Transmart 13.8 installation postgres problem

[Carolin Bruckmaier]

I am following the step by step installation guide for transmart 16.3. At the step "setting up a new database" ( https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Settingupanewdatabaseandsampledata ), executing the command 'make -j4 postgres' gives me the following error message:

make -C ddl/postgres/GLOBAL createdb

make[1]: Entering directory '/usr/local/transmart/transmart-data/ddl/postgres/GLOBAL'

test `/usr/bin/psql -v ON_ERROR_STOP=1 --single-transaction -X -d template1 -c "select exists (select datname from pg_database where datname = 'transmart')" -tA` \

= 'f' || (echo -e "\e[31mERROR\e[m: Database transmart already exists or connection error"; false)

psql: could not connect to server: No such file or directory

Is the server running locally and accepting

connections on Unix domain socket "/var/run/postgresql/.s.PGSQL.5432"?

/bin/sh: line 0: test: =: unary operator expected

ERROR: Database transmart already exists or connection error

make[1]: *** [createdb] Error 1

Makefile:45: recipe for target 'createdb' failed

make[1]: Leaving directory '/usr/local/transmart/transmart-data/ddl/postgres/GLOBAL'

make: *** [postgres] Error 2

Makefile:4: recipe for target 'postgres' failed

I checked the PSQL_BIN in the vars file, it should be set correctly.

Do you have any idea how to solve this problem?

Best,

Carolin

[Peter Rice]

Hi Carolin,

Before creating the database there is a check whether the database
already exists. The psql command failed to connect.

First thing to check is whether postgres is up and running:

sudo service postgresql status

The check, the same way the installation does, by connecting as postgres:

sudo -u postgres /usr/bin/psql -c "select datname from pg_database"

Then try to connect using your settings in vars:

/usr/bin/psql -c "select datname from pg_database"

I expect we will see the same error message 'psql: could not connect to
server: No such file or directory'

The question then is which file or directory it could be looking for.

regards,

Peter Rice
Axiomedix Inc.

On 24/09/2018 08:14, Carolin Bruckmaier wrote:
> I am following the step by step installation guide for transmart 16.3.
> At the step "setting up a new database" (
> https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Settingupanewdatabaseandsampledat

> <https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Settingupanewdatabaseandsampledata>a

> --
> For more ways to get in contact with the tranSMART community visit
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[ssm...@txbiomed.org]

I am seeing the same problem.   I honestly don't have any experience with databases.   I did check to see if the postgres was running, and it was.   

Thanks, 

Sandy

[Peter Rice]

Hi Sandy,

One possibility is "No such file or directory" means there is a problem
with the tablespaces (we have to guess which file or directory it was
looking for)

Source the transmart-data/vars file then:

printenv TABLESPACES

ls -al $TABLESPACES

sudo -u postgres ls -al $TABLESPACES

The tablespace should include transmart and indx directories, be owned
by postgres, and be accessible by user postgres (sometimes there is a
higher level directory user postgres cannot read, that could cause the
problem you see).

On 25/09/2018 15:09, ssm...@txbiomed.org wrote:
> I am seeing the same problem.   I honestly don't have any experience
> with databases.   I did check to see if the postgres was running, and it
> was.
>
> Thanks,
>
> Sandy
>
>
> On Monday, September 24, 2018 at 2:14:08 AM UTC-5, Carolin Bruckmaier wrote:
>
> I am following the step by step installation guide for transmart
> 16.3. At the step "setting up a new database" (
> https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Settingupanewdatabaseandsampledat

> <https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Settingupanewdatabaseandsampledata>a

> --
> For more ways to get in contact with the tranSMART community visit
> https://wiki.transmartfoundation.org/display/transmartwiki/Getting+Support
> ---
> You received this message because you are subscribed to the Google
> Groups "transmart-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to transmart-disc...@googlegroups.com
> <mailto:transmart-disc...@googlegroups.com>.
> To post to this group, send email to transmar...@googlegroups.com
> <mailto:transmar...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/transmart-discuss/2b2e7cad-3f8d-466c-9998-fc30eead0347%40googlegroups.com
> <https://groups.google.com/d/msgid/transmart-discuss/2b2e7cad-3f8d-466c-9998-fc30eead0347%40googlegroups.com?utm_medium=email&utm_source=footer>.

[ssm...@txbiomed.org]

Hi Peter, 

Here is my output.  

transmart@ubuntu-test:~/transmart/transmart-data/ddl/postgres/GLOBAL$ cd ~/transmart/transmart-data

transmart@ubuntu-test:~/transmart/transmart-data$ . ./vars

transmart@ubuntu-test:~/transmart/transmart-data$ printenv TABLESPACES

/var/lib/postgresql/tablespaces/

transmart@ubuntu-test:~/transmart/transmart-data$ ls -al $TABLESPACES

total 28

drwxr-xr-x 7 postgres postgres 4096 Sep 25 07:25 .

drwxr-xr-x 4 postgres postgres 4096 Sep 25 07:25 ..

drwx------ 2 postgres postgres 4096 Sep 25 07:25 biomart

drwx------ 2 postgres postgres 4096 Sep 25 07:25 deapp

drwx------ 2 postgres postgres 4096 Sep 25 07:25 indx

drwx------ 2 postgres postgres 4096 Sep 25 07:25 search_app

drwx------ 2 postgres postgres 4096 Sep 25 07:25 transmart

transmart@ubuntu-test:~/transmart/transmart-data$ 

transmart@ubuntu-test:~/transmart/transmart-data$ 

transmart@ubuntu-test:~/transmart/transmart-data$ sudo -u postgres ls -al $TABLESPACES

[sudo] password for transmart: 

total 28

drwxr-xr-x 7 postgres postgres 4096 Sep 25 07:25 .

drwxr-xr-x 4 postgres postgres 4096 Sep 25 07:25 ..

drwx------ 2 postgres postgres 4096 Sep 25 07:25 biomart

drwx------ 2 postgres postgres 4096 Sep 25 07:25 deapp

drwx------ 2 postgres postgres 4096 Sep 25 07:25 indx

drwx------ 2 postgres postgres 4096 Sep 25 07:25 search_app

drwx------ 2 postgres postgres 4096 Sep 25 07:25 transmart

transmart@ubuntu-test:~/transmart/transmart-data$ 

On Monday, September 24, 2018 at 2:14:08 AM UTC-5, Carolin Bruckmaier wrote:

[Peter Rice]

Hi Sandy,

So let's check that postgres query as reported in the output.

Source the transmart-data/vars file then (all one line):

/usr/bin/psql -v ON_ERROR_STOP=1 --single-transaction -X -d template1

-c "select exists (select datname from pg_database)"

This should give a list of database names, including 'transmart' but
when run from the Makefile (make postgres) it was giving an error

regards,

Peter Rice
Axiomedix Inc.

On 25/09/2018 15:09, ssm...@txbiomed.org wrote:

> I am seeing the same problem.   I honestly don't have any experience
> with databases.   I did check to see if the postgres was running, and it
> was.
>
> Thanks,
>
> Sandy
>
>
> On Monday, September 24, 2018 at 2:14:08 AM UTC-5, Carolin Bruckmaier wrote:
>
> I am following the step by step installation guide for transmart
> 16.3. At the step "setting up a new database" (
> https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Settingupanewdatabaseandsampledat

> <https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-Settingupanewdatabaseandsampledata>a

[Sandra Smith]

Peter,

Really appreciate all your help! Here is the output below. Should I create the posgres user in sql? Should I also create the databases?

Thanks,

sandy

transmart@ubuntu-test:~/transmart/transmart-data$ /usr/bin/psql -v ON_ERROR_STOP=1 --single-transaction -X -d template1 -c "select exists (select datname from pg_database)"
psql: FATAL: Peer authentication failed for user "postgres"

On 9/25/18, 10:23 AM, "Peter Rice" <peter...@axiomedix.com> wrote:

-c "select exists (select datname from pg_database)"

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[Peter Rice]

Hi Sandy,

Did you source the vars file?

printenv | grep PG

Something is amiss with the postgres settings. I can reproduce the
message by defining PGUSER=postgres but not defining the others.

Certainly something is suggesting postgres as the username. You may also
have settings in ~/.pgpass that it will try to use if the variables are
not defined.

Hope that helps

Peter Rice
Axiomedix Inc.