Help. I am stuck. initall fails


#1

Hello experts,

I have been fighting this for a few days.

I built the latest version 13.12 from source (successfully). I am running with postgres 8.4. I started postgres and am trying to initialize the database. But I am failing on scidb.py initall.

Here are my steps:

su postgres

Then I run
sh scidb-prepare-db.sh

Enter system catalog owner login: scidb
Enter system catalog owner password: scidb
Enter catalog database name: spectrum
User scidb already exists. Skipping creating.
Database spectrum already exists. Skipping creating
Granting privileges on database spectrum to user scidb…
Adding language C to trusted for database spectrum…
Granting user scidb usage for language C…
Done! Now connect to catalog with SciDB initialize and register cluster instance.

Now as user scidb, I have the following etc/config.ini:
[spectrum]
server-0=localhost,0
db_user=scidb
db_passwd=scidb
install_root=/home/scidb/scidb-13.12.0.6872/install
pluginsdir=/home/scidb/scidb-13.12.0.6872/install/lib/scidb/plugins
logconf=/home/scidb/scidb-13.12.0.6872/install/share/scidb/log4cxx.properties
base-path=/home/scidb/spectrum
tmp-path=/tmp
base-port=1239
interface=localhost

I now run

bin/scidb.py initall
./scidb.py initall spectrum

Which gives me the following output:

/usr/lib64/python2.6/site-packages/Crypto/Util/number.py:57: PowmInsecureWarning: Not using mpz_powm_sec. You should rebuild using libgmp >= 5 to avoid timing attack vulnerability.
_warn(“Not using mpz_powm_sec. You should rebuild using libgmp >= 5 to avoid timing attack vulnerability.”, PowmInsecureWarning)
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/spectrum/000/0 on server 0 (localhost), local instance 0
Abnormal return code: 1
error in command /home/scidb/scidb-13.12.0.6872/install/bin/scidb --register -p 1239 --initialize -i localhost -s /home/scidb/spectrum/000/0/storage.cfg -l /home/scidb/scidb-13.12.0.6872/install/share/scidb/log4cxx.properties --rle-chunk-format=True -c host=localhost port=5432 dbname=spectrum user=scidb password=scidb:
Check logs in init-stderr.log init-stdout.log

Here are what I think are relevant logs in the scidb.log file:

2014-04-02 15:32:26,273 [0x7ff5000e47e0] [INFO ]: Start SciDB instance (pid=8687). SciDB Version: 13.12.6872. Build Type: Debug. Copyright © 2008-2013 SciDB, Inc.
2014-04-02 15:32:26,273 [0x7ff5000e47e0] [INFO ]: Configuration:
precision : 6
catalog : host=localhost port=5432 dbname=spectrum user=scidb password=scidb
log-properties : /home/scidb/scidb-13.12.0.6872/install/share/scidb/log4cxx.properties
port : 1239
interface : localhost
coordinator : 0
register : 1
initialize : 1
storage : /home/scidb/spectrum/000/0/storage.cfg
plugins : /home/scidb/scidb-13.12.0.6872/install/lib/scidb/plugins

2014-04-02 15:32:26,273 [0x7ff5000e47e0] [DEBUG]: Created temp directory /home/scidb/spectrum/000/0/tmp/
2014-04-02 15:32:26,301 [0x7ff5000e47e0] [ERROR]: System catalog connection failed: SystemException in file: src/system/catalog/SystemCatalog.cpp function: connect line: 2053
Error id: scidb::SCIDB_SE_SYSCAT::SCIDB_LE_CANT_CONNECT_PG
Error description: System catalog error. Cannot connect to PostgreSQL catalog: 'FATAL: Ident authentication failed for user “scidb”

When I try to log in using psql however, I am able to do so.

psql -d spectrum -U scidb
psql (8.4.20)
Type “help” for help.

spectrum=>

Any clues about what I might have done wrong? Thank you in advance.

Ranga


#2

OK. I had to start the ident service and got a bit further. Now I get the following failure in my logs:

failed with error ERROR: could not access file “$libdir/uuid-ossp”: No such file or directory
.
2014-04-02 17:28:13,523 [0x7f534d8f67e0] [ERROR]: Failed to close header file
2014-04-02 17:28:13,523 [0x7f534d8f67e0] [ERROR]: Failed to close transaction log file
2014-04-02 17:28:13,523 [0x7f534d8f67e0] [ERROR]: Failed to close transaction log file
2014-04-02 17:28:13,523 [0x7f534d8f67e0] [INFO ]: SciDB instance. SciDB Version: 13.12.6872. Build Type: Debug. Copyright © 2008-2013 SciDB, Inc. is exiting.
461,1 Bot

What do I need to do to resolve this one?


#3

OK I installed the postgres-contrib package and it now initialized correctly so the problem is apparently resolved. On to the next step. Whew.


#4

Hi,mranga
Now I met the same problem ,you said by "installed the postgres-contrib package ",your installtion is OK ,I just wonder the command :“sudo apt-get install postgres-contrib” is what you did ?When I use the command,it says “no such package :postgres-contrib”? I run scidb in ubuntu12.04,and my scidb version is 13.10.