Install Hail 0.2.57 on AWS Spark cluster

Hail Query & hailctl
1

Hi,
I am successfully using Hail v0.2.32 on AWS EMR cluster v 5.28.0 (Spark 2.4.4)
I successfully install the dependencies (java 8, g++, python 3.6, BLAS and LAPACK)

Then I clone hail repo and run the make command :
make install-on-cluster HAIL_COMPILE_NATIVES=1 SCALA_VERSION=2.11.12 SPARK_VERSION=2.4.4

I got the following error:

...
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Wextra -fPIC -ggdb -fno-strict-aliasing -I../resources/include -I/etc/alternatives/jre/include -I/etc/alternatives/jre/include/linux ApproximateQuantiles_test.cpp -MG -M -MF build/ApproximateQuantiles_test.d -MT build/ApproximateQuantiles_test.o
make[1]: Leaving directory `/opt/broad-hail/hail/src/main/c'
make[1]: Entering directory `/opt/broad-hail/hail/src/main/c'
make[1]: *** No rule to make target `jni.h', needed by `build/NativeBoot.o'.  Stop.
make[1]: Leaving directory `/opt/broad-hail/hail/src/main/c'
make: *** [native-lib-prebuilt] Error 2

any idea what could be wrong ?

Thanks

2

What’s make --version?

3 
$ make --version
GNU Make 3.82
Built for x86_64-redhat-linux-gnu
4

hey guys, any new about that ussue ?

5

Problem solved,

The issue was a conflict between java JRE and JDK…
Hail build required jni.h that is present in JDK includes, but my system was using JRE that do not include jni.h.

Prior to Hail build I created a soft link from JRE do JDK includes and that solve the issue

sudo ln -s /etc/alternatives/java_sdk/include /etc/alternatives/jre/include