(SOLVED) executing scidb.py initall: Abnormal return code: 1


#1

I already found this problem resolved here, but the problem resists in my case. If it’s possible, I would like a help about this problem, in this case specifically below.

I’m using Ubuntu (12.04-64bit) to install a SciDB (scidb_12.12.0-5890) on a single machine (Intel® Core™2 Duo CPU T6570 @ 2.10GHz / 4GB RAM / 4GB Swap) and I having an error when I try to execute ‘./scidb.py initall scidb’:

Abnormal return code: 1
error in command /opt/scidb/12.12/bin/scidb --register -p 5432 --initialize -i localhost -s /home/scidb/data/000/0/storage.cfg -l /opt/scidb/12.12/share/scidb/log4cxx.properties --rle-chunk-format=True -c host=localhost port=5432 dbname=scidb user=scidb password=scidb: 
Check logs in init-stderr.log init-stdout.log

I try to describe the steps below:

– using the scidb user (created by ‘adduser scidb’) to configure a password-less ssh:

root@ramon-Vostro-1520:/# service ssh status
ssh start/running, process 8301


root@ramon-Vostro-1520:/# sudo -u scidb 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:
6c:6e:eb:b3:92:c0:84:f2:d7:9b:44:e9:a0:5f:b2:f1 scidb@ramon-Vostro-1520
The key's randomart image is:
+--[ RSA 2048]----+
|                 |
|                 |
|   .   .         |
|. . o o.         |
| o + =  S        |
|  o * =o         |
|   o O +o        |
|    o E...       |
|       o+o       |
+-----------------+


root@ramon-Vostro-1520:/# sudo -u scidb ssh-copy-id -i /home/scidb/.ssh/id_rsa.pub scidb@localhost
scidb@localhost's password: 
Now try logging into the machine, with "ssh 'scidb@localhost'", and check in:

  ~/.ssh/authorized_keys

to make sure we haven't added extra keys that you weren't expecting.

After configure the repository, update the apt index, and confirms that I don’t have the postgresql installed previously; I installed the scidb-all-coord:

root@ramon-Vostro-1520:/# service postgresql status
postgresql: unrecognized service
root@ramon-Vostro-1520:/# apt-get install scidb-all-coord

package list that was installed

  libscidbclient libscidbclient-python postgresql-8.4 postgresql-client-8.4 postgresql-client-common postgresql-common
  postgresql-contrib-8.4 scidb scidb-all-coord scidb-doc scidb-plugins scidb-utils

/etc/postgresql/8.4/main/pg_hba.conf

# Database administrative login by Unix domain socket
local   all         postgres                          trust 

# TYPE  DATABASE    USER        CIDR-ADDRESS          METHOD

# "local" is for Unix domain socket connections only
local   all         all                               trust
# IPv4 local connections:
host    all         all         127.0.0.1/32          trust
# IPv6 local connections:
host    all         all         ::1/128               trust

/etc/postgresql/8.4/main/postgresql.conf

# - Connection Settings -
listen_addresses = '*'
#listen_addresses = 'localhost'         # what IP address(es) to listen on;
                                        # comma-separated list of addresses;
                                        # defaults to 'localhost', '*' = all
                                        # (change requires restart)
port = 5432                             # (change requires restart)

/etc/services

root@ramon-Vostro-1520:/# grep postgresql /etc/services
postgresql	5432/tcp	postgres	# PostgreSQL Database
postgresql	5432/udp	postgres
root@ramon-Vostro-1520:/# service postgresql start
 * Starting PostgreSQL 8.4 database server                              [ OK ]

exporting environment variables (and using scidb user, I did the same – in true I put in the ~/.bashrc on /home/root and /home/scidb):

export SCIDB_VER=12.12
export PATH=/opt/scidb/$SCIDB_VER/bin:/opt/scidb/$SCIDB_VER/share/scidb:$PATH
export LD_LIBRARY_PATH=/opt/scidb/$SCIDB_VER/lib:$LD_LIBRARY_PATH

root@ramon-Vostro-1520:/# echo $SCIDB_VER
12.12
root@ramon-Vostro-1520:/# echo $PATH
/opt/scidb/12.12/bin:/opt/scidb/12.12/share/scidb:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
root@ramon-Vostro-1520:/# echo $LD_LIBRARY_PATH
/opt/scidb/12.12/lib:

/opt/scidb/12.12/etc/config.ini

[scidb]
server-0=localhost,0
db_user=scidb
db_passwd=scidb
install_root=/opt/scidb/12.12
pluginsdir=/opt/scidb/12.12/lib/scidb/plugins
logconf=/opt/scidb/12.12/share/scidb/log4cxx.properties
base-path=/home/scidb/data
tmp-path=/tmp
base-port=5432
interface=eth0
root@ramon-Vostro-1520:/opt/scidb/12.12/bin# sudo -u postgres psql -p 5432
psql (8.4.15)
Digite "help" para ajuda.
postgres=# \q

root@ramon-Vostro-1520:/opt/scidb/12.12/bin# sudo -u postgres ./scidb.py init_syscat scidb
 is the result
Adding user scidb...
CREATE ROLE
Creating language plpgsql for database ...
UPDATE 1
GRANT
Sample of connection string:
host=localhost port=5432 dbname=scidb user=scidb password=scidb

And the error is this below:

root@ramon-Vostro-1520:/opt/scidb/12.12/bin# su scidb
scidb@ramon-Vostro-1520:/opt/scidb/12.12/bin$ ./scidb.py initall scidb
checking (server 0 (localhost) local instance 0) ... 
Found 0 scidb processes
This will delete all data and reinitialize storage [n]|y: y
init(server 0 (localhost) local instance 0)
Initializing local scidb instance/storage.

Cleaning up old logs and storage files.
Removing data directory /home/scidb/data/000/0 on server 0 (localhost), local instance 0 
Abnormal return code: 1
error in command /opt/scidb/12.12/bin/scidb --register -p 5432 --initialize -i localhost -s /home/scidb/data/000/0/storage.cfg -l /opt/scidb/12.12/share/scidb/log4cxx.properties --rle-chunk-format=True -c host=localhost port=5432 dbname=scidb user=scidb password=scidb: 
Check logs in init-stderr.log init-stdout.log
scidb@ramon-Vostro-1520:/opt/scidb/12.12/bin$ tail /home/scidb/data/000/0/scidb.log 
2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add physical operator factory: physicalQuantile for logical operator: quantile
2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add logical operator factory: insert
2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add physical operator factory: physicalInsert for logical operator: insert
2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add logical operator factory: variable_window
2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add physical operator factory: PhysicalVariableWindow for logical operator: variable_window
2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Error during SciDB execution: Address already in use
2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Failed to close header file
2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Failed to close transaction log file
2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Failed to close transaction log file
2013-01-11 15:45:09,657 [0x7fc1363137c0] [INFO ]: SciDB instance. SciDB version: 12.12.0.5890 (Smile). Build type: RelWithDebInfo. Copyright (C) 2008-2012 SciDB, Inc. is exiting.

already advancing, thanks for helping me.


#2

I also met this question, too. Then, I logged into root account but I met the following problems.

root@ubuntu:~# scidb.py initall test1 ssh failure: server=localhost port=22 Authentication failed.

What’s wrong with it? Can anyone help me? Thanks!


Abnormal return code 1 stderr on -- look at scidb logs for hints
#3

The error occurred because I configured the SciDB config.ini to wait conection in the same port of the PostgreSQL.
Erroneously, I thought the variable base-port assigned the port of PostgreSQL (Line 10 below).

/opt/scidb/12.12/etc/config.ini

1   [scidb]
2   server-0=localhost,0
3   db_user=scidb
4   db_passwd=scidb
5   install_root=/opt/scidb/12.12
6   pluginsdir=/opt/scidb/12.12/lib/scidb/plugins
7   logconf=/opt/scidb/12.12/share/scidb/log4cxx.properties
8   base-path=/home/scidb/data
9   tmp-path=/tmp
10 base-port=5432   # ---> must be maintain the port 1239 (base-port=1239)
11 interface=eth0

The log showed the error in Line 7:

1    scidb@ramon-Vostro-1520:/opt/scidb/12.12/bin$ tail /home/scidb/data/000/0/scidb.log 
2    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add physical operator factory: physicalQuantile for logical operator: quantile
3    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add logical operator factory: insert
4    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add physical operator factory: physicalInsert for logical operator: insert
5    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add logical operator factory: variable_window
6    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add physical operator factory: PhysicalVariableWindow for logical operator: variable_window
7    2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Error during SciDB execution: Address already in use
8    2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Failed to close header file
9    2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Failed to close transaction log file
10  2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Failed to close transaction log file
11  2013-01-11 15:45:09,657 [0x7fc1363137c0] [INFO ]: SciDB instance. SciDB version: 12.12.0.5890 (Smile). Build type: RelWithDebInfo. Copyright (C) 2008-2012 SciDB, Inc. is exiting.

About the diaosifyp error:

Maybe the problem is because (i) the variables was not exported; (ii) SSH was not started; or (iii) the ssh-keygen was not executed:

export SCIDB_VER=12.12
export PATH=/opt/scidb/$SCIDB_VER/bin:/opt/scidb/$SCIDB_VER/share/scidb:$PATH
export LD_LIBRARY_PATH=/opt/scidb/$SCIDB_VER/lib:$LD_LIBRARY_PATH

Thank you!


#4

[quote=“rcosta”]The error occurred because I configured the SciDB config.ini to wait conection in the same port of the PostgreSQL.
Erroneously, I thought the variable base-port assigned the port of PostgreSQL (Line 10 below).

/opt/scidb/12.12/etc/config.ini

1   [scidb]
2   server-0=localhost,0
3   db_user=scidb
4   db_passwd=scidb
5   install_root=/opt/scidb/12.12
6   pluginsdir=/opt/scidb/12.12/lib/scidb/plugins
7   logconf=/opt/scidb/12.12/share/scidb/log4cxx.properties
8   base-path=/home/scidb/data
9   tmp-path=/tmp
10 base-port=5432   # ---> must be maintain the port 1239 (base-port=1239)
11 interface=eth0

The log showed the error in Line 7:

1    scidb@ramon-Vostro-1520:/opt/scidb/12.12/bin$ tail /home/scidb/data/000/0/scidb.log 
2    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add physical operator factory: physicalQuantile for logical operator: quantile
3    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add logical operator factory: insert
4    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add physical operator factory: physicalInsert for logical operator: insert
5    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add logical operator factory: variable_window
6    2013-01-11 15:45:09,642 [0x7fc1363137c0] [DEBUG]: Add physical operator factory: PhysicalVariableWindow for logical operator: variable_window
7    2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Error during SciDB execution: Address already in use
8    2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Failed to close header file
9    2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Failed to close transaction log file
10  2013-01-11 15:45:09,657 [0x7fc1363137c0] [ERROR]: Failed to close transaction log file
11  2013-01-11 15:45:09,657 [0x7fc1363137c0] [INFO ]: SciDB instance. SciDB version: 12.12.0.5890 (Smile). Build type: RelWithDebInfo. Copyright (C) 2008-2012 SciDB, Inc. is exiting.

About the diaosifyp error:

Maybe the problem is because (i) the variables was not exported; (ii) SSH was not started; or (iii) the ssh-keygen was not executed:

export SCIDB_VER=12.12
export PATH=/opt/scidb/$SCIDB_VER/bin:/opt/scidb/$SCIDB_VER/share/scidb:$PATH
export LD_LIBRARY_PATH=/opt/scidb/$SCIDB_VER/lib:$LD_LIBRARY_PATH

Thank you![/quote]

Thanks for your help! But I think I have exported since otherwise the problem would be “no command found”. I think the problem is because ssh configuration but I follow the user guide and I still could not use it. I just ran ScidDB on my own computer and how should I configure SSH? Thanks!