SciDB installation cannot find java


#1

Hi,
I am getting the following error while running ./run.py setup. I have installed all the libraries manually in /opt/scidb/15.12/3rdparty/ . But now I am getting error saying Could not find Java.
Java 1.8 is installed at /usr/lib/jvm/. Here is the error from terminal:

  • *****BEGIN dense_linear_algebra/CMakeLists.txt ***********************
    – Found MPI_C: /usr/lib/libmpi.so;/usr/lib/i386-linux-gnu/libdl.so;/usr/lib/i386-linux-gnu/libhwloc.so
    – Found MPI_CXX: /usr/lib/libmpi_cxx.so;/usr/lib/libmpi.so;/usr/lib/i386-linux-gnu/libdl.so;/usr/lib/i386-linux-gnu/libhwloc.so
    – Found MPI_Fortran: /usr/lib/libmpi_f77.so;/usr/lib/libmpi.so;/usr/lib/i386-linux-gnu/libdl.so;/usr/lib/i386-linux-gnu/libhwloc.so
    – MPI_Fortran_COMPILER=/usr/bin/mpif77
    – Debug: BLAS_LIBRARIES is /usr/lib/libblas.so
    – Debug: LAPACK_LIBRARIES is /usr/lib/liblapack.so;/usr/lib/libblas.so
    – Debug: SCALAPACK_LIBRARIES is
    – Debug: MPI_LIBRARIES is /usr/lib/libmpi_cxx.so;/usr/lib/libmpi.so;/usr/lib/i386-linux-gnu/libdl.so;/usr/lib/i386-linux-gnu/libhwloc.so
    – Debug: CMAKE_C_FLAGS is -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-long-long -Wno-unused-parameter -fPIC -D__STDC_FORMAT_MACROS
    – Debug: CMAKE_CXX_FLAGS is -std=c++14 -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-strict-aliasing -Wno-long-long -Wno-unused-parameter -Wno-variadic-macros -fPIC -D__STDC_FORMAT_MACROS -Wno-system-headers -isystem /opt/local/include/ -isystem /usr/local/include/ -D__STDC_LIMIT_MACROS -DPROJECT_ROOT="/home/purva/15.12/scidbtrunk/" -Wconversion
    – Debug: CMAKE_Fortran_FLAGS is -fno-f2c -Wline-truncation -I/opt/scidb/15.12/3rdparty/mpich2/include/mpi -I/opt/scidb/15.12/3rdparty/boost/include/boost
    – Debug: MPI_Fortran_COMPILER is /usr/bin/mpif77
    – *****END linear_algebra/CMakeLists.txt ***********************
    – **BEGIN linear_algebra/CMakeLists.txt --------------------------------
    – Debug: CMAKE_C_FLAGS is -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-long-long -Wno-unused-parameter -fPIC -D__STDC_FORMAT_MACROS
    – Debug: CMAKE_CXX_FLAGS is -std=c++14 -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-strict-aliasing -Wno-long-long -Wno-unused-parameter -Wno-variadic-macros -fPIC -D__STDC_FORMAT_MACROS -Wno-system-headers -isystem /opt/local/include/ -isystem /usr/local/include/ -D__STDC_LIMIT_MACROS -DPROJECT_ROOT="/home/purva/15.12/scidbtrunk/" -Wconversion
    – **END linear_algebra/CMakeLists.txt --------------------------------
    – Could NOT find Java (missing: Java_JAVA_EXECUTABLE Java_JAR_EXECUTABLE Java_JAVAC_EXECUTABLE Java_JAVAH_EXECUTABLE Java_JAVADOC_EXECUTABLE)
    CMake Error at src/jdbc/CMakeLists.txt:4 (message):
    Java 1.8 is currently the only supported version for building JDBC!

I have to get SciDB installed and running for an academic project. Any help is appreciated.


#2

This are the places cmake is looking in
/usr/lib/jvm/java-1.8.0-openjdk/bin
/usr/lib/jvm/java-1.8.0-openjdk-amd64/bin
/usr/lib/jvm/java-1.8.0-openjdk.x86_64/bin

and did you run deployment/deploy.sh prepare_toolchain localhost before you tried to build ?