I've just installed Ubuntu, installed Conda, several packages including Django and PostgreSQL via Conda (with Conda installed PostgreSQL). That's it, nothing else.
I'm trying to follow the instructions here: https://github.com/rdkit/OCEAN. Rather than creating a virtual environment I've created a Conda one instead. I'm not sure if that's going to make any difference.
Also please note: this is a clean build. I have not activated anything or created any DB user etc. All I've done is activate the Conda env of choice and started installing the packages listed on the link above.
I'm having problems with the initial PostgreSQL instructions recreated here...
Get a clone of OCEAN from the Repo:
git clone https://www.github.com/rdkit/OCEAN.git
cd OCEAN
Create a PostgreSQL-User, the database for OCEAN and fill the OCEAN-DB:
# create PostgreSQL-User for OCEAN
# password 'ocean_pw' should be used when asked,
# according to database-entry in settings.py
createuser -P -s -d -r -e ocean_user
# create PostgreSQL-Database for OCEAN
createdb --owner=ocean_user ocean
When I try createuser -P -s -d -r -e ocean_user and then add the required password (in the Git link) I get the error:
createuser: error: could not connect to database postgres: could not connect to server: No such file or directory. Is the server running locally or accepting connections on Unix domain socket "/tmp/.s.PGSQL.5432"?
I have a Conda environment and on a very clean Ubuntu machine. The last time I touched a DB was years ago. How can I resolve this?
Just strange, I am doing back database maintenance, I tried to to a heroku pg:pull <DB_URL> local_db --app <appname> and it says:
pg:pull is not a heroku command.
I tried to create a backup with heroku pg:backups:capture <DB_URL> and i get this:
pg:backups:capture is not a heroku command.
Just trying heroku pg:backups shows:
pg:backups is not a heroku command.
Its strange because even in the --help section, looks like all the useful commands are gone:
heroku pg --help
Usage: heroku pg [DATABASE]
-a, --app APP # app to run command against
-r, --remote REMOTE # git remote of app to run command against
Commands for pg, type "heroku help pg:COMMAND" for more details:
heroku pg [DATABASE] #
heroku pg:info [DATABASE] #
heroku pg:wait [DATABASE] #
I looked around online and didn't see anything about these pg command deprications. I checked my heroku CLI version: heroku-cli/5.3.0-5329fb8 (darwin-amd64) go1.6.2
Strange becuase I've been using these commands on this same computer many times recently and suddenly they're gone.
Have these pg been depricated (I doubt)? If not does anyone know what I am doing wrong? If so, anyone know how to do push/pull/capture in the new framework?
The answer was that my CLI version was out-of-date. I followed these instructions on my Mac:
rm -rf /usr/local/heroku
rm -rf ~/.local/share/heroku ~/.config/heroku ~/.cache/heroku
And then re-installed using homebrew:
brew update
brew install heroku
Apparently the new version of the CLI is supposed to keep itself up-to-date.
Being new to Anaconda, I am having some trouble properly setting up a conda environment. What I am interested in achieving is setting up an environment for a django application with a postgres database. The following command creates the environment:
$ conda create -n django1.7-webdev python=3.4 django=1.7 postgresql=9.1
This second command activates the environment:
$ source activate django1.7-webdev
At this point, though, when trying to run psql, I get the following error:
$ psql
psql: could not connect to server: No such file or directory
Is the server running locally and accepting
connections on Unix domain socket "/tmp/.s.PGSQL.5432"?
How can I start PostgreSQL in the conda environment? The following command starts the PostgreSQL installed outside the activated conda environment, which is not what I want:
$ sudo service postgresql start
The postgresql documentation on starting servers is at https://www.postgresql.org/docs/9.1/static/server-start.html - before that, you might also need to initialize a database: https://www.postgresql.org/docs/9.1/static/creating-cluster.html
The conda package should include any binaries necessary to follow those directions. Moreover, these binaries should already be on PATH, since you are activating the environment.
In general, if you're starting a command with sudo to interact with conda, something is wrong. Unless you are trying to do some centrally-owned install that several users use, conda should never require admin rights.
Closed. This question does not meet Stack Overflow guidelines. It is not currently accepting answers.
We don’t allow questions seeking recommendations for books, tools, software libraries, and more. You can edit the question so it can be answered with facts and citations.
Closed 1 year ago.
The community reviewed whether to reopen this question 1 year ago and left it closed:
Original close reason(s) were not resolved
Improve this question
I'm using the PostgreSQL database for my Ruby on Rails application (on Mac OS X 10.9).
Are there any detailed instructions on how to upgrade PostgreSQL database?
I'm afraid I will destroy the data in the database or mess it up.
Assuming you've used home-brew to install and upgrade Postgres, you can perform the following steps.
Stop current Postgres server:
launchctl unload ~/Library/LaunchAgents/homebrew.mxcl.postgresql.plist
Initialize a new 10.1 database:
initdb /usr/local/var/postgres10.1 -E utf8
run pg_upgrade (note: change bin version if you're upgrading from something other than below):
pg_upgrade -v \
-d /usr/local/var/postgres \
-D /usr/local/var/postgres10.1 \
-b /usr/local/Cellar/postgresql/9.6.5/bin/ \
-B /usr/local/Cellar/postgresql/10.1/bin/
-v to enable verbose internal logging
-d the old database cluster configuration directory
-D the new database cluster configuration directory
-b the old PostgreSQL executable directory
-B the new PostgreSQL executable directory
Move new data into place:
cd /usr/local/var
mv postgres postgres9.6
mv postgres10.1 postgres
Restart Postgres:
launchctl load ~/Library/LaunchAgents/homebrew.mxcl.postgresql.plist
Check /usr/local/var/postgres/server.log for details and to make sure the new server started properly.
Finally, re-install the rails pg gem
gem uninstall pg
gem install pg
I suggest you take some time to read the PostgreSQL documentation to understand exactly what you're doing in the above steps to minimize frustrations.
Despite all answers above, here goes my 5 cents.
It works on any OS and from any-to-any postgres version.
Stop any running postgres instance;
Install the new version and start it; Check if you can connect to the new version as well;
Change old version's postgresql.conf -> port from 5432 to 5433;
Start the old version postgres instance;
Open a terminal and cd to the new version bin folder;
Run pg_dumpall -p 5433 -U <username> | psql -p 5432 -U <username>
Stop old postgres running instance;
Here is the solution for Ubuntu users
First we have to stop postgresql
sudo /etc/init.d/postgresql stop
Create a new file called /etc/apt/sources.list.d/pgdg.list and add below line
deb http://apt.postgresql.org/pub/repos/apt/ utopic-pgdg main
Follow below commands
wget -q -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
sudo apt-get update
sudo apt-get install postgresql-9.4
sudo pg_dropcluster --stop 9.4 main
sudo /etc/init.d/postgresql start
Now we have everything, just need to upgrade it as below
sudo pg_upgradecluster 9.3 main
sudo pg_dropcluster 9.3 main
That's it. Mostly upgraded cluster will run on port number 5433. Check it with below command
sudo pg_lsclusters
If you are using homebrew and homebrew services, you can probably just do:
brew services stop postgresql
brew upgrade postgresql
brew postgresql-upgrade-database
brew services start postgresql
I think this might not work completely if you are using advanced postgres features, but it worked perfectly for me.
Update: This process is the same for upgrading 9.5 through at least 11.5; simply modify the commands to reflect versions 9.6 and 10, where 9.6 is the old version and 10 is the new version. Be sure to adjust the "old" and "new" directories accordingly, too.
I just upgraded PostgreSQL 9.5 to 9.6 on Ubuntu and thought I'd share my findings, as there are a couple of OS/package-specific nuances of which to be aware.
(I didn't want to have to dump and restore data manually, so several of the other answers here were not viable.)
In short, the process consists of installing the new version of PostgreSQL alongside the old version (e.g., 9.5 and 9.6), and then running the pg_upgrade binary, which is explained in (some) detail at https://www.postgresql.org/docs/9.6/static/pgupgrade.html .
The only "tricky" aspect of pg_upgrade is that failure to pass the correct value for an argument, or failure to be logged-in as the correct user or cd to the correct location before executing a command, may lead to cryptic error messages.
On Ubuntu (and probably Debian), provided you are using the "official" repo, deb http://apt.postgresql.org/pub/repos/apt/ xenial-pgdg main, and provided you haven't changed the default filesystem paths or runtime options, the following procedure should do the job.
Install the new version (note that we specify the 9.6, explicitly):
sudo apt install postgresql-9.6
Once installation succeeds, both versions will be running side-by-side, but on different ports. The installation output mentions this, at the bottom, but it's easy to overlook:
Creating new cluster 9.6/main ...
config /etc/postgresql/9.6/main
data /var/lib/postgresql/9.6/main
locale en_US.UTF-8
socket /var/run/postgresql
port 5433
Stop both server instances (this will stop both at the same time):
sudo systemctl stop postgresql
Switch to the dedicated PostgreSQL system user:
su postgres
Move into his home directory (failure to do this will cause errors):
cd ~
pg_upgrade requires the following inputs (pg_upgrade --help tells us this):
When you run pg_upgrade, you must provide the following information:
the data directory for the old cluster (-d DATADIR)
the data directory for the new cluster (-D DATADIR)
the "bin" directory for the old version (-b BINDIR)
the "bin" directory for the new version (-B BINDIR)
These inputs may be specified with "long names", to make them easier to visualize:
-b, --old-bindir=BINDIR old cluster executable directory
-B, --new-bindir=BINDIR new cluster executable directory
-d, --old-datadir=DATADIR old cluster data directory
-D, --new-datadir=DATADIR new cluster data directory
We must also pass the --new-options switch, because failure to do so results in the following:
connection to database failed: could not connect to server: No such file or directory
Is the server running locally and accepting
connections on Unix domain socket "/var/lib/postgresql/.s.PGSQL.50432"?
This occurs because the default configuration options are applied in the absence of this switch, which results in incorrect connection options being used, hence the socket error.
Execute the pg_upgrade command from the new PostgreSQL version:
/usr/lib/postgresql/9.6/bin/pg_upgrade --old-bindir=/usr/lib/postgresql/9.5/bin --new-bindir=/usr/lib/postgresql/9.6/bin --old-datadir=/var/lib/postgresql/9.5/main --new-datadir=/var/lib/postgresql/9.6/main --old-options=-cconfig_file=/etc/postgresql/9.5/main/postgresql.conf --new-options=-cconfig_file=/etc/postgresql/9.6/main/postgresql.conf
Logout of the dedicated system user account:
exit
The upgrade is now complete, but, the new instance will bind to port 5433 (the standard default is 5432), so keep this in mind if attempting to test the new instance before "cutting-over" to it.
Start the server as normal (again, this will start both the old and new instances):
systemctl start postgresql
If you want to make the new version the default, you will need to edit the effective configuration file, e.g., /etc/postgresql/9.6/main/postgresql.conf, and ensure that the port is defined as such:
port = 5432
If you do this, either change the old version's port number to 5433 at the same time (before starting the services), or, simply remove the old version (this will not remove your actual database content; you would need to use apt --purge remove postgresql-9.5 for that to happen):
apt remove postgresql-9.5
The above command will stop all instances, so you'll need to start the new instance one last time with:
systemctl start postgresql
As a final point of note, don't forget to consider pg_upgrade's good advice:
Upgrade Complete
----------------
Optimizer statistics are not transferred by pg_upgrade so,
once you start the new server, consider running:
./analyze_new_cluster.sh
Running this script will delete the old cluster's data files:
./delete_old_cluster.sh
The user manual covers this topic in depth. You can:
pg_upgrade in-place; or
pg_dump and pg_restore.
If in doubt, do it with dumps. Don't delete the old data directory, just keep it in case something goes wrong / you make a mistake; that way you can just go back to your unchanged 9.3 install.
For details, see the manual.
If you're stuck, post a detailed question explaining how you're stuck, where, and what you tried first. It depends a bit on how you installed PostgreSQL too, as there are several different "distributions" of PostgreSQL for OS X (unfortunately). So you'd need to provide that info.
Standing on the shoulders of the other poor creatures trodding through this muck, I was able to follow these steps to get back up and running after an upgrade to Yosemite:
Assuming you've used home-brew to install and upgrade Postgres, you can perform the following steps.
Stop current Postgres server:
launchctl unload ~/Library/LaunchAgents/homebrew.mxcl.postgresql.plist
Initialize a new 9.4 database:
initdb /usr/local/var/postgres9.4 -E utf8
Install postgres 9.3 (as it was no longer present on my machine):
brew install homebrew/versions/postgresql93
Add directories removed during Yosemite upgrade:
mkdir -p /usr/local/var/postgres/{pg_tblspc,pg_twophase,pg_stat_tmp}/touch /usr/local/var/postgres/{pg_tblspc,pg_twophase,pg_stat_tmp}/.keep
run pg_upgrade:
pg_upgrade -v -d /usr/local/var/postgres -D /usr/local/var/postgres9.4 -b /usr/local/Cellar/postgresql93/9.3.5/bin/ -B /usr/local/Cellar/postgresql/9.4.0/bin/
Move new data into place:
cd /usr/local/var
mv postgres postgres9.3
mv postgres9.4 postgres
Restart Postgres:
launchctl load ~/Library/LaunchAgents/homebrew.mxcl.postgresql.plist
Check /usr/local/var/postgres/server.log for details and to make sure the new server started properly.
Finally, re-install related libraries?
pip install --upgrade psycopg2
gem uninstall pg
gem install pg
Looks like the solution has been baked into Homebrew now:
$ brew info postgresql
...
==> Caveats
To migrate existing data from a previous major version of PostgreSQL run:
brew postgresql-upgrade-database
....
On Windows I kept facing different errors messages when trying to use pg_upgrade.
Saved a lot of time for me to just:
Backup DB
Uninstall all copies of PostgreSQL
Install 9.5
Restore DB
This did it for me.
https://gist.github.com/dideler/60c9ce184198666e5ab4
Short and to the point. I honestly don't aim to understand the guts of PostgreSQL, I want to get stuff done.
My solution for upgrading from Postgresql 11 to Postgresql 12 on Windows 10 is the following.
As a first remark you will need to be able stop and start the Postgresql service. You can do this by the following commands in Powershell.
Start:
pg_ctl start -D “d:\postgresql\11\data”
Stop:
pg_ctl stop -D “d:\postgresql\11\data”
Status:
pg_ctl status -D “d:\postgresql\11\data”
It would be wise to make a backup before doing the upgrade. The Postgresql 11 instance must be running. Then to copy the globals do
pg_dumpall -U postgres -g -f d:\bakup\postgresql\11\globals.sql
and then for each database
pg_dump -U postgres -Fc <database> > d:\backup\postgresql\11\<database>.fc
or
pg_dump -U postgres -Fc -d <database> -f d:\backup\postgresql\11\<database>.fc
If not already done install Postgresql 12 (as Postgresql 11 is also installed this will be on port 5433)
Then to do the upgrade as follows:
1) Stop Postgresql 11 service (see above)
2) Edit the postgresql.conf file in d:\postgresql\12\data and change port = 5433 to port = 5432
3) Edit the windows user environment path (windows start then type env) to point to Postgresql 12 instead of Postresql 11
4) Run upgrade by entering the following command.
pg_upgrade `
-b “c:\program files\postgresql\11\bin” `
-B “c:\program files\postgresql\12\bin” `
-d “d:\postgresql\11\data” `
-D “d:\postgresql\12\data” --username=postgres
(In powershell use backtick (or backquote) ` to continue the command on the next line)
5) and finally start the new Postgresql 12 service
pg_ctl start -D “d:\postgresql\12\data”
My solution was to do a combination of these two resources:
https://gist.github.com/tamoyal/2ea1fcdf99c819b4e07d
and
http://www.gab.lc/articles/migration_postgresql_9-3_to_9-4
The second one helped more then the first one. Also to not, don't follow the steps as is as some are not necessary.
Also, if you are not being able to backup the data via postgres console, you can use alternative approach, and backup it with pgAdmin 3 or some other program, like I did in my case.
Also, the link: https://help.ubuntu.com/stable/serverguide/postgresql.html
Helped to set the encrypted password and set md5 for authenticating the postgres user.
After all is done, to check the postgres server version run in terminal:
sudo -u postgres psql postgres
After entering the password run in postgres terminal:
SHOW SERVER_VERSION;
It will output something like:
server_version
----------------
9.4.5
For setting and starting postgres I have used command:
> sudo bash # root
> su postgres # postgres
> /etc/init.d/postgresql start
> /etc/init.d/postgresql stop
And then for restoring database from a file:
> psql -f /home/ubuntu_username/Backup_93.sql postgres
Or if doesn't work try with this one:
> pg_restore --verbose --clean --no-acl --no-owner -h localhost -U postgres -d name_of_database ~/your_file.dump
And if you are using Rails do a bundle exec rake db:migrate after pulling the code :)
For Mac via homebrew:
brew tap petere/postgresql,
brew install <formula> (eg: brew install petere/postgresql/postgresql-9.6)
Remove old Postgres:
brew unlink postgresql
brew link -f postgresql-9.6
If any error happen, don't forget to read and follow brew instruction in each step.
Check this out for more: https://github.com/petere/homebrew-postgresql
On Windows 10 since I had npm, I installed rimraf package. npm install rimraf -g
Backup all your databases one by one using command pg_dump -U $username --format=c --file=$mydatabase.sqlc $dbname
Then Installed Latest PostgreSQL Version i.e. 11.2 which prompted me to use port 5433 this time.
Followed by Uninstall of older versions of PostgreSQL mine was 10. Note the uninstaller may give a warning of not deleting folder C:\PostgreSQL\10\data. That's why we have the next step using rimraf to permanently delete the folder and it's sub-folders.
change into PostgreSQL install directory and ran the command rimraf 10. 10 is a directory name. Note use your older version of PostgreSQL i.e. 9.5 or something.
Now add C:\PostgreSQL\pg11\bin, C:\PostgreSQL\pg11\lib into the Windows environmental variables. Note my new installed version is 11 thus why I am using pg11.
Navigate to C:\PostgreSQL\data\pg11 then open postgresql.conf edit port = 5433 to port = 5432
That's it. Open cmd and type psql -U postgres
You can now restore all your backed databases one by one using the command pg_restore -U $username --dbname=$databasename $filename
I think this is best link for your solution to update postgres to 9.6
https://sandymadaan.wordpress.com/2017/02/21/upgrade-postgresql9-3-9-6-in-ubuntu-retaining-the-databases/