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12-30-2016, 05:55 PM
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#1
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Member
Registered: Apr 2015
Posts: 217
Rep: 
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Installing gridengine in centos 7
Hi there,
I was trying to install gridengine in my centos 7 server. I have downloaded all the rpm files and run
Code:
gridengine-8.1.8-1.el6.x86_64.rpm gridengine-execd-8.1.8-1.el6.x86_64.rpm gridengine-qmon-8.1.8-1.el6.x86_64.rpm
gridengine-debuginfo-8.1.8-1.el6.x86_64.rpm gridengine-qmaster-8.1.8-1.el6.x86_64.rpm
Then I installed the gridengine running sripts at /opt/sge ;
Code:
install_execd install_qmaster inst_sge
And finally got:
Code:
/home/zillur/Desktop/zillur/phd/gridengine/sge
[zillur@genomics sge]$ ps -ef | grep sge
zillur 17809 8994 0 19:50 pts/45 00:00:00 grep --color=auto sge
zillur 29491 1 0 Dec29 ? 00:00:29 /opt/sge/bin/lx-amd64/sge_qmaster
zillur 30216 1 0 Dec29 ? 00:00:20 /opt/sge/bin/lx-amd64/sge_execd
But if I run qsub:
Code:
bash: qsub: command not found...
If I want to restart the daemon:
Code:
[zillur@genomics sge]$ service sgeexec.p6444 stop && sgeexec.p6444 start
Redirecting to /bin/systemctl stop sgeexec.p6444.service
Failed to stop sgeexec.p6444.service: Unit sgeexec.p6444.service not loaded.
Any help with the installation?
Best Regards
Zillur
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12-30-2016, 06:22 PM
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#2
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Senior Member
Registered: Aug 2006
Location: Detroit, MI
Distribution: GNU/Linux systemd
Posts: 4,278
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What do you get if you:
Code:
cd /opt/sge
find . -name qsub*
systemctl list-unit-files | grep sge
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1 members found this post helpful.
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12-30-2016, 06:40 PM
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#3
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Member
Registered: Apr 2015
Posts: 217
Original Poster
Rep: 
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Thank you very much for your reply. Here is the output:
Code:
[zillur@genomics ~]$ cd /opt/sge/
[zillur@genomics sge]$ find . -name qsub*
./man/man1/qsub.1
./bin/lx-amd64/qsub
[zillur@genomics sge]$ systemctl list-unit-files | grep sge
[zillur@genomics sge]$
The last command didn't give anything. Thanks again.
Best Regards
Zillur
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12-30-2016, 07:29 PM
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#4
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Senior Member
Registered: Aug 2006
Location: Detroit, MI
Distribution: GNU/Linux systemd
Posts: 4,278
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Ok. Lets find the name of the service file that was supposed to be installed and its filename.
Code:
for p in $(rpm -qa | grep gridengine); do
rpm -ql $p | grep service
done
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1 members found this post helpful.
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12-30-2016, 08:17 PM
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#5
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Member
Registered: Apr 2015
Posts: 217
Original Poster
Rep: 
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Thank you very much for your reply. Here it is:
Code:
[zillur@genomics sge]$ for p in $(rpm -qa | grep gridengine); do
> rpm -ql $p | grep service
> done
/opt/sge/util/rctemplates/systemd/sgeexecd.service
/opt/sge/util/rctemplates/systemd/sgemaster.service
/opt/sge/util/rctemplates/systemd/sgeshadowd.service
Best Regards
Zillur
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12-30-2016, 09:03 PM
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#6
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Senior Member
Registered: Aug 2006
Location: Detroit, MI
Distribution: GNU/Linux systemd
Posts: 4,278
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Ok so lets add /opt/sge/bin/lx-amd64/ to the system path,. you can do this by user(add to .bash_profile) or system wide(add to /etc/environment).
Code:
echo "PATH=$PATH:/opt/sge/bin/lx-amd64/" >> /etc/environment
or
echo "PATH=$PATH:/opt/sge/bin/lx-amd64/" >> /home/YOURUSER/.bash_profile
Log out, log back in. 'qsub' should work as a command now.
And then use the correct systemd service to start, which looks to me like sgemaster, but might be one of the others according to your output above:
Code:
systemctl start sgemaster
systemctl status sgemaster
Last edited by szboardstretcher; 12-31-2016 at 01:05 PM.
Reason: change semicolon to colon :/
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1 members found this post helpful.
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12-30-2016, 11:25 PM
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#7
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Member
Registered: Apr 2015
Posts: 217
Original Poster
Rep: 
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Thank you very much. Here is current situation:
Code:
[zillur@genomics ~]$ echo "PATH=$PATH;/opt/sge/bin/lx-amd64/" >> /home/zillur/.bash_profile
[zillur@genomics ~]$ logout
Connection to 136.145.231.38 closed.
MacBook-Pro-55:final_project ZILLURRAHMAN$ sudo ssh zillur@136.145.231.38
zillur@136.145.231.38's password:
Last login: Sat Dec 31 01:15:02 2016 from 67.224.154.165
-bash: /opt/sge/bin/lx-amd64/: Is a directory
[zillur@genomics ~]$ qsub
bash: qsub: command not found...
[zillur@genomics ~]$ systemctl start sgemaster
==== AUTHENTICATING FOR org.freedesktop.systemd1.manage-units ===
Authentication is required to manage system services or units.
Authenticating as: Zillur (zillur)
Password:
==== AUTHENTICATION COMPLETE ===
Failed to start sgemaster.service: Unit not found.
[zillur@genomics ~]$ systemctl status sgemaster
Unit sgemaster.service could not be found.
Then again:
Code:
[zillur@genomics ~]$ echo "PATH=$PATH;/opt/sge/bin/lx-amd64/" >> /etc/environment
-bash: /etc/environment: Permission denied
[zillur@genomics ~]$ sudo echo "PATH=$PATH;/opt/sge/bin/lx-amd64/" >> /etc/environment
-bash: /etc/environment: Permission denied
[zillur@genomics ~]$ sudo echo "PATH=$PATH;/opt/sge/bin/lx-amd64/" >> /etc/environment
-bash: /etc/environment: Permission denied
[zillur@genomics ~]$ su
Password:
[root@genomics zillur]# echo "PATH=$PATH;/opt/sge/bin/lx-amd64/" >> /etc/environment
[root@genomics zillur]# exit
exit
[zillur@genomics ~]$ logout
Connection to 136.145.231.38 closed.
MacBook-Pro-55:final_project ZILLURRAHMAN$ sudo ssh zillur@136.145.231.38
zillur@136.145.231.38's password:
Last login: Sat Dec 31 01:16:36 2016 from 67.224.154.165
-bash: /opt/sge/bin/lx-amd64/: Is a directory
[zillur@genomics ~]$ qsub
bash: qsub: command not found...
[zillur@genomics ~]$ systemctl start sgemaster
==== AUTHENTICATING FOR org.freedesktop.systemd1.manage-units ===
Authentication is required to manage system services or units.
Authenticating as: Zillur (zillur)
Password:
==== AUTHENTICATION COMPLETE ===
Failed to start sgemaster.service: Unit not found.
What should I do now?
Best Regards
Zillur
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12-31-2016, 07:56 AM
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#8
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Senior Member
Registered: Dec 2011
Location: Simplicity
Distribution: Mint/MATE
Posts: 3,052
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There was a mistake in the advice given. Should have been
Code:
echo "PATH=$PATH:/opt/sge/bin/lx-amd64/"
Please change the semicolon to a colon! (with a text editor)
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1 members found this post helpful.
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12-31-2016, 12:56 PM
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#9
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Member
Registered: Apr 2015
Posts: 217
Original Poster
Rep: 
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Thank you very much. I think bash_profile related problem is solved. Now I have another problem:
Code:
Unable to initialize environment because of error: Please set the environment variable SGE_ROOT.
Exiting.
99 jobs submitted as array task
Job ID:
Thank you again. What should I do now?
Best Regards
Zillur
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12-31-2016, 01:07 PM
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#10
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Senior Member
Registered: Aug 2006
Location: Detroit, MI
Distribution: GNU/Linux systemd
Posts: 4,278
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You are going to have to read about the gridengine and how it works to decide where to put SGE_ROOT, i cannot do that for you. http://gridscheduler.sourceforge.net...e_shadowd.html
Setting it is as easy as the PATH variable, just throw it in bash_profile like:
SGE_ROOT=/some/path
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1 members found this post helpful.
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12-31-2016, 04:41 PM
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#11
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Senior Member
Registered: Dec 2011
Location: Simplicity
Distribution: Mint/MATE
Posts: 3,052
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I guess it is
Code:
export SGE_ROOT=/opt/sge
to be added to the bash_profile as well.
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1 members found this post helpful.
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01-04-2017, 02:33 PM
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#12
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Member
Registered: Apr 2015
Posts: 217
Original Poster
Rep: 
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Thank you very much for your kind suggestions. after
Code:
export SGE_ROOT=/opt/sge
I got a new problem. Here it is:
Code:
[zillur@genomics idmapping]$ perl split_blast_queries_edwardsSteve.pl -f /home/zillur/Desktop/zillur/phd/orthofinder/fasta/PlasmoDB-28_Pfalciparum3D7_AnnotatedProteins.fasta -db /home/zillur/Desktop/zillur/phd/blast/blast/db/nrdb -d output/ -n 100
Unable to run job: denied: host "genomics.rrp.campus" is not submit host
Exiting.
99 jobs submitted as array task
Job ID:
Here is my host:
Code:
[zillur@genomics idmapping]$ hostnamectl status
Static hostname: genomics
Icon name: computer-server
Chassis: server
Machine ID: ****
Boot ID: &*****
Operating System: CentOS Linux 7 (Core)
CPE OS Name: cpe:/o:centos:centos:7
Kernel: Linux 3.10.0-514.2.2.el7.x86_64
Architecture: x86-64
What should I do now?
Best Regards
Zillur
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01-04-2017, 03:37 PM
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#13
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LQ Muse
Registered: Aug 2005
Location: A2 area Mi.
Posts: 17,710
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you are aware that this is a CentOS 6 ( el6) rpm on CentOS 7 !
this will likely cause major problems
one being rhel6 uses systemV and rhel7 uses systemD
use the cent7 rpm ( el7 )
Last edited by John VV; 01-04-2017 at 03:38 PM.
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1 members found this post helpful.
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01-04-2017, 03:58 PM
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#14
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Member
Registered: Apr 2015
Posts: 217
Original Poster
Rep: 
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Thank you very much for your comments. How can I get el7 rpms? I got the latest rpm from here:
Code:
https://arc.liv.ac.uk/downloads/SGE/releases/8.1.9/
Best Regards
Zillur
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01-04-2017, 04:08 PM
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#15
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LQ Muse
Registered: Aug 2005
Location: A2 area Mi.
Posts: 17,710
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grab the source and build it
rhel6 and rhel7 ( or centos and sl ) are VERY VERY different operating systems
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1 members found this post helpful.
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