Issues with PostgresSQL

PBS Pro Installation with source code - Users-Site Administrators - PBS Professional Open Source Project

sxy

By default pbs expect the user postgres to exist in server node.

I have successfully installed open PBS Pro from source code on our EHRL7 cluster server.
I specified these options on the line,

configure --prefix=/usr/physics/pbspro --with-python=/usr/physics/python/anaconda2 --with-pbs-server-home=/var/spool/pbspro --with-pbs-conf-file=/var/spool/pbspro

but I can't see the directory /var/spool/pbspro created and I can't find pbs.conf anywhere.

Thanks,

Sue

ashwathraop

Aug '16

Hello,

Did you run post-install script after "make install"? You should be able to find the script installed under /usr/physics/pbspro/libexec/pbs_postinstall. This script is responsible for creating and/or updating the PBS Pro configuration file and the PBS_HOME directory.

Hope this helps. Also you can refer pbspro/INSTALL file for installation instructions.

Regards,
Ashwath

sxy

Aug '16

thanks.

I would like to put pbs.conf in a different place with a different name. therefore on the building line, I specify this option,

configure ..... --with-pbs-conf-file=/var/spool/pbspro/pbspro.conf

it doesn't work. still /etc/pbs.conf.14.0.1 was created.

Sue

dilip-krishnan

Aug '16

Hi Sxy,
This option seems to be broken, you can raise a bug ticket here
https://pbspro.atlassian.net/secure/Dashboard.jspa4

Regards
Dilip

mkaro

Aug '16

Please set the environment variable PBS_CONF_FILE prior to running pbs_postinstall. It should point to the location where you want the configuration file to live (e.g. /var/spool/pbs/pbs.conf). Make sure you export the environment variable so that it is visible to the script. After you run pbs_postinstall, you will likely need to update /etc/profile.d/pbs.sh and /etc/profile.d/pbs.csh to export PBS_CONF_FILE when users log in.

sxy

Mar 31

Cont.

my PBS_HOME directory doesn't have subdirectory datastore.

Sue

dilip-krishnan

Apr 4

Hi,

By default pbs expect the user postgres to exist in server node. But if you want to use a different user, please use --with-database-user=USER option ( Specify any non-root user account that owns the PBS database,.)
in configure.

Datastore directory is created when dataservice is initialized properly. In your case it failed hence never created.

Regards

mkaro

Apr 5

@dilip-krishnan is correct. I'll add that installing the PostgreSQL package supplied for your Linux distribution should automatically create an account named "postgres". This account only needs to exist on the node where the pbs_server runs. Keep in mind that settings in files like /etc/nsswitch.conf will affect how user accounts are configured.

sxy

Apr 6

Hi, thanks.

I have tried a fresh installation again with this configuration eg.

$ configure --prefix=/usr/physics/pbspro --with-python=/usr/physics/python/anaconda2 --with-database-user=sxy

then

$ /etc/init.d/pbs start
Starting PBS
PBS Home directory /var/spool/pbs needs updating.
Running /usr/physics/pbspro/libexec/pbs_habitat to update it.

---

*** Error initializing the PBS dataservice
Error details:
/usr/bin exists, binaries missing...exiting

pbs_habitat is calling install_db which in turn calls /usr/bin/initdb. However no initdb available on our RHEL7. postgresql-devel-9.2.18-1.el7.x86_64 has been installed on our system via yum. but as shown in my previous email, user postgres does not exist.

is initdb part of postgresql?

any suggestions please? thanks,

Sue

dilip-krishnan

Apr 6

Hi,
Can you check if these postgresql-9.2.18-1.el7.x86_64 & postgresql-server-9.2.18-1.el7.x86_64 packages are installed, if not please install and then try installing PBS. I suspect you missed the 2 step in INSTALL docs, and that these packages are not installed.

Regards.
Dilip

sxy

Apr 10

Hi,

thanks. now postgresql-server-9.2.18-1.el7.x86_64 has been installed.

try it again:

/etc/init.d/pbs start

Starting PBS
PBS Home directory /var/spool/pbspro needs updating.
Running /usr/physics/pbspro/libexec/pbs_habitat to update it.

---

/usr/physics/pbspro/pgsql/pg_upgrade not found
Failed to upgrade PBS Datastore

---

there is no directory in $PBS_EXEC/pgsql on the server.
the following packages were installed via "yum install ..."

rpm -qa | grep postgresql

postgresql-libs-9.2.18-1.el7.x86_64
postgresql-server-9.2.18-1.el7.x86_64
postgresql-devel-9.2.18-1.el7.x86_64
postgresql-9.2.18-1.el7.x86_64

any suggestions? thanks,

Sue

mkaro

Apr 10

CAUTION: The following suggestion will result in deleting your existing PBS Pro configuration. Do NOT follow this suggestion unless you are willing to delete your existing PBS Pro configuration.

You are experiencing this problem due to ticket PP-3063.

The reason PBS Pro is trying to upgrade your database is because it detects a previous installation has already created it. You should be able to delete PBS_HOME (/var/spool/pbs by default) and try restarting by issuing "/etc/init.d/pbs restart".

As noted above, this will delete any previous configuration you have created.

A better suggestion might be to move (mv) /var/spool/pbs to /var/spool/pbs.old so that you can put it back if you need to.

sxy

May 2

Hi,

our pbspro server was rebooted. when I tried to start pbspro:

/etc/init.d/pbs start

Starting PBS
PBS comm
/usr/physics/pbspro/sbin/pbs_comm ready (pid=175159), Proxy Name:headnode.physics.usyd.edu.au:17001, Threads:4
PBS sched
Connecting to PBS dataservice...Failed to start PBS dataservice:[Failed to acquire lock on /var/spool/pbspro/datastore/pbs_dblock. Lock seems to be held by pid: 175438 running on host: headnode.physics.usyd.edu.au - cannot start]
.Failed to start PBS dataservice:[Failed to acquire lock on /var/spool/pbspro/datastore/pbs_dblock. Lock seems to be held by pid: 175438 running on host: headnode.physics.usyd.edu.au - cannot start]
.Failed to start PBS dataservice:[Failed to acquire lock on /var/spool/pbspro/datastore/pbs_dblock. Lock seems to be held by pid: 175438 running on host: headnode.physics.usyd.edu.au - cannot start]
.continuing in background.
PBS server

any ideas about what caused the failure of pbs dataservice?

thanks,

Sue

mkaro

May 2

Hi Sue,

Could you please provide the output of "ps -ef | grep pbs" on your headnode? It's possible there is another instance of the PBS data service already running. If you are certain this is not the case, you could try removing the lock file and restarting PBS.

Thanks,

Mike

sxy

May 3

Hi Mike,

thanks. the problem has been identified.

after system is rebooted (rhel7), system creates directory /var/run/postgresql with postgres as the owner.

however, when pbspro was installed, an existing user was chosen as database user, who is not "postgres".

therefore, the user can not create lock file in /var/run/postgresql owned by "postgres". that caused the failure of starting pbs dataservice.

I suggest that a few lines be added in pbspro/sbin/pbs_dataservice to check the ownership of /var/run/postgresql.

if it is different from the database user defined in /var/spool/pbspro/server_priv/db_user, the ownership should be changed accordingly.

thanks,

Sue

sxy

May 3

are there any options in configurations of dataservice for pbspro to store the lock file within $PBS_HOME?

Sue

sxy

May 4

Hi Micheal,

in your previous email, you mentioned,

actually if the database user name was not specified in pbspro compilation assuming user postgres is used, we would receive a message saying that postgres is not an existing user on the system.

Sue

mkaro

May 7

Hello Sue,

That is an excellent suggestion. As a fellow member of the community, I encourage you to file a ticket on http://pbspro.atlassian.net1

If you are unable to do so, please let me know and I'll file one on your behalf.

Thanks,

Mike

Recommended Links

Softpanorama Recommended

Top articles

Sites

Top articles

Sites

...

Etc

Society

Groupthink : Two Party System as Polyarchy : Corruption of Regulators : Bureaucracies : Understanding Micromanagers and Control Freaks : Toxic Managers :   Harvard Mafia : Diplomatic Communication : Surviving a Bad Performance Review : Insufficient Retirement Funds as Immanent Problem of Neoliberal Regime : PseudoScience : Who Rules America : Neoliberalism  : The Iron Law of Oligarchy : Libertarian Philosophy

Quotes

War and Peace : Skeptical Finance : John Kenneth Galbraith :Talleyrand : Oscar Wilde : Otto Von Bismarck : Keynes : George Carlin : Skeptics : Propaganda  : SE quotes : Language Design and Programming Quotes : Random IT-related quotes :  Somerset Maugham : Marcus Aurelius : Kurt Vonnegut : Eric Hoffer : Winston Churchill : Napoleon Bonaparte : Ambrose Bierce :  Bernard Shaw : Mark Twain Quotes

Bulletin:

Vol 25, No.12 (December, 2013) Rational Fools vs. Efficient Crooks The efficient markets hypothesis : Political Skeptic Bulletin, 2013 : Unemployment Bulletin, 2010 :  Vol 23, No.10 (October, 2011) An observation about corporate security departments : Slightly Skeptical Euromaydan Chronicles, June 2014 : Greenspan legacy bulletin, 2008 : Vol 25, No.10 (October, 2013) Cryptolocker Trojan (Win32/Crilock.A) : Vol 25, No.08 (August, 2013) Cloud providers as intelligence collection hubs : Financial Humor Bulletin, 2010 : Inequality Bulletin, 2009 : Financial Humor Bulletin, 2008 : Copyleft Problems Bulletin, 2004 : Financial Humor Bulletin, 2011 : Energy Bulletin, 2010 : Malware Protection Bulletin, 2010 : Vol 26, No.1 (January, 2013) Object-Oriented Cult : Political Skeptic Bulletin, 2011 : Vol 23, No.11 (November, 2011) Softpanorama classification of sysadmin horror stories : Vol 25, No.05 (May, 2013) Corporate bullshit as a communication method  : Vol 25, No.06 (June, 2013) A Note on the Relationship of Brooks Law and Conway Law

History:

Fifty glorious years (1950-2000): the triumph of the US computer engineering : Donald Knuth : TAoCP and its Influence of Computer Science : Richard Stallman : Linus Torvalds  : Larry Wall  : John K. Ousterhout : CTSS : Multix OS Unix History : Unix shell history : VI editor : History of pipes concept : Solaris : MS DOS :  Programming Languages History : PL/1 : Simula 67 : C : History of GCC development :  Scripting Languages : Perl history   : OS History : Mail : DNS : SSH : CPU Instruction Sets : SPARC systems 1987-2006 : Norton Commander : Norton Utilities : Norton Ghost : Frontpage history : Malware Defense History : GNU Screen : OSS early history

Classic books:

The Peter Principle : Parkinson Law : 1984 : The Mythical Man-Month :  How to Solve It by George Polya : The Art of Computer Programming : The Elements of Programming Style : The Unix Hater’s Handbook : The Jargon file : The True Believer : Programming Pearls : The Good Soldier Svejk : The Power Elite

Most popular humor pages:

Manifest of the Softpanorama IT Slacker Society : Ten Commandments of the IT Slackers Society : Computer Humor Collection : BSD Logo Story : The Cuckoo's Egg : IT Slang : C++ Humor : ARE YOU A BBS ADDICT? : The Perl Purity Test : Object oriented programmers of all nations : Financial Humor : Financial Humor Bulletin, 2008 : Financial Humor Bulletin, 2010 : The Most Comprehensive Collection of Editor-related Humor : Programming Language Humor : Goldman Sachs related humor : Greenspan humor : C Humor : Scripting Humor : Real Programmers Humor : Web Humor : GPL-related Humor : OFM Humor : Politically Incorrect Humor : IDS Humor : "Linux Sucks" Humor : Russian Musical Humor : Best Russian Programmer Humor : Microsoft plans to buy Catholic Church : Richard Stallman Related Humor : Admin Humor : Perl-related Humor : Linus Torvalds Related humor : PseudoScience Related Humor : Networking Humor : Shell Humor : Financial Humor Bulletin, 2011 : Financial Humor Bulletin, 2012 : Financial Humor Bulletin, 2013 : Java Humor : Software Engineering Humor : Sun Solaris Related Humor : Education Humor : IBM Humor : Assembler-related Humor : VIM Humor : Computer Viruses Humor : Bright tomorrow is rescheduled to a day after tomorrow : Classic Computer Humor

The Last but not Least Technology is dominated by two types of people: those who understand what they do not manage and those who manage what they do not understand ~Archibald Putt. Ph.D

The statements, views and opinions presented on this web page are those of the author (or referenced source) and are not endorsed by, nor do they necessarily reflect, the opinions of the Softpanorama society. We do not warrant the correctness of the information provided or its fitness for any purpose. The site uses AdSense so you need to be aware of Google privacy policy. You you do not want to be tracked by Google please disable Javascript for this site. This site is perfectly usable without Javascript.

Last modified: March, 12, 2019