SciDB 14.3 build error on Ubuntu 12.04


#1

Hi,

G’day! Just before trying to recompile my plugin to work under SciDB 14.3 on Ubuntu 12.04, I got errors while building from the SciDB source. Looks like something related to Java? I haven’t got this while building 13.12.

I am doing a local build only with run.py setup followed by run.py make. Tried with run.py make -j2 and the build would stop even earlier.

Any recommendations? Thanks!

Cheers,
Patrick

scidb@ubuntu:~/scidb-14.3.0.7383$ ./run.py setup
WARNING: Deleting old CMakeCache file:/home/scidb/scidb-14.3.0.7383/stage/build/CMakeCache.txt
WARNING: about to delete *all* contents of /home/scidb/scidb-14.3.0.7383/stage/build/* [y]|n: y
-- ****************** BEGIN CMakeLists.txt ******************
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- The Fortran compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- CMAKE_INSTALL_PREFIX not Initialized to default keeping: /home/scidb/scidb-14.3.0.7383/stage/install
-- Found Subversion: /usr/bin/svn (found version "1.6.17")
-- Found Git: /usr/bin/git 
-- Reading revision from file: 7383
-- Build type (use -DCMAKE_BUILD_TYPE=[RelWithDebInfo]/Debug/Release/Profile/CC/Valgrind): RelWithDebInfo
WARNING:executable will have RPATH set to $ORIGIN:/home/scidb/scidb-14.3.0.7383/stage/install/lib
-- DISTRO_NAME_VER is Ubuntu-12.04.4
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   system
--   program_options
--   serialization
--   regex
--   filesystem
--   thread
-- Found Protobuf: /usr/include/google/protobuf 
-- GPB - /usr/lib/libprotobuf.so
-- Found Log4CXX: /usr/lib/liblog4cxx.so 
-- LOG4CXX - /usr/lib/liblog4cxx.so
-- Found Doxygen: /usr/bin/doxygen 
-- Found LibPQXX: /usr/lib 
-- Found LibPQ: /usr/bin/pg_config 
-- Found LibPQ: /usr/lib 
-- checking for module 'cppunit'
--   found cppunit, version 1.12.1
-- Found LibRT: /usr/lib/x86_64-linux-gnu/librt.so 
-- Found SWIG: /usr/bin/swig2.0 (found suitable version "2.0.4", required is "2.0")
-- Found PythonLibs: /usr/lib/libpython2.7.so 
-- Found FLEX: /usr/bin/flex 
-- Found BISON: /usr/bin/bison 
-- Found SED: /bin/sed 
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.3.4")
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so 
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so - found
-- Found LibReadline: /usr/lib/x86_64-linux-gnu/libreadline.so 
-- Looking for include files CMAKE_HAVE_PTHREAD_H
-- Looking for include files CMAKE_HAVE_PTHREAD_H - found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE 
-- Found PythonInterp: /usr/bin/python (found version "2.7.3")
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- A library with BLAS API found.
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Found XSLTPROC: /usr/bin/xsltproc 
-- Found FOP: /usr/bin/fop 
-- Found docbook.xsl: /usr/share/xml/docbook/stylesheet/docbook-xsl/fo/docbook.xsl 
-- Looking for malloc_stats
-- Looking for malloc_stats - found
-- ****************** BEGIN src/CMakeLists.txt ******************
-- SWIG 2 and Python found. Python module will built
-- Configuring /home/scidb/scidb-14.3.0.7383/src/system/Constants.cpp.in as /home/scidb/scidb-14.3.0.7383/stage/build/src/system/Constants.cpp
-- Configuring /home/scidb/scidb-14.3.0.7383/src/system/System.h.in as /home/scidb/scidb-14.3.0.7383/stage/build/src/system/System.h
-- Configuring /home/scidb/scidb-14.3.0.7383/src/util/scidb-sample.conf.in as /home/scidb/scidb-14.3.0.7383/stage/build/bin/packaging_only/scidb-sample.conf
-- ****************** BEGIN src/mpi/CMakeLists.txt ******************
-- WARNING-- using locally installed MPICH2
-- Local MPICH2 path: /opt/scidb/14.3/3rdparty/mpich2
-- WARNING-- using locally installed ScaLAPACK for MPICH2
-- Debug: To refresh/rebuild the local copy of scalapack, remove /home/scidb/scidb-14.3.0.7383/stage/build/src/mpi/local_scalapack/container.
-- ****************** 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-14.3.0.7383/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2
-- DEBUG-- MPICH2_SUFFIX=.mpich2
-- DEBUG-- MPI_INCLUDE=-I /opt/scidb/14.3/3rdparty/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/14.3/3rdparty/mpich2
-- Debug: SCALAPACK_LIBRARIES is /home/scidb/scidb-14.3.0.7383/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install/lib/libscalapack.a
-- Debug: SCALAPACK_INC_DIR is /home/scidb/scidb-14.3.0.7383/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install/lib/include
-- Debug: FINAL PACKAGE SETTINGS src/mpi ================================>
-- Debug: SCALAPACK_LIBRARIES is /home/scidb/scidb-14.3.0.7383/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install/lib/libscalapack.a
-- Debug: LAPACK_LIBRARIES is /usr/lib/liblapack.so;/usr/lib/libblas.so
-- Debug: BLAS_LIBRARIES is /usr/lib/libblas.so
-- Debug: MPI_LIBRARIES is /opt/scidb/14.3/3rdparty/mpich2/lib/libmpichf90.a
-- Debug: MPI_INCLUDE is -I /opt/scidb/14.3/3rdparty/mpich2/include/mpich2
-- Debug: MPI_Fortran_COMPILER is /opt/scidb/14.3/3rdparty/mpich2/bin/mpif77.mpich2
-- Debug: CMAKE_C_FLAGS is  -pedantic -W -Wextra -Wall -Wno-long-long -Wno-unused-parameter -fPIC -D__STDC_FORMAT_MACROS
-- Debug: CMAKE_CXX_FLAGS is  -std=c++98 -pedantic -W -Wextra -Wall -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/scidb/scidb-14.3.0.7383/\" -DOMPI_IGNORE_CXX_SEEK
-- Debug: CMAKE_Fortran_FLAGS is  -fno-f2c -Wline-truncation -I/opt/scidb/14.3/3rdparty/mpich2/include/mpi -I/opt/scidb/14.3/3rdparty/boost/include/boost 
-- Debug: CMAKE_Fortran_COMPLIER is /usr/bin/gfortran
-- Debug: CMAKE_CXX_COMPILER is /usr/bin/c++
-- Debug: FINAL PACKAGE SETTINGS <================================
-- Debug: Building MPI Slave
-- ****************** BEGIN mpi/slaving/CMakeLists.txt ******************
-- Debug: CMAKE_CXX_COMPLIER is /opt/scidb/14.3/3rdparty/mpich2/bin/mpic++.mpich2
-- Debug: CMAKE_Fortran_COMPLIER is /opt/scidb/14.3/3rdparty/mpich2/bin/mpif77.mpich2
-- Debug: CMAKE_C_FLAGS is  -pedantic -W -Wextra -Wall -Wno-long-long -Wno-unused-parameter -fPIC -D__STDC_FORMAT_MACROS -I /opt/scidb/14.3/3rdparty/mpich2/include/mpich2 -I /home/scidb/scidb-14.3.0.7383/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install/lib/include
-- Debug: SCALAPACK_BUILD_DIR  is /home/scidb/scidb-14.3.0.7383/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build
-- Debug: SCALAPACK_INC_DIR  is /home/scidb/scidb-14.3.0.7383/stage/build/src/mpi/local_scalapack/container/src/scalapackForMPICH2-build/install/lib/include
-- ****************** END mpi/slaving/CMakeLists.txt ******************
-- ****************** END src/mpi/CMakeLists.txt ******************
-- *****BEGIN linear_algebra/CMakeLists.txt ***********************
-- Found MPI_C: /opt/scidb/13.12/3rdparty/mpich2/lib/libmpich.so;/opt/scidb/13.12/3rdparty/mpich2/lib/libopa.a;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/librt.so 
-- Found MPI_CXX: /opt/scidb/13.12/3rdparty/mpich2/lib/libmpichcxx.so;/opt/scidb/13.12/3rdparty/mpich2/lib/libmpich.so;/opt/scidb/13.12/3rdparty/mpich2/lib/libopa.a;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/librt.so 
-- Found MPI_Fortran: /opt/scidb/13.12/3rdparty/mpich2/lib/libmpich.so;/opt/scidb/13.12/3rdparty/mpich2/lib/libopa.a;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/librt.so 
-- MPI_Fortran_COMPILER=/opt/scidb/14.3/3rdparty/mpich2/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 /opt/scidb/13.12/3rdparty/mpich2/lib/libmpichcxx.so;/opt/scidb/13.12/3rdparty/mpich2/lib/libmpich.so;/opt/scidb/13.12/3rdparty/mpich2/lib/libopa.a;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/librt.so
-- Debug: CMAKE_C_FLAGS is  -pedantic -W -Wextra -Wall -Wno-long-long -Wno-unused-parameter -fPIC -D__STDC_FORMAT_MACROS
-- Debug: CMAKE_CXX_FLAGS is  -std=c++98 -pedantic -W -Wextra -Wall -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/scidb/scidb-14.3.0.7383/\"
-- Debug: CMAKE_Fortran_FLAGS is  -fno-f2c -Wline-truncation -I/opt/scidb/14.3/3rdparty/mpich2/include/mpi -I/opt/scidb/14.3/3rdparty/boost/include/boost 
-- Debug: MPI_Fortran_COMPILER is /opt/scidb/14.3/3rdparty/mpich2/bin/mpif77
-- *****END linear_algebra/CMakeLists.txt ***********************
-- Found Java6: /usr/lib/jvm/java-1.6.0-openjdk-amd64/bin/java 
-- PROTO_DIR = /home/scidb/scidb-14.3.0.7383/src/clients/java/../../../src/network/proto/
-- ****************** END src/CMakeLists.txt ******************
-- Configuring /home/scidb/scidb-14.3.0.7383/doc/api/Doxyfile.in as /home/scidb/scidb-14.3.0.7383/stage/build/doc/api/Doxyfile
-- Documentation will not be generated automatically. Use -DSCIDB_DOC_TYPE={NONE,FULL,API} to set type of generated documentation. Use make doc to generate FULL documentation manually.
-- ****************** END CMakeLists.txt ******************
-- Configuring done
-- Generating done
-- Build files have been written to: /home/scidb/scidb-14.3.0.7383/stage/build
scidb@ubuntu:~/scidb-14.3.0.7383$ 
scidb@ubuntu:~/scidb-14.3.0.7383$ ./run.py make
[  1%] Built target json_lib
[  2%] Built target bsdiff
[  2%] Built target bs_tests
[  2%] Built target MurmurHash_lib
[  8%] Built target util_lib
[  8%] Built target genmeta
[  8%] Built target catalog_lib
[  8%] Built target scidb_msg_lib
[ 11%] Built target array_lib
[ 14%] Built target system_lib
[ 16%] Built target compression_lib
[ 16%] Built target delta_lib
[ 52%] Built target ops_lib
[ 54%] Built target scalar_proc_lib
[ 60%] Built target qproc_lib
[ 61%] Built target io_lib
[ 62%] Built target network_lib
[ 63%] Built target scidb
[ 68%] Built target scidbclient
[ 68%] Built target scidbpython
[ 68%] Built target mpi_common
[ 70%] Built target mpi
[ 71%] Built target scalapackForMPICH2
[ 72%] Built target mpi_slave_common
[ 73%] Built target mpi_slave_direct
[ 73%] Built target mpi_slave_scidb
[ 79%] Built target dense_linear_algebra
Buildfile: /home/scidb/scidb-14.3.0.7383/src/clients/java/build.xml
  [taskdef] Could not load definitions from resource net/sf/antcontrib/antcontrib.properties. It could not be found.

configure:

BUILD FAILED
/home/scidb/scidb-14.3.0.7383/src/clients/java/build.xml:39: Problem: failed to create task or type if
Cause: The name is undefined.
Action: Check the spelling.
Action: Check that any custom tasks/types have been declared.
Action: Check that any <presetdef>/<macrodef> declarations have taken place.


Total time: 0 seconds
make[2]: *** [jdbc_build] Error 1
make[1]: *** [src/clients/java/CMakeFiles/jdbc_build.dir/all] Error 2
make: *** [all] Error 2
./run.py: ERROR: Command make failed: Abnormal return code: 2 on command ['/usr/bin/make', '-j1']
Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests
scidb@ubuntu:~/scidb-14.3.0.7383$ 

#2

Okay solved that myself - reinstalled OpenJDK 6, ant, ant-contrib package and it’s all working now :smile:


#3

I also cannot build SciDB, but on Ubuntu 14.04 LTS.

I am using “How to Build, Install, and Test SciDB 14.3” guide and I am stuck at subsection “6.2 Build”.

scidb@ubuntutest:~/Build/scidbtrunk$ ./run.py setup WARNING: about to delete *all* contents of /home/scidb/Build/scidbtrunk/stage/build/* [y]|n: y ./run.py: ERROR: Command setup failed: [Errno 2] No such file or directory Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests

Please help. I am new with SciDB.


#4

Have you tried:

cd deployment
./deploy.sh prepare_toolchain localhost

#5

I have also tried to deploy toolchain but got the same error:

[code]scidb@ubuntutest:~/Build/scidbtrunk$ cd deployment/
scidb@ubuntutest:~/Build/scidbtrunk/deployment$ ./deploy.sh prepare_toolchain localhost
Source path: /home/scidb/Build/scidbtrunk
Script common path: /home/scidb/Build/scidbtrunk/deployment/common
Build path: /home/scidb/Build/scidbtrunk/stage/build
SciDB version: 14.3
Executing: prepare_toolchain localhost

Prepare toolchain @localhost
Register SciDB 3rdparty repository on localhost
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment && mkdir -p /tmp/root
spawn scp -r -q -o StrictHostKeyChecking=no /home/scidb/Build/scidbtrunk/deployment/common root@localhost:/tmp/root/deployment
spawn ssh -o StrictHostKeyChecking=no root@localhost cd /tmp/root/deployment && ./register_3rdparty_scidb_repository.sh
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment && mkdir -p /tmp/root
spawn scp -r -q -o StrictHostKeyChecking=no /home/scidb/Build/scidbtrunk/deployment/common root@localhost:/tmp/root/deployment
spawn ssh -o StrictHostKeyChecking=no root@localhost cd /tmp/root/deployment && ./prepare_toolchain.sh 14.3
scidb@ubuntutest:~/Build/scidbtrunk/deployment$
scidb@ubuntutest:~/Build/scidbtrunk/deployment$
scidb@ubuntutest:~/Build/scidbtrunk/deployment$ ./run.py setup
bash: ./run.py: No such file or directory
scidb@ubuntutest:~/Build/scidbtrunk/deployment$ cd …
scidb@ubuntutest:~/Build/scidbtrunk$ ./run.py setup
WARNING: about to delete all contents of /home/scidb/Build/scidbtrunk/stage/build/* [y]|n: y
./run.py: ERROR: Command setup failed: [Errno 2] No such file or directory
Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests
scidb@ubuntutest:~/Build/scidbtrunk$ [/code]

This is my current process of installation:

[code]# Create scidb linux user:
sudo groupadd scidb
sudo useradd -d /home/scidb -m -g scidb -G adm,cdrom,sudo,dip,plugdev,lpadmin scidb
sudo passwd scidb # Set to “scidb”

Log out and login with scidb user

Remove previously installed version if necessary

sudo dpkg --list | grep scidb | awk '{print $2}' | xargs sudo dpkg --purge

Save latest version of scidb to ~/Build/scidbtrunk

cd ~/Build; 
tar -zxvf scidbXXXX.tgz
mv scidbXXXX scidbtrunk

Install sshd

sudo apt-get install expect openssh-server openssh-client
# Edit:   /etc/ssh/sshd_config : PermitRootLogin yes; 
sudo service ssh restart  #or reset server

Enable passwordless login to itself

ssh-keygen # DO NOT enter a passphrase; accept the default. 
ssh-add
ssh-copy-id -i ~/.ssh/id_rsa.pub scidb@localhost
ssh-copy-id -i ~/.ssh/id_rsa.pub root@localhost

Toolchain

./deployment/deploy.sh prepare_toolchain localhost

Install Postgres

sudo apt-get install -y postgresql
deployment/deploy.sh prepare_postgresql postgres postgres 10.0.0.0/8 localhost
sudo usermod -G scidb -a postgres
chmod g+rx scidbtrunk
# Check access: sudo -u postgres ls scidbtrunk

Set environment variables

# Add following lines to /home/scidb/.bashrc:
export SCIDB_VER=14.3
export SCIDB_INSTALL_PATH=/home/scidb/Build/scidbtrunk/stage/install
export SCIDB_BUILD_PATH=/home/scidb/Build/scidbtrunk/stage/install  # not in manual
export PATH=$SCIDB_INSTALL_PATH/bin:$PATH
# Close and reopen console

Build

cd /home/scidb/Build/scidbtrunk
./run.py -h # to learn its usage.
./run.py setup # to configure build directories and cmake infrastructure

I am stuck here ###[/code]


#6

I wanted to give SciDB a try but I am still unable to install it.

What combination of operating system and SciDB version did you use to successfully install and use SciDB? Did you use any other installation manual? Does anyone have different installation steps or (even better) installation script.


#7

I successfully built SciDB 14.3 on Ubuntu 12.04 yesterday. One thing that I did differently than your install script was to run deploy.sh access after generating ssh keys, as per section 4.1 of the build instructions. Looks like you’re using ssh-copy-id for this step; I don’t know if deploy access does anything in addition to installing the identify file.

% deployment/deploy.sh access root "" "" localhost
% deployment/deploy.sh access root "" "" localhost

I did run into a problem running deploy.sh access: the script hung as it were waiting for input. The problem is that an “expect” call was waiting for a prompt that must have changed recently . I was able to resolve the problem with the following patch:

--- deploy.sh.bk	2014-05-21 16:25:56.882073234 +0000
+++ deploy.sh	2014-05-21 16:26:06.002072895 +0000
@@ -240,7 +240,7 @@
 set timeout -1
 spawn $@
 expect {
-  "${username}@${hostname}'s password:" { send "${password}\r"; exp_continue }
+  "Password:" { send "${password}\r"; exp_continue }
   eof                                   { }
 }
 catch wait result

When I run prepare_toolchain I get much more output than what you posted:

scidb@ip-10-47-130-205:~/scidb-14.3.0.7383/deployment$ ./deploy.sh prepare_toolchain localhost
Source path: /home/scidb/scidb-14.3.0.7383
Script common path: /home/scidb/scidb-14.3.0.7383/deployment/common
Build path: /home/scidb/scidb-14.3.0.7383/deployment
SciDB version: 14.3
Executing: prepare_toolchain localhost

Prepare toolchain @localhost
Register SciDB 3rdparty repository on localhost
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment && mkdir -p /tmp/root
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
spawn scp -r -q -o StrictHostKeyChecking=no /home/scidb/scidb-14.3.0.7383/deployment/common root@localhost:/tmp/root/deployment
spawn ssh -o StrictHostKeyChecking=no root@localhost cd /tmp/root/deployment && ./register_3rdparty_scidb_repository.sh
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
--2014-05-22 17:25:12--  http://downloads.paradigm4.com/key
Resolving downloads.paradigm4.com (downloads.paradigm4.com)... 74.50.61.106
Connecting to downloads.paradigm4.com (downloads.paradigm4.com)|74.50.61.106|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1699 (1.7K) [text/plain]
Saving to: `STDOUT'

     0K .                                                     100%  152M=0s

2014-05-22 17:25:12 (152 MB/s) - written to stdout [1699/1699]

OK
deb http://downloads.paradigm4.com/ ubuntu12.04/3rdparty/
Hit http://us-east-1.ec2.archive.ubuntu.com precise Release.gpg
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates Release.gpg
Hit http://us-east-1.ec2.archive.ubuntu.com precise Release
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates Release
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main Sources
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe Sources
Hit http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Release.gpg
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main amd64 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe amd64 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main i386 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe i386 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main TranslationIndex
Hit http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Release
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe TranslationIndex
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main Sources
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe Sources
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main amd64 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe amd64 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main i386 Packages
Hit http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe i386 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main TranslationIndex
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe TranslationIndex
Get:1 http://security.ubuntu.com precise-security Release.gpg [198 B]
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe Translation-en
Get:2 http://security.ubuntu.com precise-security Release [49.6 kB]
Ign http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Translation-en_US
Ign http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Translation-en
Get:3 http://security.ubuntu.com precise-security/main Sources [105 kB]
Get:4 http://security.ubuntu.com precise-security/universe Sources [30.9 kB]
Get:5 http://security.ubuntu.com precise-security/main amd64 Packages [388 kB]
Get:6 http://security.ubuntu.com precise-security/universe amd64 Packages [93.1 kB]
Get:7 http://security.ubuntu.com precise-security/main i386 Packages [415 kB]
Get:8 http://security.ubuntu.com precise-security/universe i386 Packages [97.6 kB]
Hit http://security.ubuntu.com precise-security/main TranslationIndex
Hit http://security.ubuntu.com precise-security/universe TranslationIndex
Hit http://security.ubuntu.com precise-security/main Translation-en
Hit http://security.ubuntu.com precise-security/universe Translation-en
Fetched 1,179 kB in 2s (433 kB/s)
Reading package lists...
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment && mkdir -p /tmp/root
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
spawn scp -r -q -o StrictHostKeyChecking=no /home/scidb/scidb-14.3.0.7383/deployment/common root@localhost:/tmp/root/deployment
spawn ssh -o StrictHostKeyChecking=no root@localhost cd /tmp/root/deployment && ./prepare_toolchain.sh 14.3
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
Prepare Ubuntu 12.04 for build SciDB
Hit http://us-east-1.ec2.archive.ubuntu.com precise Release.gpg
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates Release.gpg
Hit http://us-east-1.ec2.archive.ubuntu.com precise Release
Hit http://security.ubuntu.com precise-security Release.gpg
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates Release
Hit http://security.ubuntu.com precise-security Release
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main Sources
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe Sources
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main amd64 Packages
Hit http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Release.gpg
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe amd64 Packages
Hit http://security.ubuntu.com precise-security/main Sources
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main i386 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe i386 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main TranslationIndex
Hit http://security.ubuntu.com precise-security/universe Sources
Hit http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Release
Hit http://security.ubuntu.com precise-security/main amd64 Packages
Hit http://security.ubuntu.com precise-security/universe amd64 Packages
Hit http://security.ubuntu.com precise-security/main i386 Packages
Hit http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Packages
Hit http://security.ubuntu.com precise-security/universe i386 Packages
Hit http://security.ubuntu.com precise-security/main TranslationIndex
Hit http://security.ubuntu.com precise-security/universe TranslationIndex
Hit http://security.ubuntu.com precise-security/main Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe TranslationIndex
Hit http://security.ubuntu.com precise-security/universe Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main Sources
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe Sources
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main amd64 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe amd64 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main i386 Packages
Ign http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Translation-en_US
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe i386 Packages
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main TranslationIndex
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe TranslationIndex
Ign http://downloads.paradigm4.com ubuntu12.04/3rdparty/ Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com precise/main Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com precise/universe Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/main Translation-en
Hit http://us-east-1.ec2.archive.ubuntu.com precise-updates/universe Translation-en
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
ant is already the newest version.
ant-contrib is already the newest version.
ant-optional is already the newest version.
bison is already the newest version.
debhelper is already the newest version.
doxygen is already the newest version.
expect is already the newest version.
flex is already the newest version.
gfortran is already the newest version.
junit is already the newest version.
libbz2-dev is already the newest version.
libcppunit-1.12-1 is already the newest version.
libcppunit-dev is already the newest version.
liblapack-dev is already the newest version.
libpqxx-3.1 is already the newest version.
libpqxx3-dev is already the newest version.
libprotobuf-dev is already the newest version.
libprotobuf7 is already the newest version.
libreadline6 is already the newest version.
libreadline6-dev is already the newest version.
protobuf-compiler is already the newest version.
swig2.0 is already the newest version.
zlib1g-dev is already the newest version.
liblog4cxx10 is already the newest version.
liblog4cxx10-dev is already the newest version.
libopenmpi-dev is already the newest version.
libprotobuf-java is already the newest version.
libscalapack-mpi1 is already the newest version.
build-essential is already the newest version.
cmake is already the newest version.
openjdk-6-jdk is already the newest version.
python-crypto is already the newest version.
python-paramiko is already the newest version.
subversion is already the newest version.
sudo is already the newest version.
xsltproc is already the newest version.
scidb-14.3-libboost1.54-all-dev is already the newest version.
scidb-14.3-libmpich2-dev is already the newest version.
scidb-14.3-mpich2 is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 205 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
ccache is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 205 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
docbook-xsl is already the newest version.
fop is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 205 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
postgresql-8.4 is already the newest version.
postgresql-contrib-8.4 is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 205 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
time is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 205 not upgraded.
DONE
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment && mkdir -p /tmp/root
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
spawn scp -r -q -o StrictHostKeyChecking=no /home/scidb/scidb-14.3.0.7383/deployment/common root@localhost:/tmp/root/deployment
spawn ssh -o StrictHostKeyChecking=no root@localhost cd /tmp/root/deployment && ./stop_virbr0.sh
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
Attempting to shut down virbr0 ...
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
scidb@ip-10-47-130-205:~/scidb-14.3.0.7383/deployment$

#8

I used ssh-copy-id because after using

deployment/deploy.sh access root "" "" localhost deployment/deploy.sh access scidb "" "" localhost
paswordless ssh to the same machine wouldn’t work.

I’ve retried but it is still the same. The script deosn’t hang, but it asks for password:

scidb@ubuntutest:~/Build/scidbtrunk$ ssh-keygen
Generating public/private rsa key pair.
Enter file in which to save the key (/home/scidb/.ssh/id_rsa): 
/home/scidb/.ssh/id_rsa already exists.
Overwrite (y/n)? y
Enter passphrase (empty for no passphrase): 
Enter same passphrase again: 
Your identification has been saved in /home/scidb/.ssh/id_rsa.
Your public key has been saved in /home/scidb/.ssh/id_rsa.pub.
The key fingerprint is:
ba:21:98:c6:3c:b5:87:cc:29:e5:a5:6e:1d:91:60:b9 scidb@ubuntutest
The key's randomart image is:
+--[ RSA 2048]----+
|     .           |
|    +            |
|   . o .         |
|    E o          |
|    o ..S        |
| o O *..         |
|  O X.+.         |
| . +.o.o         |
|   .. .          |
+-----------------+
scidb@ubuntutest:~/Build/scidbtrunk$ deployment/deploy.sh access root "" "" localhost
Source path: /home/scidb/Build/scidbtrunk
Script common path: /home/scidb/Build/scidbtrunk/deployment/common
Build path: /home/scidb/Build/scidbtrunk/stage/build
SciDB version: 14.3
Executing: access root   localhost

Enter root's password (only once):Provide access by ~/.ssh/id_rsa.pub to root@localhost
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment && mkdir -p /tmp/root
root@localhost's password: 
spawn scp -r -q -o StrictHostKeyChecking=no /home/scidb/Build/scidbtrunk/deployment/common root@localhost:/tmp/root/deployment
root@localhost's password: 
spawn ssh -o StrictHostKeyChecking=no root@localhost cd /tmp/root/deployment && ./user_access.sh "root" "ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDaNXyLNPFkgswh7awq2j1dDzbggMUxriMsVlN7Z6/uiMfT9NlHqIiy0xukGnnhKKLT++92i/T2BZ7Z+JxTcCmTM1qqd70r+x5POAmF8CmvDYVzhhKgwsKwquYSCyi/idf0tD2dZISvEbo0o+oCd1CyqNxDo+PnAttKKRnqDZn9KsLE60eXz5CX/II8XHiLSJ0bPkKEmc8SJegb3wsWgmzf37r1kbfyiQ8tplbeMuCSVGelJenU7t2GOnzLFpW1UKLirWE806msZ85fgs7IkT1t6dEtSu9v5JkBFB3N4ArbZyOdZUOAU4jk1NxQ4Kzap3iTXhz5djHQ3AHt5JWJSgR5 scidb@ubuntutest"
root@localhost's password: 
scidb@ubuntutest:~/Build/scidbtrunk$ 
scidb@ubuntutest:~/Build/scidbtrunk$ 
scidb@ubuntutest:~/Build/scidbtrunk$ deployment/deploy.sh access scidb "" "" localhost
Source path: /home/scidb/Build/scidbtrunk
Script common path: /home/scidb/Build/scidbtrunk/deployment/common
Build path: /home/scidb/Build/scidbtrunk/stage/build
SciDB version: 14.3
Executing: access scidb   localhost

Enter scidb's password (only once):Provide access by ~/.ssh/id_rsa.pub to scidb@localhost
spawn ssh -o StrictHostKeyChecking=no scidb@localhost rm -rf /tmp/scidb/deployment && mkdir -p /tmp/scidb
scidb@localhost's password: 
spawn scp -r -q -o StrictHostKeyChecking=no /home/scidb/Build/scidbtrunk/deployment/common scidb@localhost:/tmp/scidb/deployment
scidb@localhost's password: 
spawn ssh -o StrictHostKeyChecking=no scidb@localhost cd /tmp/scidb/deployment && ./user_access.sh "scidb" "ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDaNXyLNPFkgswh7awq2j1dDzbggMUxriMsVlN7Z6/uiMfT9NlHqIiy0xukGnnhKKLT++92i/T2BZ7Z+JxTcCmTM1qqd70r+x5POAmF8CmvDYVzhhKgwsKwquYSCyi/idf0tD2dZISvEbo0o+oCd1CyqNxDo+PnAttKKRnqDZn9KsLE60eXz5CX/II8XHiLSJ0bPkKEmc8SJegb3wsWgmzf37r1kbfyiQ8tplbeMuCSVGelJenU7t2GOnzLFpW1UKLirWE806msZ85fgs7IkT1t6dEtSu9v5JkBFB3N4ArbZyOdZUOAU4jk1NxQ4Kzap3iTXhz5djHQ3AHt5JWJSgR5 scidb@ubuntutest"
scidb@localhost's password: 
scidb@ubuntutest:~/Build/scidbtrunk$ 
scidb@ubuntutest:~/Build/scidbtrunk$ ssh localhost date
scidb@localhost's password: 
Pet Svi 23 09:26:15 CEST 2014

Because of that also “prepare toolchain” fails:

scidb@ubuntutest:~/Build/scidbtrunk$ deployment/deploy.sh prepare_toolchain localhost
Source path: /home/scidb/Build/scidbtrunk
Script common path: /home/scidb/Build/scidbtrunk/deployment/common
Build path: /home/scidb/Build/scidbtrunk/stage/build
SciDB version: 14.3
Executing: prepare_toolchain localhost

Prepare toolchain @localhost
Register SciDB 3rdparty repository on localhost
spawn ssh -o StrictHostKeyChecking=no root@localhost rm -rf /tmp/root/deployment && mkdir -p /tmp/root
root@localhost's password: 
Permission denied, please try again.
root@localhost's password: 
Permission denied, please try again.
root@localhost's password: 
Permission denied (publickey,password).
scidb@ubuntutest:~/Build/scidbtrunk$ 

I have also tried with this commands, but is still the same:

  ssh-keygen # DO NOT enter a passphrase; accept the default. 
  ssh-add
  ssh-copy-id -i ~/.ssh/id_rsa.pub scidb@localhost
  ssh-copy-id -i ~/.ssh/id_rsa.pub root@localhost
  deployment/deploy.sh access root "" "" localhost
  deployment/deploy.sh access scidb "" "" localhost