Ubuntu SciDB 15.7 build error


#1

I’m getting a build error on the scalapack build step:

– verifying file…
file=’/home/dolson/scidb-15.7.0.9267/src/mpi/local_scalapack/container/src/scalapack_installer.tgz’
– verifying file… warning: did not verify file - no URL_HASH specified?
– extracting…
src=’/home/dolson/scidb-15.7.0.9267/src/mpi/local_scalapack/container/src/scalapack_installer.tgz’
dst=’/home/dolson/scidb-15.7.0.9267/src/mpi/local_scalapack/container/src/scalapackForMPICH2’
– extracting… [tar xfz]
– extracting… [analysis]
– extracting… [rename]
– extracting… [clean up]
– extracting… done
[ 66%] Performing patch step for ‘scalapackForMPICH2’
[ 66%] No update step for ‘scalapackForMPICH2’
[ 67%] No configure step for ‘scalapackForMPICH2’
[ 67%] Performing build step for 'scalapackForMPICH2’
SETUP_DIR is /home/dolson/scidb-15.7.0.9267/src/mpi/local_scalapack/container/src/scalapackForMPICH2
PATCH is /home/dolson/scidb-15.7.0.9267/src/mpi/local_scalapack/scalapack.patch
ARGS#: 6
ARG1: -I /opt/scidb/15.7/3rdparty/mpich2/include/mpich2
ARG2: /opt/scidb/15.7/3rdparty/mpich2/bin
ARG3: /usr/lib/liblapack.so /usr/lib/libf77blas.so /usr/lib/libatlas.so
ARG4: /usr/lib/libf77blas.so
ARG5: /usr/lib/libatlas.so
patching file script/framework.py
patching file script/utils.py
patching file script/scalapack.py

Setting up the framework
ScaLAPACK installer version (1, 0, 2)
MPI bin dir is /opt/scidb/15.7/3rdparty/mpich2/bin
mpirun is /opt/scidb/15.7/3rdparty/mpich2/bin/mpiexec.hydra
mpicc is /opt/scidb/15.7/3rdparty/mpich2/bin/mpicc/usr/lib/libatlas.so
mpif90 is /opt/scidb/15.7/3rdparty/mpich2/bin/mpif90/usr/lib/libatlas.so
MPI include dir is -I /opt/scidb/15.7/3rdparty/mpich2/include/mpich2
NOOPT flags are -fPIC -g -O0
Creating directory /bigdata/backup/home/dolson/scidb-15.7.0.9267/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install
Install directory is… /bigdata/backup/home/dolson/scidb-15.7.0.9267/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install
Creating directory /bigdata/backup/home/dolson/scidb-15.7.0.9267/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/build
Build directory is… /bigdata/backup/home/dolson/scidb-15.7.0.9267/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/build
Checking if mpicc works…

COMMON: mpicc not working! aborting…
stderr:


/bin/sh: 1: /opt/scidb/15.7/3rdparty/mpich2/bin/mpicc/usr/lib/libatlas.so: not found


It looks like the issue is something in the build configuration is appending ‘/usr/lib/libatlas.so’ to mpicc’s path.
mpicc is /opt/scidb/15.7/3rdparty/mpich2/bin/mpicc/usr/lib/libatlas.so
mpif90 is /opt/scidb/15.7/3rdparty/mpich2/bin/mpif90/usr/lib/libatlas.so


#2

Can you show me the output of “run.py setup”? I am particularly interested in the following section:
– ****************** BEGIN mpi/local_scalapack/CMakeLists.txt ******************
– DEBUG BLAS_FOUND=TRUE LAPACK_FOUND=TRUE MPICH_FOUND=1
– WARNING-- using locally built libscalapack.a
– DEBUG-- UNTAR_DIR=/home/scidb/scidb/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2
– DEBUG-- MPICH2_SUFFIX=.mpich2
– DEBUG-- MPI_INCLUDE=-I /opt/scidb/15.7/3rdparty/mpich2/include/mpich2
– DEBUG-- BLAS_LIBRARIES=/usr/lib/libblas.so
– DEBUG-- LOCAL_LAPACK_LIBRARIES=/usr/lib/liblapack.so /usr/lib/libblas.so
– DEBUG-- LOCAL_MPI_PATH=/opt/scidb/15.7/3rdparty/mpich2
– DEBUG-- PRIMARY_STATUS=0
www.netlib.org is up.


#3

Also can you tell me what version of Ubuntu you are running ?