Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
On 2012-04-26 05:32, Greg Landrum wrote:
I continue to be unable to reproduce these problems.
Running on a 64bit Ubuntu 11.10 VM I installed the following packages
using apt-get:
sudo apt-get install postgresql
sudo apt-get install postgresql-contrib postgresql-server-dev-all
I build the cartridge:
glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make
Install it (notice the sudo):
glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo make install
Create a postgresql account for my user:
glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo su postgres
postgres@ubuntu:/home/glandrum/RDKit_2012_03_1/Code/PgSQL/rdkit$
createuser glandrum
Shall the new role be a superuser? (y/n) y
And then run the tests:
glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck
/usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress
--inputdir=. --psqldir='/usr/lib/postgresql/9.1/bin'
--dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91
sfpgist slfpgist fps
(using postmaster on Unix socket, default port)
== dropping database contrib_regression ==
NOTICE: database contrib_regression does not exist, skipping
DROP DATABASE
== creating database contrib_regression ==
CREATE DATABASE
ALTER DATABASE
== running regression test queries==
test rdkit-91 ... ok
test props... ok
test btree... ok
test molgist ... ok
test bfpgist-91 ... ok
test sfpgist ... ok
test slfpgist ... ok
test fps ... ok
=
All 8 tests passed.
=
Can you please check your configuration to make sure that the packages
are all installed and the appropriate accounts are there?
-greg
Dear Greg,
On my Ubuntu 10.04 I can build against and install into Postgres 9.0
without any issues. I did a createuser jhje as postgres and then ran
the test suite.
jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck
/opt/postgres/9.0/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress
--inputdir=. --psqldir=/opt/postgres/9.0/bin --dbname=contrib_regression
rdkit-pre91 props btree molgist bfpgist-pre91 sfpgist slfpgist fps
(using postmaster on Unix socket, port 5432)
== dropping database contrib_regression ==
DROP DATABASE
== creating database contrib_regression ==
CREATE DATABASE
ALTER DATABASE
== running regression test queries==
test rdkit-pre91 ... ok
test props... ok
test btree... ok
test molgist ... ok
test bfpgist-pre91... ok
test sfpgist ... ok
test slfpgist ... ok
test fps ... ok
=
All 8 tests passed.
=
jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$
After having installed the cartridge as the postgres user with psql
/opt/postgres/9.0/share/postgresql/contrib/rdkit.sql:
postgres@ubuntu-lynet-test:~$ psql
Password:
psql (9.0.4)
Type help for help.
postgres=# select mol_amw('');
mol_amw
-
58.124
(1 row)
postgres=# show rdkit.tanimoto_threshold;
rdkit.tanimoto_threshold
--
0.5
(1 row)
postgres=#
But against postgres 9.1 both the test suite and the attempt to do
create extension rdkit fails with
FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
On the Linux Mint VM I found that I didn't have the postgresql-contrib
package installed. I added it but it didn't make a difference.
Both of the VMs I have used are 32-bit and you are using a 64-bit VM. I
wonder if that is significant. I don't have a 64-bit Linux VM ready for
test building at the moment but let me see if I can establish one.
Kind regards
-- Jan Holst Jensen
--
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Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
On Thu, Apr 26, 2012 at 8:26 AM, Jan Holst Jensen j...@biochemfusion.com wrote: jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ After having installed the cartridge as the postgres user with psql /opt/postgres/9.0/share/postgresql/contrib/rdkit.sql: I am not able to dig details now, but IIRC there are two different cartridges, one for 8.x and another one for 9.x. Just to be sure, I'd double check you are installing the right one in there. -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
On 2012-04-26 08:37, Gianluca Sforna wrote: On Thu, Apr 26, 2012 at 8:26 AM, Jan Holst Jensenj...@biochemfusion.com wrote: jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ After having installed the cartridge as the postgres user with psql /opt/postgres/9.0/share/postgresql/contrib/rdkit.sql: I am not able to dig details now, but IIRC there are two different cartridges, one for 8.x and another one for 9.x. Just to be sure, I'd double check you are installing the right one in there. Dear Gianluca, The cartridge is indeed postgres-version specifc. Which one is built depends on your postgres environment when you run make. On one machine I have both postgres 9.0 and 9.1 installed and so if I setup the 9.0 environment and run make, it will build the 9.0 cartridge. And vice versa. Like this (the third line in each block sources the version-specific postgres environment): jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export RDBASE=/home/jhje/RDKit_2012_03_1 jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export LD_LIBRARY_PATH=/home/jhje/RDKit_2012_03_1/lib/ jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ . /opt/postgres/9.1/pg91-openscg.env jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make clean rm -f rdkit.so librdkit.a rm -f rdkit_io.o mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o cache.o adapter.o rm -f rdkit--3.1.sql rm -rf results/ regression.diffs regression.out tmp_check/ log/ jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make cp rdkit.sql91.in rdkit--3.1.sql gcc -I/usr/local/include -I/home/jhje/RDKit_2012_03_1/Code -DRDKITVER='004100' -I. -I. -I/opt/postgres/9.1/include/postgresql/server -I/opt/postgres/9.1/include/postgresql/internal -D_GNU_SOURCE -I/usr/local/include/libxml2 -I/usr/local/openssl/include -I/usr/local/ldap-2.4.23/include -I/usr/local/include -fPIC -c -o rdkit_io.o rdkit_io.c ... jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export RDBASE=/home/jhje/RDKit_2012_03_1 jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export LD_LIBRARY_PATH=/home/jhje/RDKit_2012_03_1/lib/ jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ . /opt/postgres/9.0/pg90-openscg.env jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make clean rm -f rdkit.so librdkit.a rm -f rdkit.sql rm -f rdkit_io.o mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o guc.o cache.o adapter.o rm -rf results tmp_check log rm -f regression.diffs regression.out regress.out run_check.out jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make sed 's,MODULE_PATHNAME,$libdir/rdkit,g' rdkit.sql.in rdkit.sql gcc -I/usr/local/include -I/home/jhje/RDKit_2012_03_1/Code -DRDKITVER='004100' -I. -I. -I/opt/postgres/9.0/include/postgresql/server -I/opt/postgres/9.0/include/postgresql/internal -D_GNU_SOURCE -I/usr/local/include/libxml2 -I/usr/local/include -fPIC -c -o rdkit_io.o rdkit_io.c ... And you also have to take care that when you do make install as root that the environment is setup to point to your correct postgres version. You can verify that is the case by checking the output of make install and see what directories the library and SQL scripts are installed into, e.g. here I am installing into postgres 9.0: root@ubuntu-lynet-test:~# cd /home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/ root@ubuntu-lynet-test:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# . /opt/postgres/9.0/pg90-openscg.env root@ubuntu-lynet-test:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# make install /bin/mkdir -p '/opt/postgres/9.0/lib/postgresql' /bin/mkdir -p '/opt/postgres/9.0/share/postgresql/contrib' /bin/sh /opt/postgres/9.0/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 755 rdkit.so '/opt/postgres/9.0/lib/postgresql/rdkit.so' /bin/sh /opt/postgres/9.0/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./uninstall_rdkit.sql '/opt/postgres/9.0/share/postgresql/contrib' /bin/sh /opt/postgres/9.0/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 644 rdkit.sql '/opt/postgres/9.0/share/postgresql/contrib' root@ubuntu-lynet-test:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# So yes, it can certainly get mixed up, but if you only have a single postgres version installed and you build and test on that same machine this should not be an issue. I haven't seen any differences in behavior between the 8.4 and 9.0 series. I think the build script only changes when you go to 9.1 (?). I have the cartridge running fine in postgres 9.0 for a while now and I also recently got it installed on a postgres 8.4.5 in an emulated Raspberry Pi (ARM architecture) without any issues. Kind regards -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond.
Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
Dear Greg, The same thing happens when I try to enable the 'rdkit' extension directly. postgres@linux-dev-x86 ~ $ psql psql (9.1.3) Type help for help. postgres=# create extension rdkit; FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 The connection to the server was lost. Attempting reset: Succeeded. postgres=# This is an error message that's been reported before, but we never really did find a root cause. I will start from scratch on my VM with Ubuntu 11.10 and take careful notes as I'm doing the installation, then post those on the wiki. I don't have time to do it this morning, but I'll try and get to it tonight or tomorrow a.m. Best, -greg Thanks. Meanwhile, I got RDKit_2012_03_1 running fine in Postgres 9.0.4 (the OpenSCG version) on an Ubuntu 10.04 build server. I will try to install Postgres 9.1 on that server and see if the error can be reproduced with that setup. Kind regards -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1. [Follow-up - testing on Ubuntu 10.04]
Meanwhile, I got RDKit_2012_03_1 running fine in Postgres 9.0.4 (the OpenSCG version) on an Ubuntu 10.04 build server. I will try to install Postgres 9.1 on that server and see if the error can be reproduced with that setup. Dear Greg, I have now installed Postgres 9.1 on the mentioned build server. Postgres 9.1 was installed via the DEB package from http://www.openscg.com/se/postgresql/packages.jsp I got RDKit_2012_03_1 compiled after implementing the one-line patch I sent a little earlier. The Postgres install error seems reproducible as I also get it here, which is a configuration quite different from the Linux Mint 12 developer VM I originally saw the issue on. postgres@ubuntu-lynet-test:~$ cat /etc/issue Ubuntu 10.04.2 LTS \n \l postgres@ubuntu-lynet-test:~$ uname -a Linux ubuntu-lynet-test 2.6.32-28-generic-pae #55-Ubuntu SMP Mon Jan 10 22:34:08 UTC 2011 i686 GNU/Linux postgres@ubuntu-lynet-test:~$ psql Password: psql.bin (9.1.3) Type help for help. postgres=# create extension rdkit; FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 The connection to the server was lost. Attempting reset: Succeeded. postgres=# Cheers -- Jan -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
I continue to be unable to reproduce these problems. Running on a 64bit Ubuntu 11.10 VM I installed the following packages using apt-get: sudo apt-get install postgresql sudo apt-get install postgresql-contrib postgresql-server-dev-all I build the cartridge: glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make Install it (notice the sudo): glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo make install Create a postgresql account for my user: glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo su postgres postgres@ubuntu:/home/glandrum/RDKit_2012_03_1/Code/PgSQL/rdkit$ createuser glandrum Shall the new role be a superuser? (y/n) y And then run the tests: glandrum@ubuntu:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=. --psqldir='/usr/lib/postgresql/9.1/bin' --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps (using postmaster on Unix socket, default port) == dropping database contrib_regression == NOTICE: database contrib_regression does not exist, skipping DROP DATABASE == creating database contrib_regression == CREATE DATABASE ALTER DATABASE == running regression test queries== test rdkit-91 ... ok test props... ok test btree... ok test molgist ... ok test bfpgist-91 ... ok test sfpgist ... ok test slfpgist ... ok test fps ... ok = All 8 tests passed. = Can you please check your configuration to make sure that the packages are all installed and the appropriate accounts are there? -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
Hi, I am having problems install the Postgres cartridge in Postgres 9.1 on Linux Mint 12 (which is based on Ubuntu 11.10). RDKit 2012_03_1 builds without any issues and all tests pass. The PgSQL cartridge builds fine too, and installs fine as seen below. jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ sudo make install /bin/mkdir -p '/usr/lib/postgresql/9.1/lib' /bin/mkdir -p '/usr/share/postgresql/9.1/extension' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 755 rdkit.so '/usr/lib/postgresql/9.1/lib/rdkit.so' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit.control '/usr/share/postgresql/9.1/extension/' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit--3.1.sql '/usr/share/postgresql/9.1/extension/' jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ However, the make installcheck step fails. In the regression.diffs I see: [... tons of lines ...] --- 4,9 -- SET client_min_messages = warning; \set ECHO none ! FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 ! FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 ! connection to server was lost The same thing happens when I try to enable the 'rdkit' extension directly. postgres@linux-dev-x86 ~ $ psql psql (9.1.3) Type help for help. postgres=# create extension rdkit; FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 The connection to the server was lost. Attempting reset: Succeeded. postgres=# /var/log/postgresql/postgres-9.1-main-log doesn't tell me anything extra: 2012-04-24 18:23:32 CEST LOG: invalid value for parameter rdkit.tanimoto_threshold: 0.5 2012-04-24 18:23:32 CEST STATEMENT: create extension rdkit; 2012-04-24 18:23:32 CEST FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 2012-04-24 18:23:32 CEST STATEMENT: create extension rdkit; Being in Denmark, I suspected regional settings, but apparently it is not the issue (?): postgres=# select 7.0/3; ?column? 2. (1 row) postgres=# \q The decimal separator used in Postgres is a period, not a comma as I feared. Any help appreciated :-). Cheers -- Jan Holst Jensen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Trouble install 2012_03_1's PgSQL cartridge in Postgres 9.1.
Dear Jan, On Tue, Apr 24, 2012 at 6:55 PM, Jan Holst Jensen j...@biochemfusion.com wrote: Hi, I am having problems install the Postgres cartridge in Postgres 9.1 on Linux Mint 12 (which is based on Ubuntu 11.10). RDKit 2012_03_1 builds without any issues and all tests pass. good so far. The PgSQL cartridge builds fine too, and installs fine as seen below. jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ sudo make install /bin/mkdir -p '/usr/lib/postgresql/9.1/lib' /bin/mkdir -p '/usr/share/postgresql/9.1/extension' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 755 rdkit.so '/usr/lib/postgresql/9.1/lib/rdkit.so' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit.control '/usr/share/postgresql/9.1/extension/' /bin/sh /usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit--3.1.sql '/usr/share/postgresql/9.1/extension/' jhje@linux-dev-x86 ~/RDKit_2012_03_1/Code/PgSQL/rdkit $ That also looks ok The same thing happens when I try to enable the 'rdkit' extension directly. postgres@linux-dev-x86 ~ $ psql psql (9.1.3) Type help for help. postgres=# create extension rdkit; FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5 The connection to the server was lost. Attempting reset: Succeeded. postgres=# This is an error message that's been reported before, but we never really did find a root cause. I will start from scratch on my VM with Ubuntu 11.10 and take careful notes as I'm doing the installation, then post those on the wiki. I don't have time to do it this morning, but I'll try and get to it tonight or tomorrow a.m. Best, -greg -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
