Build Error


#1

I am trying to build scidb on ubuntu 12.04. I have tried with both 14.3 and 13.12. I keep getting an error regarding the mpicc on both builds similar to this:

[code]MPI bin dir is /opt/scidb/13.12/3rdparty/mpich2/bin
mpirun is /opt/scidb/13.12/3rdparty/mpich2/bin/mpiexec.hydra
mpicc is /opt/scidb/13.12/3rdparty/mpich2/bin/mpicc/usr/lib/libatlas.so.3gf
mpif90 is /opt/scidb/13.12/3rdparty/mpich2/bin/mpif90/usr/lib/libatlas.so.3gf
MPI include dir is -I /opt/scidb/13.12/3rdparty/mpich2/include/mpich2
NOOPT flags are -fPIC -g -O0
Creating directory /usr/local/scidb-13.12.0.6872/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install
Install directory is… /usr/local/scidb-13.12.0.6872/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install
Creating directory /usr/local/scidb-13.12.0.6872/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/build
Build directory is… /usr/local/scidb-13.12.0.6872/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/build
Checking if mpicc works…

COMMON: mpicc not working! aborting…
stderr:


/bin/sh: 1: /opt/scidb/13.12/3rdparty/mpich2/bin/mpicc/usr/lib/libatlas.so.3gf: not found
[/code]

I used the prepare_toolchain script to set up the requirements.

It looks like the final line saying the file cannot be found is the merging of to paths that do exist:

/opt/scidb/13.12/3rdparty/mpich2/bin/mpicc
/usr/lib/libatlas.so.3gf

Any thoughts?


#2

I’ve done some more digging into this. Here is the published build log from

downloads.paradigm4.com/ubuntu12 … /build.log

pertaining to the error:

[ 2%] No patch step for 'scalapackForMPICH2' [ 2%] No update step for 'scalapackForMPICH2' [ 2%] No configure step for 'scalapackForMPICH2' [ 2%] Performing build step for 'scalapackForMPICH2' SETUP_DIR is /tmp/buildd/scidb-14.3-0/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2 PATCH is /tmp/buildd/scidb-14.3-0/src/mpi/local_scalapack/scalapack.patch ARGS#: 5 ARG1: -I /opt/scidb/14.3/3rdparty/mpich2/include/mpich2 ARG2: /opt/scidb/14.3/3rdparty/mpich2/bin ARG3: /usr/lib/liblapack.so /usr/lib/libblas.so ARG4: /usr/lib/libblas.so ARG5: .mpich2 patching file script/framework.py patching file script/utils.py ==============================

my build is passing a different argument set:

[ 71%] No patch step for 'scalapackForMPICH2' [ 71%] No update step for 'scalapackForMPICH2' [ 71%] No configure step for 'scalapackForMPICH2' [ 71%] Performing build step for 'scalapackForMPICH2' SETUP_DIR is /home/scidb/scidbtrunk/src/mpi/local_scalapack/container/src/scalapackForMPICH2 PATCH is /home/scidb/scidbtrunk/src/mpi/local_scalapack/scalapack.patch ARGS#: 6 ARG1: -I /opt/scidb/14.3/3rdparty/mpich2/include/mpich2 ARG2: /opt/scidb/14.3/3rdparty/mpich2/bin ARG3: /usr/lib/liblapack.so /usr/lib/libf77blas.so.3gf /usr/lib/libatlas.so.3gf ARG4: /usr/lib/libf77blas.so.3gf ARG5: /usr/lib/libatlas.so.3gf patching file script/framework.py patching file script/utils.py

Any idea how to adjust this?


#3

I was having this same issue (on Ubuntu 12.04 with SciDB 14.8). I fixed it by removing these packages:

sudo apt-get remove libatlas-base-dev libatlas3gf-base

The installer was getting confused by the presence of these libraries, failing to build the local scalapack during the ‘run.py make’ stage. Now it builds to 100%. Hope that helps.