] Makefile:42: recipe for target ‘build/Encoder.o’ failed
16:46:57.016 [DEBUG] [org.gradle.process.internal.DefaultExecHandle] Changing state to: FAILED
16:46:57.016 [DEBUG] [org.gradle.process.internal.DefaultExecHandle] Process ‘command ‘make’’ finished with exit value 2 (state: FAILED)
16:46:57.017 [DEBUG] [org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter] Finished executing task ‘:nativeLib’
16:46:57.017 [LIFECYCLE] [class org.gradle.TaskExecutionLogger] :nativeLib FAILED
16:46:57.018 [INFO] [org.gradle.execution.taskgraph.AbstractTaskPlanExecutor] :nativeLib (Thread[main,5,main]) completed. Took 0.184 secs.
16:46:57.018 [DEBUG] [org.gradle.execution.taskgraph.AbstractTaskPlanExecutor] Task worker [Thread[main,5,main]] finished, busy: 0.257 secs, idle: 0.0 secs
16:46:57.025 [ERROR] [org.gradle.BuildExceptionReporter]
16:46:57.025 [ERROR] [org.gradle.BuildExceptionReporter] FAILURE: Build failed with an exception.
16:46:57.025 [ERROR] [org.gradle.BuildExceptionReporter]
16:46:57.025 [ERROR] [org.gradle.BuildExceptionReporter] * What went wrong:
16:46:57.026 [ERROR] [org.gradle.BuildExceptionReporter] Execution failed for task ‘:nativeLib’.
16:46:57.026 [ERROR] [org.gradle.BuildExceptionReporter] > Process ‘command ‘make’’ finished with non-zero exit value 2
16:46:57.026 [ERROR] [org.gradle.BuildExceptionReporter]
16:46:57.026 [ERROR] [org.gradle.BuildExceptionReporter] * Try:
16:46:57.026 [ERROR] [org.gradle.BuildExceptionReporter] Run with --stacktrace option to get the stack trace.
16:46:57.026 [LIFECYCLE] [org.gradle.BuildResultLogger]
16:46:57.026 [LIFECYCLE] [org.gradle.BuildResultLogger] BUILD FAILED
16:46:57.026 [LIFECYCLE] [org.gradle.BuildResultLogger]
16:46:57.026 [LIFECYCLE] [org.gradle.BuildResultLogger] Total time: 6.844 secs
16:46:57.028 [DEBUG] [org.gradle.cache.internal.btree.BTreePersistentIndexedCache] Closing cache fileSnapshots.bin (/home/ubuntu/hail/hail/.gradle/2.14.1/taskArtifacts/fileSnapshots.bin)
16:46:57.028 [DEBUG] [org.gradle.cache.internal.btree.BTreePersistentIndexedCache] Closing cache taskArtifacts.bin (/home/ubuntu/hail/hail/.gradle/2.14.1/taskArtifacts/taskArtifacts.bin)
16:46:57.028 [DEBUG] [org.gradle.cache.internal.btree.BTreePersistentIndexedCache] Closing cache fileSnapshotsToTreeSnapshotsIndex.bin (/home/ubuntu/hail/hail/.gradle/2.14.1/taskArtifacts/fileSnapshotsToTreeSnapshotsIndex.bin)
16:46:57.028 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Releasing lock on task history cache (/home/ubuntu/hail/hail/.gradle/2.14.1/taskArtifacts).
16:46:57.030 [DEBUG] [org.gradle.api.internal.artifacts.ivyservice.resolveengine.store.CachedStoreFactory] Resolution result cache closed. Cache reads: 0, disk reads: 1 (avg: 0.027 secs, total: 0.027 secs)
16:46:57.102 [DEBUG] [org.gradle.api.internal.artifacts.ivyservice.resolveengine.store.CachedStoreFactory] Resolution result cache closed. Cache reads: 0, disk reads: 0 (avg: 0.0 secs, total: 0.0 secs)
16:46:57.102 [DEBUG] [org.gradle.api.internal.artifacts.ivyservice.resolveengine.store.ResolutionResultsStoreFactory] Deleted 2 resolution results binary files in 0.072 secs
16:46:57.102 [DEBUG] [org.gradle.cache.internal.DefaultCacheAccess] Cache Generated Gradle JARs cache (/root/.gradle/caches/2.14.1/generated-gradle-jars) was closed 0 times.
16:46:57.102 [DEBUG] [org.gradle.cache.internal.btree.BTreePersistentIndexedCache] Closing cache module-metadata.bin (/root/.gradle/caches/modules-2/metadata-2.16/module-metadata.bin)
16:46:57.102 [DEBUG] [org.gradle.cache.internal.btree.BTreePersistentIndexedCache] Closing cache artifact-at-repository.bin (/root/.gradle/caches/modules-2/metadata-2.16/artifact-at-repository.bin)
16:46:57.102 [DEBUG] [org.gradle.cache.internal.btree.BTreePersistentIndexedCache] Closing cache module-artifacts.bin (/root/.gradle/caches/modules-2/metadata-2.16/module-artifacts.bin)
16:46:57.102 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Releasing lock on artifact cache (/root/.gradle/caches/modules-2).
16:46:57.103 [DEBUG] [org.gradle.api.internal.artifacts.ivyservice.ivyresolve.memcache.InMemoryCachedRepositoryFactory] In-memory dependency metadata cache closed. Repos cached: 18, cache instances: 6, modules served from cache: 526, artifacts: 504
16:46:57.103 [DEBUG] [org.gradle.cache.internal.btree.BTreePersistentIndexedCache] Closing cache plugin-use-metadata.bin (/root/.gradle/caches/2.14.1/plugin-resolution/plugin-use-metadata.bin)
16:46:57.103 [DEBUG] [org.gradle.cache.internal.DefaultFileLockManager] Releasing lock on Plugin Resolution Cache (/root/.gradle/caches/2.14.1/plugin-resolution).
16:46:57.103 [DEBUG] [org.gradle.api.internal.tasks.compile.daemon.CompilerDaemonManager] Stopping 0 compiler daemon(s).
16:46:57.103 [INFO] [org.gradle.api.internal.tasks.compile.daemon.CompilerDaemonManager] Stopped 0 compiler daemon(s).


#2

see here: NativeLib compilation now requires lz4


#3

Indeed, it worked! Thank you.
Sorry, I had missed that one.


#4

just made it in response to your post :slight_smile:

A few others had the same problem and posted all the places (GitHub issue, Zulip, …)