albhasan / docker_scidb Goto Github PK

Shim is enabled, users can connect through it

After ssh into docker and running ~./containerSetup.sh

output:

Creating a new generic function for ‘phyper’ in package ‘scidb’
Creating a new generic function for ‘qhyper’ in package ‘scidb’
Creating a new generic function for ‘reshape’ in package ‘scidb’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

• DONE (scidb)

The downloaded source packages are in
‘/tmp/Rtmp0AgMf5/downloaded_packages’
Generating public/private rsa key pair.
Created directory '/root/.ssh'.
Your identification has been saved in /root/.ssh/id_rsa.
Your public key has been saved in /root/.ssh/id_rsa.pub.
The key fingerprint is:
60:93:3c:5f:f1:1b:d9:f6:0e:6e:d7:58:5a:d1:ec:91 root@98a3d238b63b
The key's randomart image is:
+--[ RSA 2048]----+
| . |
| . . o o .o|
| B . + oEo|
| . = . + oo|
| S . . =|
| . B.|
| = +|
| . . |
| |
+-----------------+
Generating public/private rsa key pair.
Created directory '/home/scidb/.ssh'.
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:
e4:c6:a8:cd:40:16:f8:32:64:a2:54:64:a6:b6:1c:7f scidb@98a3d238b63b
The key's randomart image is:
+--[ RSA 2048]----+
| o_. |
|..B . |
|oB .o . |
|+ *o. = |
| o +.E. S |
| .= . |
| . o |
| |
| |
+-----------------+
scidbtrunk
run.py: ERROR: Command setup failed: [Errno 2] No such file or directory
run.py: ERROR: Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests
WARNING: about to delete *all_ contents of /home/scidb/dev_dir/scidbtrunk/stage/build/* [y]|n: Source path: /home/scidb/dev_dir/scidbtrunk
Script common path: /home/scidb/dev_dir/scidbtrunk/deployment/common
Build path: /home/scidb
SciDB version: 15.7
Executing: build_fast /tmp/packages

~/dev_dir/scidbtrunk ~
~
~/dev_dir/scidbtrunk ~
Extracting version
Extracting revision from file.
~
Version: 15.7.0
Revision: 9267
Preparing result dir
Cleaning old packages
Preparing sources from /home/scidb/debian to /home/scidb/debian
Building binary packages locally
~ ~
dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security
dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): -D_FORTIFY_SOURCE=2
dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security
dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions -Wl,-z,relro
dpkg-buildpackage: source package scidb-15.7
dpkg-buildpackage: source version 0-9267
dpkg-buildpackage: source changed by SciDB support list [email protected]
dpkg-buildpackage: host architecture amd64
dpkg-buildpackage: warning: debian/rules is not executable: fixing that.
dpkg-source --before-build scidb
dpkg-checkbuilddeps: Unmet build dependencies: cmake g++-4.9 gfortran-4.9 bison flex libcppunit-dev libpqxx3-dev libprotobuf-dev protobuf-compiler liblog4cxx10-dev fop xsltproc doxygen ant ant-contrib ant-optional libprotobuf-java openjdk-8-jdk junit libpam-dev swig2.0 docbook-xsl libscalapack-mpi1 libopenmpi-dev scidb-15.7-libcsv scidb-15.7-libmpich2-dev scidb-15.7-mpich2 scidb-15.7-libboost1.54-all-dev scidb-15.7-ant scidb-15.7-cityhash
dpkg-buildpackage: warning: Build dependencies/conflicts unsatisfied; aborting.
dpkg-buildpackage: warning: (Use -d flag to override.)
dpkg-buildpackage failed
Source path: /home/scidb/dev_dir/scidbtrunk
Script common path: /home/scidb/dev_dir/scidbtrunk/deployment/common
Build path: /home/scidb
SciDB version: 15.7
Executing: scidb_install /tmp/packages localhost

Coordinator IP: 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.
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).
cp: cannot create regular file `/opt/scidb/15.7/etc/config.ini': No such file or directory
Source path: /home/scidb/dev_dir/scidbtrunk
Script common path: /home/scidb/dev_dir/scidbtrunk/deployment/common
Build path: /home/scidb
SciDB version: 15.7
Executing: scidb_prepare scidb scidb xxxx.xxxx.xxxx scidb_docker /home/scidb/data 2 default 1 localhost

[scidb_docker]
server-0=localhost,1
db_user=scidb
redundancy=1
install_root=/opt/scidb/15.7
pluginsdir=/opt/scidb/15.7/lib/scidb/plugins
logconf=/opt/scidb/15.7/share/scidb/log4cxx.properties
base-path=/home/scidb/data
base-port=1239
interface=eth0
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/dev_dir/scidbtrunk/deployment/common scidb@localhost:/tmp/scidb/deployment
scidb@localhost's password:
spawn ssh -o StrictHostKeyChecking=no scidb@localhost cd /tmp/scidb/deployment && ./scidb_prepare.sh 15.7
scidb@localhost's password:
export SCIDB_VER=15.7
spawn ssh -o StrictHostKeyChecking=no scidb@localhost rm -rf /tmp/scidb/deployment
scidb@localhost's password:
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).
bash: line 4: scidb.py: command not found
bash: line 9: iquery: command not found
bash: line 10: iquery: command not found
bash: line 11: iquery: command not found
bash: line 12: scidb.py: command not found
root@98a3d238b63b:~#

Include additional SciDB configuration files with more instances(16 & 32 & 64)

Move files to the real root home folder.

File management would be easier if container-users' IDs match specific host-users' IDs

DOCKERFILE
1 - Retrieve the ID of user postgres and store it:
RUN OLD_POSTGRES_ID=$(id -u postgres)

2 - Change the IDs of container-user postgres to match host-user postgres
RUN usermod -u 109 -U postgres
RUN groupmod -g 117 postgres

3 - Update owner of old files
RUN find / -uid $OLD_POSTGRES_ID -exec chown postgres {} ;