Thread: [Rdkit-discuss] Trouble installing 2012_03_1's PgSQL cartridge in Postgres 9.1. [Follow-up #2- on 6
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From: Jan H. J. <ja...@bi...> - 2012-04-26 22:30:49
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Dear Greg, I can again reproduce the Postgres 9.1 issue, this time in a brand new 64-bit VM. Ubuntu 10.04.2 x86_64 server installed from scratch. gnome-desktop-environment installed, VMware tools installed. jhje@ubuntu-x64-build:~$ cat /etc/issue Ubuntu 10.04.2 LTS \n \l jhje@ubuntu-x64-build:~$ uname -a Linux ubuntu-x64-build 2.6.32-28-server #55-Ubuntu SMP Mon Jan 10 23:57:16 UTC 2011 x86_64 GNU/Linux jhje@ubuntu-x64-build:~$ Packages build-essential, bison, flex, boost libraries, numpy, cmake installed. RDKit_2012_03_1 builds (after the needed one-line patch to Wrap.h) and all tests pass. Installed OpenSCG postgresql 9.1.3 package (latest postgres for Ubuntu 10.04.2 is Pg 8.5, so not interesting). Set "trust" authentication for local connections in pg_hba.conf so rdkit postgres test suite can run without prompting for password. postgres@ubuntu-x64-build:~$ createuser jhje Shall the new role be a superuser? (y/n) y postgres@ubuntu-x64-build:~$ jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ . /opt/postgres/9.1/pg91-openscg.env jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make ... builds with the usual 3-4 warnings ... jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo su - [sudo] password for jhje: root@ubuntu-x64-build:~# cd /home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/ root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# . /opt/postgres/9.1/pg91-openscg.env root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# make install /bin/mkdir -p '/opt/postgres/9.1/lib/postgresql' /bin/mkdir -p '/opt/postgres/9.1/share/postgresql/extension' /bin/sh /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 755 rdkit.so '/opt/postgres/9.1/lib/postgresql/rdkit.so' /bin/sh /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit.control '/opt/postgres/9.1/share/postgresql/extension/' /bin/sh /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh -c -m 644 ./rdkit--3.1.sql '/opt/postgres/9.1/share/postgresql/extension/' root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=. --psqldir='/opt/postgres/9.1/bin' --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps (using postmaster on Unix socket, port 5432) ============== 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 ... FAILED (test process exited with exit code 2) test props ... FAILED test btree ... FAILED test molgist ... FAILED test bfpgist-91 ... FAILED test sfpgist ... FAILED test slfpgist ... FAILED test fps ... FAILED ====================== 8 of 8 tests failed. ====================== The differences that caused some tests to fail can be viewed in the file "/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.diffs". A copy of the test summary that you see above is saved in the file "/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.out". make: *** [installcheck] Error 1 jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ less regression.diffs [... ...] --- 4,9 ---- -- SET client_min_messages = warning; \set ECHO none ! FATAL: failed to initialize rdkit.dice_threshold to 0.5 ! FATAL: failed to initialize rdkit.dice_threshold to 0.5 ! connection to server was lost OK, this time around it is the dice_threshold instead of the tanimoto_threshold that cannot be initialized, but still... Hmmm... 'less' is reporting a linking issue, but only when the postgres environment has been loaded: jhje@ubuntu-x64-build:~$ less Missing filename ("less --help" for help) jhje@ubuntu-x64-build:~$ . /opt/postgres/9.1/pg91-openscg.env jhje@ubuntu-x64-build:~$ less less: Symbol `ospeed' has different size in shared object, consider re-linking Missing filename ("less --help" for help) jhje@ubuntu-x64-build:~$ echo $LD_LIBRARY_PATH /opt/postgres/9.1/lib: jhje@ubuntu-x64-build:~$ Could a library conflict be what causes rdkit to abort ? Kind regards -- Jan |
From: Adrian S. <adr...@gm...> - 2012-04-27 09:03:20
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Hi, I'm using the RDKit PostgreSQL cartridge on the same Ubuntu architecture. I think it is a problem with the OpenSCG package, you should use the following repository instead: ppa:pitti/postgresql. He is also the official maintainer of the Ubuntu PostgreSQL packages; with those everything works as expected. Adrian On Thu, Apr 26, 2012 at 23:31, Jan Holst Jensen <ja...@bi...> wrote: > Dear Greg, > > I can again reproduce the Postgres 9.1 issue, this time in a brand new > 64-bit VM. > > Ubuntu 10.04.2 x86_64 server installed from scratch. > gnome-desktop-environment installed, VMware tools installed. > > > jhje@ubuntu-x64-build:~$ cat /etc/issue > Ubuntu 10.04.2 LTS \n \l > > jhje@ubuntu-x64-build:~$ uname -a > Linux ubuntu-x64-build 2.6.32-28-server #55-Ubuntu SMP Mon Jan 10 > 23:57:16 UTC 2011 x86_64 GNU/Linux > jhje@ubuntu-x64-build:~$ > > > Packages build-essential, bison, flex, boost libraries, numpy, cmake > installed. > > RDKit_2012_03_1 builds (after the needed one-line patch to Wrap.h) and > all tests pass. > > Installed OpenSCG postgresql 9.1.3 package (latest postgres for Ubuntu > 10.04.2 is Pg 8.5, so not interesting). > > Set "trust" authentication for local connections in pg_hba.conf so rdkit > postgres test suite can run without prompting for password. > > > postgres@ubuntu-x64-build:~$ createuser jhje > Shall the new role be a superuser? (y/n) y > postgres@ubuntu-x64-build:~$ > > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ . > /opt/postgres/9.1/pg91-openscg.env > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make > ... builds with the usual 3-4 warnings ... > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ > > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo su - > [sudo] password for jhje: > root@ubuntu-x64-build:~# cd /home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/ > root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# . > /opt/postgres/9.1/pg91-openscg.env > root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# make > install > /bin/mkdir -p '/opt/postgres/9.1/lib/postgresql' > /bin/mkdir -p '/opt/postgres/9.1/share/postgresql/extension' > /bin/sh > /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh > -c -m 755 rdkit.so '/opt/postgres/9.1/lib/postgresql/rdkit.so' > /bin/sh > /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh > -c -m 644 ./rdkit.control '/opt/postgres/9.1/share/postgresql/extension/' > /bin/sh > /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh > -c -m 644 ./rdkit--3.1.sql '/opt/postgres/9.1/share/postgresql/extension/' > root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# > > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck > /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress > --inputdir=. --psqldir='/opt/postgres/9.1/bin' > --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 > sfpgist slfpgist fps > (using postmaster on Unix socket, port 5432) > ============== 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 ... FAILED (test process exited with exit > code 2) > test props ... FAILED > test btree ... FAILED > test molgist ... FAILED > test bfpgist-91 ... FAILED > test sfpgist ... FAILED > test slfpgist ... FAILED > test fps ... FAILED > > ====================== > 8 of 8 tests failed. > ====================== > > The differences that caused some tests to fail can be viewed in the > file "/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.diffs". A > copy of the test summary that you see > above is saved in the file > "/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.out". > > make: *** [installcheck] Error 1 > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ > > > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ less > regression.diffs > [... ...] > --- 4,9 ---- > -- > SET client_min_messages = warning; > \set ECHO none > ! FATAL: failed to initialize rdkit.dice_threshold to 0.5 > ! FATAL: failed to initialize rdkit.dice_threshold to 0.5 > ! connection to server was lost > > OK, this time around it is the dice_threshold instead of the > tanimoto_threshold that cannot be initialized, but still... > > Hmmm... 'less' is reporting a linking issue, but only when the postgres > environment has been loaded: > > jhje@ubuntu-x64-build:~$ less > Missing filename ("less --help" for help) > jhje@ubuntu-x64-build:~$ . /opt/postgres/9.1/pg91-openscg.env > jhje@ubuntu-x64-build:~$ less > less: Symbol `ospeed' has different size in shared object, consider > re-linking > Missing filename ("less --help" for help) > jhje@ubuntu-x64-build:~$ echo $LD_LIBRARY_PATH > /opt/postgres/9.1/lib: > jhje@ubuntu-x64-build:~$ > > Could a library conflict be what causes rdkit to abort ? > > 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 > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss |
From: Jan H. J. <ja...@bi...> - 2012-04-27 11:58:26
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On 2012-04-27 11:02, Adrian Schreyer wrote: > Hi, > > I'm using the RDKit PostgreSQL cartridge on the same Ubuntu > architecture. I think it is a problem with the OpenSCG package, you > should use the following repository instead: ppa:pitti/postgresql. He > is also the official maintainer of the Ubuntu PostgreSQL packages; > with those everything works as expected. > > Adrian Hi Adrian, Thanks for the pointer! This solves it for my Ubuntu 10.04.2 server. And Greg - I could successfully build and run the cartridge on a plain vanilla Ubuntu 11.10; see below. On Linux Mint 12 I wasn't able to get this solution to work. The ppa repositories conflict with the packages on Linux Mint. Even though I pinned the ppa repository to have a higher priority than Ubuntu packages - here in /etc/apt/preferences: Package: * Pin: release o=linuxmint Pin-Priority: 700 Package: * Pin: origin packages.linuxmint.com Pin-Priority: 700 Package: * Pin: origin ppa.launchpad.net Pin-Priority: 650 Package: * Pin: release o=Ubuntu Pin-Priority: 600 This only resulted in postgresql-common being installed from ppa.launchpad.net - the postgres server package was still being installed from the Ubuntu archives and I still have the rdkit install failure. I think I will just note that Linux Mint doesn't play nice with RDKit and move on :-). Cheers -- Jan ________________________ Ubuntu 11.10 x64 basic server install in VMware 7.1.5. add packages gnome-desktop-environment xinit build-essential install vmware-tools add packages cmake flex bison libboost-dev libboost-regex-dev libboost-python-dev python-numpy Build RDKit_2012_03_1 - all tests pass. add packages postgresql-9.1 postgresql-server-dev-9.1 run "createuser jhje" as the postgres user - make the new user a superuser cd to the rdkit cartridge dir - as the "jhje" user. run "make" run "make install" run "make installcheck" - all tests pass. _________________________ Ubuntu 10.04.2 server with OpenSCG Postgres 9.1 installed. The rdkit cartridge was failing to install. I stopped the OpenSCG Postgres 9.1 service. Then added the following to /etc/apt/sources.list: deb http://ppa.launchpad.net/pitti/postgresql/ubuntu lucid main deb-src http://ppa.launchpad.net/pitti/postgresql/ubuntu lucid main apt-get update apt-get install postgresql-9.1 postgresql-server-dev-9.1 Re-built the rdkit cartridge using the new 9.1 postgres package. jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export RDBASE=/home/jhje/RDKit_2012_03_1/ jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export LD_LIBRARY_PATH=/home/jhje/RDKit_2012_03_1/lib/ jhje@ubuntu-x64-build:~/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-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make ... bla bla bla ... jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo make install [sudo] password for jhje: /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@ubuntu-x64-build:~/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. ===================== jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ jhje@ubuntu-x64-build:~$ ldd /usr/lib/postgresql/9.1/lib/rdkit.so linux-vdso.so.1 => (0x00007fff2f1bc000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f7581515000) libm.so.6 => /lib/libm.so.6 (0x00007f7581292000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f758107a000) libc.so.6 => /lib/libc.so.6 (0x00007f7580cf7000) /lib64/ld-linux-x86-64.so.2 (0x00007f7581c0d000) jhje@ubuntu-x64-build:~$ |
From: Greg L. <gre...@gm...> - 2012-04-27 12:24:16
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Dear Jan, On Fri, Apr 27, 2012 at 1:58 PM, Jan Holst Jensen <ja...@bi...> wrote: > > And Greg - I could successfully build and run the cartridge on a plain > vanilla Ubuntu 11.10; see below. I'm glad to hear it! > This only resulted in postgresql-common being installed from > ppa.launchpad.net - the postgres server package was still being installed > from the Ubuntu archives and I still have the rdkit install failure. I think > I will just note that Linux Mint doesn't play nice with RDKit and move on > :-). That's a good data point to have. -greg |