PBS Pro (public version) Installation on Ubuntu 18.04.2 LTS (Bionic Beaver)


#1

Hi All,

I am currently installing PBS Pro on my workstation. It seems it has been installed properly but it has still an issue regarding to permission and connection to the server. The corresponding log files are as follows:

The installation log:


*** PBS Installation Summary


*** Postinstall script called as follows:
*** /opt/pbs/libexec/pbs_postinstall ‘’


*** Existing configuration file found: /etc/pbs.conf


*** Saving /etc/pbs.conf as /etc/pbs.conf.pre.19.0.0.20190308094945
*** Replacing /etc/pbs.conf with /etc/pbs.conf.19.0.0
*** /etc/pbs.conf has been modified.
*** The original contents have been saved to /etc/pbs.conf.pre.19.0.0.20190308094945


*** Registering PBS Pro as a service.
Synchronizing state of pbs.service with SysV service script with /lib/systemd/systemd-sysv-install.
Executing: /lib/systemd/systemd-sysv-install enable pbs


*** PBS_HOME is /var/spool/pbs
*** Creating new file /var/spool/pbs/pbs_environment
*** WARNING: TZ not set in /var/spool/pbs/pbs_environment


*** The PBS Pro server has been installed in /opt/pbs/sbin.
*** The PBS Pro scheduler has been installed in /opt/pbs/sbin.


*** The PBS Pro communication agent has been installed in /opt/pbs/sbin.


*** The PBS Pro MOM has been installed in /opt/pbs/sbin.


*** The PBS commands have been installed in /opt/pbs/bin.


*** End of /opt/pbs/libexec/pbs_postinstall


The Start PBS log:

Starting PBS
PBS Home directory /var/spool/pbs needs updating.
Running /opt/pbs/libexec/pbs_habitat to update it.


*** Setting default queue and resource limits.


Connecting to PBS dataservice…connected to PBS dataservice@Ehsan
pbs_iff: cannot connect to host
pbs_iff: cannot connect to host
No Permission.
qmgr: cannot connect to server
Connection refused
qmgr: cannot connect to server
Connection refused
qterm: could not connect to server (111)
*** End of /opt/pbs/libexec/pbs_habitat
Home directory /var/spool/pbs updated.
/opt/pbs/sbin/pbs_comm ready (pid=22252), Proxy Name:ehsan:17001, Threads:4
PBS comm
PBS mom
Creating usage database for fairshare.
PBS sched
Connecting to PBS dataservice…connected to PBS dataservice@Ehsan
Licenses valid for 10000000 Floating hosts
PBS server

It would be great if you can give me your comments about the issue.

Thanks in advance for your time and attention.


#2

Try the following steps

  • Some file permissions must be modified to add SUID privilege.
    sudo chmod 4755 /opt/pbs/sbin/pbs_iff /opt/pbs/sbin/pbs_rcp
  • Start the PBS Pro services.
    sudo /etc/init.d/pbs start

#3

Dear kjakkali,
Thanks for your response. I have checked your points so far, but it did not work.

-rwsr-xr-x 1 root root 77704 Mar 7 20:53 pbs_rcp
-rwsr-xr-x 1 root root 1100760 Mar 7 20:53 pbs_iff

bash$ sudo /etc/init.d/pbs start
Starting PBS
/opt/pbs/sbin/pbs_comm ready (pid=871), Proxy Name:ehsanam:17001, Threads:4
PBS comm
PBS mom
Creating usage database for fairshare.
PBS sched
Connecting to PBS dataservice…connected to PBS dataservice@ehsanam
Licenses valid for 10000000 Floating hosts
PBS server


#4

Hi,
Are you still getting following error while starting PBS.

or while executing any pbs commands like ‘pbsnodes -av’ ?


#5

Dear kjakkali,

A the moment, I dont see any error when I start PBS and it says even it connected to dataserver@hotname. However, when I use a PBS command like qstat -B, I face a Error. The log file is as follows:

bash$ . /etc/profile.d/pbs.sh
bash$ sudo /etc/init.d/pbs start
Starting PBS
/opt/pbs/sbin/pbs_comm ready (pid=32097), Proxy Name:ehsan:17001, Threads:4
PBS comm
Creating usage database for fairshare.
PBS sched
Connecting to PBS dataservice…connected to PBS dataservice@Ehsan
Licenses valid for 10000000 Floating hosts
PBS server
bash$ qstat -B
Connection refused
qstat: cannot connect to server Ehsan (errno=111)


#6

@ehsanam : One issue might be due to loop back ip-address.
Can you try adding non loop back IP address of the hostname entry into /etc/hosts file and try restart PBS?


#7

Dear kjakkali,

Tnx again for your help. Now I can run the PBS commands using non-loop IP address. However, I face a problem regarding default queue:

bash$ echo “sleep 60” | qsub
bash$ qsub: No default queue specified.

I am wondering the default queue should be specified during installation or after installation?


#8

@ehsanam : Good to know that.
Please run the pbs_postinstall (ex: libexec/pbs_postinstall) script which will create default queue.


#9

@kjakkali As you suggested, I used the pbs_postinstall script and it solved the issue. Thanks a lot!
However, the job is not executed by qsub and its status is in Q mode. For example:

bash$ echo “sleep 60” | qsub
bash$ qstat -a

S = Q

Should I configure something else in PBS Pro?


#10

@kjakkali

I guess it might be due to lack of resources. When I use pbsnodes -a command, it gives:

pbsnodes: Server has no node list

P.S: I am trying to install PBS Pro on my workstation which has 8 cores.


#11

@kjakkali It got solved by:

root$ # source /etc/profile.d/pbs.sh
root$ # qmgr -c “create node hostname”