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:
yum install *.rpm 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 Code:
install_execd install_qmaster inst_sge Code:
/home/zillur/Desktop/zillur/phd/gridengine/sge Code:
bash: qsub: command not found... Code:
[zillur@genomics sge]$ service sgeexec.p6444 stop && sgeexec.p6444 start Best Regards Zillur |
What do you get if you:
Code:
cd /opt/sge |
Thank you very much for your reply. Here is the output:
Code:
[zillur@genomics ~]$ cd /opt/sge/ Best Regards Zillur |
Ok. Lets find the name of the service file that was supposed to be installed and its filename.
Code:
for p in $(rpm -qa | grep gridengine); do |
Thank you very much for your reply. Here it is:
Code:
[zillur@genomics sge]$ for p in $(rpm -qa | grep gridengine); do Zillur |
Ok so lets add /opt/sge/bin/lx-amd64/ to the system path,. you can do this by user(add to .bash_profile) or system wide(add to /etc/environment).
Code:
echo "PATH=$PATH:/opt/sge/bin/lx-amd64/" >> /etc/environment 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 |
Thank you very much. Here is current situation:
Code:
[zillur@genomics ~]$ echo "PATH=$PATH;/opt/sge/bin/lx-amd64/" >> /home/zillur/.bash_profile Code:
[zillur@genomics ~]$ echo "PATH=$PATH;/opt/sge/bin/lx-amd64/" >> /etc/environment Best Regards Zillur |
There was a mistake in the advice given. Should have been
Code:
echo "PATH=$PATH:/opt/sge/bin/lx-amd64/" |
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. Best Regards Zillur |
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 |
I guess it is
Code:
export SGE_ROOT=/opt/sge |
Thank you very much for your kind suggestions. after
Code:
export SGE_ROOT=/opt/sge 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 Code:
[zillur@genomics idmapping]$ hostnamectl status Best Regards Zillur |
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 ) |
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/ Zillur |
grab the source and build it
rhel6 and rhel7 ( or centos and sl ) are VERY VERY different operating systems |
Thank you very much for your comment. How can I get the source?
Quote:
Zillur |
how to get the source
read the page you posted the link to https://arc.liv.ac.uk/downloads/SGE/releases/8.1.9/ there is a LOT of information on that link ( under the rpm's ) there is a SRC file " gridengine-8.1.9-1.el5.src.rpm" that you can use "rpmbuild" on in cent7.3 to build a rpm from there is the "sge-8.1.9.tar.gz" you can also read the README file on that page https://arc.liv.ac.uk/downloads/SGE/...1.9/README.txt |
2 Attachment(s)
Thank you very much for your comments. I was trying to install from "sge-8.1.9.tar.gz" but it didn't go well. I don't what I need to do after "./aimk". So I tried to use the GUI installer. It is also showing me the attached error "Can't resolve user name from current directory". Is there any way so I can install gridengine.
Best regards Zillur |
for starters you REALLY do not want to install that on your normal users DESKTOP
SElinux will likely through a temper tantrum ( terrible 2's type ) normally you would use a install directory like /usr /usr/opt or /usr/www to install something like this also keep in mind that rhel( cent) 7 uses SystemD !!!!!! and rhel5 & 6 uses SystemV !!! are there errors when fallowing the instructions ? https://arc.liv.ac.uk/trac/SGE/#Building and have you read the README from the tarbal ? sge-8.1.9/source/README.BUILD |
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