Bug #2983: Update PostgreSQL from 7.4 to 8.2 in knb.msi - Metacat - Ecoinformatics Redmine

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Bug #2983

closed

Update PostgreSQL from 7.4 to 8.2 in knb.msi

Added by Jing Tao almost 17 years ago. Updated about 16 years ago.

Status:

Resolved

Priority:

Normal

Assignee:

Jing Tao

Category:

metacat

Target version:

1.8.1

Start date:

10/11/2007

Due date:

% Done:

Estimated time:

Bugzilla-Id:

2983

Description

Here is the email from matt:
Jing,

I see no problem, so go ahead. However, you should be sure to absolutely minimize the downtime for the KNB server, and if at all possible do the upgrade when few
people will need access to the server (some evening, or on a weekend). Try to limit the outage to just a minute or two if possible -- can you install both databases
side by side so that the version 7 db can continue to run while you set up version 8? Also, can the version 8 db use the db structure from version 7, so that you
don't have to do time-consuming table copies?

Could you try the upgrade on a test machine first, and develop a proposed upgrade plan that outlines the steps you plan to complete, and how long each step would
require to move from 7 to 8? I'd like to review that plan before you proceed.

Thanks,

Matt

Jing Tao wrote:

Hi, matt and other devs:

Since postgresql 8 has a better performance than 7 and postgresql 8 works so far so good at LTER metacat, I am thinking to upgrade postgresql to 8 in knb.msi. For
example, during % search, postgresql 7 couldn't handle one query which contains a list of all documents(because the query is too long), we have to cut the list into
couple subset and run queries couple times. It is not efficient. However, postgresql 8 can run this long query.

Do you see any problem or have some suggestion for the update?

Thanks,

Jing

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Updated by Jing Tao almost 17 years ago

In my test machine, I did succesfully installed 8 while 7 was running. In order to do so, we need install 8 from source code (If we use binary installation, some files of version 7 will be overwritten). Since data file structure of 8 is different to 7, I have to dump the data to a sql file from 7 and import the sql file to postgresql 8.

Procedure:
1. Install postgresql 8.2.5 from source code
root@localhost postgresql-8.2.5]# ./configure --prefix /usr/local/pgsql/8.2.5
root@localhost postgresql-8.2.5]# gmake
root@localhost postgresql-8.2.5]# gmake install

2. Start postgresql at another port:
root@localhost postgresql-8.2.5]# cd /usr/local/pgsql/8.2.5/
[root@localhost 8.2.5]# mkdir data
[root@localhost 8.2.5]# chown postgres data
[root@localhost 8.2.5]# su - postgres
-bash-3.00$ cd /usr/local/pgsql/8.2.5/
-bash-3.00$ ./bin/initdb data
edit pg_hba.conf and it looks like:

local all postgres trust
local knb metacat password
local kepler kepler password
host all all 127.0.0.1 255.255.255.255 password

-bash-3.00$ export LD_LIBRARY_PATH=/usr/local/pgsql/8.2.5/lib
-bash-3.00$ ./bin/postgres -i -p 5433 -D data >/dev/null 2>&1 &

3. Create knb and kepler databases, metacat and kepler role in version 8
-bash-3.00$ /usr/local/pgsql/8.2.5/bin/createdb -p 5433 knb
-bash-3.00$ /usr/local/pgsql/8.2.5/bin/createdb -p 5433 kepler
-bash-3.00$ ./bin/psql -p 5433 knb
knb=# CREATE ROLE metacat LOGIN PASSWORD 'password';
knb=# CREATE ROLE kepler LOGIN PASSWORD 'password';
knb=# \q

4. Dump knb 7.4 posgresql to a file in KNB machine
bash-3.00$ pg_dump knb > knbbackup (6.8G)
Start 6:00, end 6:20
pg_dump kepler > keplerbackup (45M)
couple seconds

5. Restore database into 8.2
-bash-3.00$./bin/psql -p 5433 knb < /tmp/knbbackup

before export data file to db:
Filesystem Size Used Avail Use% Mounted on
/dev/hda1 54G 35G 18G 67% /
none 506M 0 506M 0% /dev/shm

started at 9:15 PM ended (?) overnight (but > 3 hours)
Filesystem Size Used Avail Use% Mounted on
/dev/hda1 54G 51G 443M 100% /
none 506M 0 506M 0% /dev/shm

6. Modify the metacat.properties:
defaultDB=jdbc:postgresql://localhost:5433/knb

7. Restart tomcat (took 1 minute)

8. Test the new metacat. Since my local machine couldn't handle so huge data (I always get out of memory error for searching), I use ant "registery-schemas" for testing.

9. Shut down the 7.4 postgres

10. Test metacat again.

11. Add a file psql.sh in /etc/profile.d. The file looks like -

Settings for PostgreSQL database #
PSQL=/usr/local/pgsql/8.2.5
export PSQL

PATH=$PSQL/bin:$PATH
export PATH

MANPATH=$PSQL/man:$MANPATH
export MANPATH

LD_LIBRARY_PATH=$PSQL/lib
export LD_LIBRARY_PATH

12. Modify the postgresql in /etc/init.d
a. cp postgresql to postgresql.backup
b. Modify those parameters:
PGVERSION=8.2.5 # Set defaults for configuration variables
PGENGINE=/usr/local/pgsql/8.2.5/bin
PGPORT=5433
export PGDATA=/usr/local/pgsql/8.2.5/data
if [ -f $PGDATA/PG_VERSION ] && [ -d $PGDATA/base/template1 ]
then
echo "Using old-style directory structure"
else
export PGDATA=/usr/local/pgsql/8.2.5/data
fi

13. Restart postgresql by /etc/init.d/postgresql restart (Couple seconds)

14. Check process - ps -ef | grep post

15. Check by "netstat -plt"

16. Restart tomcat

17. Test metacat again.

18. Remove postgresql 7.4 (waiting...)

19. Remove data directory of 7.4 (waiting...)

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Updated by Jing Tao almost 17 years ago

Here is the time issue:
Since we can install postgresql 8 while 7 is running, installation time is not a big issue. However, in order to keep the databases identical, there shouldn't be any insert, update or delete activies in the version 7 database when we dump data from 7 to sql file and restore the sql file to version 8 database. The first activity (dump data from 7 to sql file) in knb.msi will take about 20 minutes. The second activity (restore the sql file to version 8 database) is unkown in knb.msi(but in my machine it took > 3 hours - overnight). So let's guess there would be an hour which should NOT allow any nsert, update or delete activies in database. I think it is good to do this job in a weekend while shutdown metacat.

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Updated by Matt Jones almost 17 years ago

The disadvantage of installing pg8 from source code is that security patches will not be automatically applied. So, given that you have to shut down the metacat in order to export the db and reimport it into pg 8, I think we might as well go with an RPM upgrade of pg8, so that automatic updates will continue to work.

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Updated by Jing Tao almost 17 years ago

Another issue is about the install dir and the database data dir. The space
needed to install postgresql is about 30 M (without data directory). So
Postgresql 8 can be installed to anywhere. The default installation directory
is /usr/local/pgsql (from source). I propose the installation directory will be
/usr/local/pgsql/8.2.5

Let's find a place for data directory. Here is the information of disk usage in
knb.msi:
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/vg01-sysroot
4.0G 1.3G 2.6G 33% /
/dev/sda1 471M 54M 394M 12% /boot
none 4.0G 0 4.0G 0% /dev/shm
/dev/mapper/vg02-home
9.8G 6.8G 2.5G 74% /home
/dev/mapper/vg02-tmp 7.9G 2.2G 5.3G 30% /tmp
/dev/mapper/vg01-usr 29G 6.2G 22G 23% /usr
/dev/mapper/vg02-var 7.9G 4.2G 3.4G 56% /var
/dev/mapper/vg03-pgsql
184G 84G 91G 48% /var/lib/pgsql
/dev/mapper/vg04-metacat
184G 61G 113G 36% /var/metacat
/dev/mapper/vg05-www 46G 4.6G 39G 11% /var/www

Since current size of knb database is about 16 G and we should consider future
usage, it seems /var/lib/pgsql is a good place for data directory.
Here is the file structure of this dir:
[root@knb lib]# ls pgsql/
backups data initdb.i18n knb-backup-05-31-2006 lost+found nohup.out null
postgres-backup-05-31-2006

It already has a data directory used by postgresql 7. I propose to create new
directory named /var/lib/pgsql/8.2.5/data as the data directory for postgresql
8.

Any suggestion and comment will be appreciated.

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Updated by Jing Tao almost 17 years ago

Consider auto update, RPM upgrade is better chioce. No matter rpm or source instllation, we have to shutdown metacat to export and inport data :(

How about the data directory for 8? Do you think /var/lib/pgsql/8.2.5/data is fine?

Thanks.

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Updated by Jing Tao over 16 years ago

Here is my propose for the updating by rpms.
1. Download packages :
postgresql-8.2.5-1PGDG.rhel4.i686.rpm
postgresql-contrib-8.2.5-1PGDG.rhel4.i686.rpm
postgresql-devel-8.2.5-1PGDG.rhel4.i686.rpm
postgresql-docs-8.2.5-1PGDG.rhel4.i686.rpm
postgresql-libs-8.2.5-1PGDG.rhel4.i686.rpm
postgresql-plperl-8.2.5-1PGDG.rhel4.i686.rpm
postgresql-plpython-8.2.5-1PGDG.rhel4.i686.rpm
postgresql-pltcl-8.2.5-1PGDG.rhel4.i686.rpm
postgresql-server-8.2.5-1PGDG.rhel4.i686.rpm
postgresql-test-8.2.5-1PGDG.rhel4.i686.rpm

2. Showdown tomcat

3. Dump knb and kepler database into files
bash-3.00$ pg_dump knb >/tmp/knbbackup (6.8G)
Start 6:00, end 6:20
pg_dump kepler > /tmp/keplerbackup (45M)
couple seconds
4. Showdown postgreSQL 7.4

5. Update postgreSQL from 7.4 to 8.2
rpm ~~Uvh postgresql~~*

6. Create a dir - /var/lib/pgsql/8.2.5/ by user postgres

7. Modify the /etc/init.d/postgresql file:
export PGDATA=/usr/local/pgsql/8.2.5/data
if [ -f $PGDATA/PG_VERSION ] && [ -d $PGDATA/base/template1 ]
then
echo "Using old-style directory structure"
else
export PGDATA=/usr/local/pgsql/8.2.5/data
fi

8. Start postgresql - /etc/init.d/postgresql start

9. Create knb and kepler databases (as unix user postgres), metacat and kepler role in version 8
-bash-3.00$ createdb knb
-bash-3.00$ createdb kepler
-bash-3.00$ ./bin/psql -p 5433 knb
knb=# CREATE ROLE metacat LOGIN PASSWORD 'password';
knb=# CREATE ROLE kepler LOGIN PASSWORD 'password';
knb=# \q

10. Restore database into 8.2
-bash-3.00$psql knb < /tmp/knbbackup
-bash-3.00$psql kepler < /tmp/keplerbackup

11. Edit pg_hba.conf in /usr/local/pgsql/8.2.5/data and it should look like:
local all postgres trust
local knb metacat password
local kepler kepler password
host all all 127.0.0.1 255.255.255.255 password

12. Restart posgreSQL

13. Restart tomcat

14. Test metacat

15. Delete data directory of 7.4 (/var/lib/pgsql/data) after a while (one week late?)

Notes:
1. Since my redhat box is pretty old - Fedora Core 3:(, I couldn't find proper rpms and didn't run it.
2. Could you double check the rpm files are completed? In 7.4, there are jdbc and odbc packages. But I couldn't find them in 8.2
3. Backup plan: if rpm failed. I can go to the installation from source code.

Any suggestion and comment will be appreciated.

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Updated by Jing Tao over 16 years ago

Here is my new propose for the updating by rpms.

Main change:
a. Install postgresql 8.3.0 rather than 8.2.5
b. We should deleted the data in /var/lib/pgsql since no space for two copies.
(Partition have 184 G space, but it is used 107 G).
c. Base on my experience in dev, I added a step to remove postgresql 7.4 before installation of 8.3.

1. Download packages :

compat-postgresql-libs-3-2PGDG.rhel4.i686.rpm 2008-02-05 01:11:10 54.3 KB
compat-postgresql-libs-debuginfo-3-2PGDG.rhel4.i686.rpm 2008-02-05 01:11:12 131.3 KB
postgresql-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:22:00 1.7 MB
postgresql-contrib-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:22:07 347.6 KB
postgresql-debuginfo-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:27:52 12.3 MB
postgresql-devel-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:28:22 1.3 MB
postgresql-docs-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:32:50 10.2 MB
postgresql-libs-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:32:54 185.3 KB
postgresql-plperl-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:32:55 33.4 KB
postgresql-plpython-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:32:56 24.5 KB
postgresql-pltcl-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:32:57 23.3 KB
postgresql-server-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:34:08 4.4 MB
postgresql-test-8.3.0-1PGDG.rhel4.i686.rpm 2008-02-02 02:34:36 1.2 MB

2. Showdown tomcat

3. Dump knb and kepler database into files
bash-3.00$ pg_dump knb >/var/lib/pgsql/knbbackup (6.8G)
Start 6:00, end 6:20
pg_dump kepler > /var/lib/pgsql/keplerbackup (45M)
couple seconds

4. Showdown postgreSQL 7.4

5. Reomve postgresql 7.4
rpm Âe `/bin/rpm Âqa|grep postgresql*` --ÂÂnodeps

6. Install postgreSQL 8.3
rpm -ivh compat*.rpm
rpm -ivh postgres*.rpm

7. Delete /usr/lib/pgsql/data by user postgres
rm data -rf

8. Initialize a PostgreSQL database cluster
initdb data

9. Start postgresql - /etc/init.d/postgresql start

10. Create knb and kepler databases (as unix user postgres), metacat and kepler
roles in version 8
-bash-3.00$ createdb knb
-bash-3.00$ createdb kepler
-bash-3.00$ ./bin/psql -p 5433 knb
knb=# CREATE ROLE metacat LOGIN PASSWORD 'password';
knb=# CREATE ROLE kepler LOGIN PASSWORD 'password';
knb=# \q

11. Restore database in 8.3
-bash-3.00$psql knb < /tmp/knbbackup
-bash-3.00$psql kepler < /tmp/keplerbackup

12. Edit pg_hba.conf in /usr/local/pgsql/8.2.5/data and it should look like:
local all postgres trust
local knb metacat password
local kepler kepler password
host all all 127.0.0.1 255.255.255.255 password

13. Restart posgreSQL

14. Restart tomcat

15. Test metacat

Backup plan:
If 8.3 installation fails, we can use up2date to install 7.4 again. Then use saved script to restore database.

Note:
1. Metacat 1.8.0 has s sql command which isn't compatible to 8.3. However cvs head does work. Currently, dev machine is running cvs metacat with postgresql 8.3.
2. Postgresql 8.3 has the new feature of free test search.

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Updated by Jing Tao about 16 years ago

In step 5, i first ran:
[root@knb postgres-8.3.3]# rpm -ef `rpm -qa | grep postgresql`
error: Failed dependencies:
libpq.so.3 is needed by (installed) perl-DBD-Pg-1.31-6.i386
libpq.so.3 is needed by (installed) mod_auth_pgsql-2.0.1-7.1.i386
libpq.so.3 is needed by (installed) php-pgsql-4.3.9-3.22.9.i386

Then ran:
[root@knb postgres-8.3.3]# rpm -ef `rpm -qa | grep postgresql` --nodeps

Note: the command in step has some errors. the above command is correct.

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Updated by Jing Tao about 16 years ago

I have some issues about compat-postgresql-libs-3-2PGDG.rhel4.i686.rpm and compat-postgresql-libs-4-1PGDG.rhel4.i686.rpm.

Talked with nick we decided only to install compat-postgresql-libs-3-2PGDG.rhel4.i686.rpm

Here is the process:
rpm ~~ivh compat-postgresql-libs~~*.rpm
warning: compat-postgresql-libs-3-2PGDG.rhel4.i686.rpm: V3 DSA signature: NOKEY, key ID 442df0f8
warning: package compat-postgresql-libs = 3-2PGDG.rhel4 was already added, replacing with compat-postgresql-libs <= 4-1PGDG.rhel4
warning: package compat-postgresql-libs-debuginfo = 3-2PGDG.rhel4 was already added, replacing with compat-postgresql-libs-debuginfo <= 4-1PGDG.rhel4
Preparing... ########################################### [100%]
1:compat-postgresql-libs-########################################### [ 50%]
2:compat-postgresql-libs ########################################### [100%]

It seems only 4-1 being installed.

I unstalled 4-1 and install 3-2.

Here are the des[root@knb postgres-8.3.3]# rpm -qilp compat-postgresql-libs-3-2PGDG.rhel4.i686.rpm
warning: compat-postgresql-libs-3-2PGDG.rhel4.i686.rpm: V3 DSA signature: NOKEY, key ID 442df0f8
Name : compat-postgresql-libs Relocations: (not relocatable)
Version : 3 Vendor: (none)
Release : 2PGDG.rhel4 Build Date: Sun 13 Jan 2008 09:32:51 PM PST
Install Date: (not installed) Build Host: koji-centos4-i386-pg83
Group : Applications/Databases Source RPM: compat-postgresql-libs-3-2PGDG.rhel4.src.rpm
Size : 111100 License: BSD
Signature : DSA/SHA1, Fri 01 Feb 2008 04:35:49 PM PST, Key ID 1f16d2e1442df0f8
URL : http://www.postgresql.org/
Summary : PostgreSQL client programs and libraries
Description :
This package provides compatibility libraries for PostgreSQL
/usr/lib/libpq.so.3.1
[root@knb postgres-8.3.3]# rpm -qilp compat-postgresql-libs-4-1PGDG.rhel4.i686.rpm
Name : compat-postgresql-libs Relocations: (not relocatable)
Version : 4 Vendor: (none)
Release : 1PGDG.rhel4 Build Date: Sun 08 Jun 2008 01:44:38 PM PDT
Install Date: (not installed) Build Host: DBI-XEN0
Group : Applications/Databases Source RPM: compat-postgresql-libs-4-1PGDG.rhel4.src.rpm
Size : 115388 License: BSD
Signature : (none)
URL : http://www.postgresql.org/
Summary : PostgreSQL client programs and libraries
Description :
This package provides compatibility libraries for PostgreSQL
/usr/lib64/libpq.so.4.1
cription about the two files: