Re: [SGE-discuss] Fwd: Error at the time of Distribution staging
On Tue, Nov 15, 2016 at 4:17 PM, William Hay <w@ucl.ac.uk> wrote: > On Tue, Nov 15, 2016 at 10:44:01AM +0530, Himanshu Joshi wrote: > >On Mon, Nov 14, 2016 at 8:41 PM, William Hay <w@ucl.ac.uk> wrote: > > > > On Mon, Nov 14, 2016 at 06:03:43PM +0530, Himanshu Joshi wrote: > > >Thanks William > > >On Fri, Nov 11, 2016 at 10:31 PM, William Hay <w@ucl.ac.uk > > > > wrote: > > > > > > On Thu, Nov 10, 2016 at 02:26:35PM +0530, Himanshu Joshi > wrote: > > > > I suspect you probably want to use inst_sge to > configure > > the node > > > as an > > > > execd as well. > > > > > > > >Is there any documentation available for doing that > because > > I do > > > not have > > > >any idea how to do it > > > http://arc.liv.ac.uk/SGE/howto/commontasks.html > > > If you are just making the initial qmaster into an execution > host > > as > > > well > > > then changing to $SGE_ROOT and running ./install_execd > should do > > it. > > > > > > > > >It worked, Now Execution daemon installed successfully. But I > am > > not sure > > >whether the nodes are configured or not... > > > > > > Make sure you have SGE_ROOT set correctly first (see below) > > > > > > >And I tried some computations with the current setup but > > some of > > > the > > > >errors were > > > > > > > >Error: which: no qconf in (/usr/local.. ) > > > >Warning SGE_ROOT environment variable is set but Grid > Engine > > > software is > > > >not found, will run locally > > > If you installed Dave's packages then they install into > /opt/sge > > by > > > default so set the > > > SGE_ROOT environment variable to point to that. > > > > > > sourcing /opt/sge/default/common/seetings.sh should set up > the > > > enironment. > > > changes done in .bashrc file as suggested > > > > > > > >And there is no folder gridengine in usr/share/doc > > > >Thus it indicates the software is not at all installed > > > Dave's packages are designed to be installed under /opt and > don't > > > stick things into /usr/share/doc. > > > > > > William > > > > > >Please find below the outputs of few of the configuration > commands > > >(without using sudo) in my terminal > > > > > >"qconf -sh" shows > > >mbialjpj > > > > > >"qconf -sel" shows > > >no execution host defined > > > > > >"qconf -ae" shows > > >denied: "JPJ" must be manager for this operation" > > iRunning qconf -ae as root so you can add a host should do it. > > > >If I understand this one liner correctly, you mean to say the qconf > -ae > >newhost can add "newhost". But as a root using this command says > qconf: > >Command not found. > As root: > source /opt/sge/default/common/settings.sh > qconf -ae > Thanks,Please find the outputs and advise [root@mbialjpj ~]# source /opt/sge/default/common/settings.sh SGE_ROOT=/opt/sge: Command not found. export: Command not found. SGE_ROOT: Undefined variable. [root@mbialjpj ~]# qconf -ae qconf: Command not found. [root@mbialjpj ~]# $SGE_ROOT SGE_ROOT: Undefined variable. [root@mbialjpj ~]# which $SGE_ROOT SGE_ROOT: Undefined variable. and without sudo -i..the outputs are like this [JPJ@mbialjpj ~]$ $SGE_ROOT bash: /opt/sge: Is a directory [JPJ@mbialjpj ~]$ which $SGE_ROOT /usr/bin/which: no sge in (/opt [JPJ@mbialjpj ~]$ qconf -ae denied: "JPJ" must be manager for this operation [JPJ@mbialjpj ~]$ qconf -ae newhost denied: "JPJ" must be manager for this operation Regards > > > > > > > William > > > >Kindly suggest the needful > >-- > >Himanshu Joshi > >M.Tech. Cognitive & Neuroscience. > >Ph.D Scholar, > >Department of Psychiatry > >NIMHANS, Bangalore > >Publications > >Multimodal Brain Image Analysis Laboratory > Kindly advise the needful -- Himanshu Joshi ___ SGE-discuss mailing list SGE-discuss@liv.ac.uk https://arc.liv.ac.uk/mailman/listinfo/sge-discuss
Re: [SGE-discuss] Fwd: Error at the time of Distribution staging
Dear all, Can you please edit my_configuration.conf file and help help in setting up the nodes as an execd. so I can use the following command for the entire installation ./inst_sge -m -auto /opt/sge/util/install_modules/my_configuration.conf Please find attached my_configuration.conf file and do the needful Regards Himanshu On Thu, Nov 10, 2016 at 2:26 PM, Himanshu Joshi <anshuhi...@gmail.com> wrote: > > > On Wed, Nov 9, 2016 at 6:56 PM, William Hay <w@ucl.ac.uk> wrote: > >> On Wed, Nov 09, 2016 at 04:59:18PM +0530, Himanshu Joshi wrote: >> >On Wed, Nov 9, 2016 at 2:18 PM, William Hay <w@ucl.ac.uk> wrote: >> > >> > On Wed, Nov 09, 2016 at 11:25:42AM +0530, Himanshu Joshi wrote: >> > >On Tue, Nov 8, 2016 at 9:38 PM, William Hay <w@ucl.ac.uk> >> > wrote: >> > > >> > > On Tue, Nov 08, 2016 at 11:30:35AM +0530, Himanshu Joshi >> wrote: >> > > > I'd try running the command >> > > > >> > > > /usr/lib/lsb/install_initd >> > /etc/init.d/sgemaster.mbialjpj55||echo >> > > $? >> > > > >> > > > To see if it produces any output. >> > > > >> > > >Yes the output for this command is >> > > >1 >> > > Annoyingly silent error. >> > > >> > >Ya true.. >> > > >> > > What does >> > > ls -l /etc/rc.d/rc3.d/*sge* >> > > output if anything? >> > > >> > >It says " no match" >> > > i.e. /etc/rc.d/rc3.d folder has no file with *sge* >> > > >> > > > >> > > >command "ps ax |grep sge" says >> > > > >> > > >17870 pts/4S+ 0:00 grep --color=auto sge >> > > >26341 ?S10557:34 /bin/sh ./inst_sge -m -x >> > > You have a copy of inst_sge running eating that amount of >> cpu >> > time? Was >> > > that intentionally still running? >> > > >> > >I was not running it intentionally , and system monitor also >> does >> > not show >> > >any process with name "inst_sge". I had tried closing all the >> > terminals >> > >and restarted the system >> > > >> > >now the output is >> > >8160 pts/0S+ 0:00 grep --color=auto sge >> > IIRC the installation of the init script is the last thing >> inst_sge does >> > so >> > if this is the only thing blocking the install then you just need >> to >> > set the file up by hand >> > >> > Try the install_initd command by hand again now that there isn't a >> > running inst_sge >> > >> >The ./install_initd says >> If you leave out the ./ it will search the path. >> >> >Command not found >> >I think this file (install_initd) is not available in /opt/sge that >> is why >> >command not found >> > >> > >> > If that doesn't work try: >> > >> > chkconfig --add sgemaster.mbialjpj55 >> > chkconfig sgemaster.mbialjpj55 on >> > service sgemaster.mbialjpj55 start >> > >> > >> > >> > Try running >> > /etc/init.d/sgemaster.mbialjpj55 start >> > by hand does it produce output? >> > >> >It worked and then the output of "ps ax | grep sge" is >> >29305 ?Sl 0:00 /opt/sge/bin/lx-amd64/sge_qmaster >> >29974 pts/0S+ 0:00 grep --color=auto sge >> > >> >Now the below 3 commands are immaterial >> >chkconfig --add sgemaster.mbialjpj55 >> >chkconfig sgemaster.mbialjpj55 on >> >service sgemaster.mbialjpj55 start >> >as these commands say >> Well the first two make sure it will start on reboot. >> >> > >> >"sge_qmaster with PID 29305 is already running" >> > >> > >> > >> > cat /etc/init.d/sgemaster.mbialjpj55 >> > >> > >> > >> > This command displays the contents of sgemas
Re: [SGE-discuss] Fwd: Error at the time of Distribution staging
> > I'd try running the command > > /usr/lib/lsb/install_initd /etc/init.d/sgemaster.mbialjpj55||echo $? > > To see if it produces any output. > Yes the output for this command is 1 > > > > > >Command failed: /usr/lib/lsb/install_initd > >/etc/init.d/sgemaster.mbialjpj55 > > > >Probably a permission problem. Please check file access permissions. > >Check root read/write permission. Check if SGE daemons are running. > > > >I have found the file "sgeqmaster.mbialjpj55" in the location > described > >as /etc/init.d > > and ls -l command gives the file permissions as > > > >-rwxr-xr-x. 1 root root 24883 Nov 7 17:27 sgemaster.mbialjpj55 > > > >How to check if SGE Daemons is running because command "service > >--status-all" reveals > ps ax |grep sge > > should reveal any sge daemons > command "ps ax |grep sge" says 17870 pts/4S+ 0:00 grep --color=auto sge 26341 ?S10557:34 /bin/sh ./inst_sge -m -x > > William > -- Himanshu Joshi ___ SGE-discuss mailing list SGE-discuss@liv.ac.uk https://arc.liv.ac.uk/mailman/listinfo/sge-discuss
Re: [SGE-discuss] Fwd: Error at the time of Distribution staging
On Mon, Nov 7, 2016 at 3:09 PM, William Hay <w@ucl.ac.uk> wrote: > On Sat, Nov 05, 2016 at 10:55:38AM +0530, Himanshu Joshi wrote: > >Redhat enterprise Linux 7.2 with X86-64 architecture > >Please find the requested information with other relevant info > >hostnamectl status > > Static hostname: mbialjpj > > Pretty hostname: MBIALJPJ > > Icon name: computer-desktop > > Chassis: desktop > >Machine ID: 431da268159243088e0e02874e8d36bf > > Boot ID: 24057a4a63554a72b9c7b4b7d9e72b74 > > Operating System: Red Hat Enterprise Linux > > CPE OS Name: cpe:/o:redhat:enterprise_linux:7.2:GA:workstation > >Kernel: Linux 3.10.0-327.el7.x86_64 > > Architecture: x86-64 > > > >I was able to initiate the installation but now stuck up in the same > error > >reported on October 20 > > > > >qmaster startup script > >-- > > > >We can install the startup script that will > >start qmaster at machine boot (y/n) [y] >> > > > >cp /opt/sge/default/common/sgemaster /etc/init.d/sgemaster.mbialjpj55 > >/usr/lib/lsb/install_initd /etc/init.d/sgemaster.mbialjpj55 > > > >Command failed: /usr/lib/lsb/install_initd > >/etc/init.d/sgemaster.mbialjpj55 > Does /usr/lib/lsb/install_initd exist? > Yes it is a folder owned by root On my RHEL7 box this is a relative symlink pointing to /sbin/chkconfig. > Yes exactly because the command " ls -la /usr/lib/lsb | grep "\->" " provides the output as lrwxrwxrwx. 1 root root23 Jun 1 2015 install_initd -> ../../../sbin/chkconfig lrwxrwxrwx. 1 root root23 Jun 1 2015 remove_initd -> ../../../sbin/chkconfig Does it exist on your machine and to what does it point? > Yes it exists with file permissions and it points to /sbin/chkconfig > What are the permissions on the file to which it points? > The following command "ls -l /sbin/chkconfig" says -rwxr-xr-x. 1 root root 41136 Apr 29 2016 /sbin/chkconfig > > > >Probably a permission problem. Please check file access permissions. > >Check root read/write permission. Check if SGE daemons are running. > How to check whether SGE daemons is running? > > > >Looking forward to receive binary packages from Dave because I do not > know > >how to look for the one which my distribution provides > > > Dave's packages for RHEL7 are available by downloading the file at: > https://copr.fedorainfracloud.org/coprs/loveshack/SGE/repo/ > epel-7/loveshack-SGE-epel-7.repo > and placing it in /etc/yum.repos.d > I had made a document file named "loveshack-SGE.repo" and pasted it in /etc/yum.repos.d > Then > yum install gridengine gridengine-qmaster gridengine-qmon gridengine-execd > Then I went into /opt/sge and followed the above command This resolved many dependencies and enabled sufficient repositories > > These install into /opt/sge so if you do switch to using these (which will > simplify future > upgrades) then remove any grid engine install you have there first. > > Again the command "./inst_sge -m -x"" reached upto the process of We can install the startup script that will start qmaster at machine boot (y/n) [y] >> but landed up in the same error i.e. cp /opt/sge/default/common/sgemaster /etc/init.d/sgemaster.mbialjpj55 /usr/lib/lsb/install_initd /etc/init.d/sgemaster.mbialjpj55 Command failed: /usr/lib/lsb/install_initd /etc/init.d/sgemaster.mbialjpj55 Probably a permission problem. Please check file access permissions. Check root read/write permission. Check if SGE daemons are running. I have found the file "sgeqmaster.mbialjpj55" in the location described as /etc/init.d and ls -l command gives the file permissions as -rwxr-xr-x. 1 root root 24883 Nov 7 17:27 sgemaster.mbialjpj55 *How to check if SGE Daemons is running *because command "service --status-all" reveals netconsole module not loaded Configured devices: lo Profile_2 enp0s25 p1p1 Currently active devices: lo p1p1 enp0s25 virbr0 ● rhnsd.service - LSB: Starts the Spacewalk Daemon Loaded: loaded (/etc/rc.d/init.d/rhnsd) Active: active (running) since Thu 2016-10-13 15:44:00 IST; 3 weeks 4 days ago Docs: man:systemd-sysv-generator(8) Main PID: 2453 (rhnsd) CGroup: /system.slice/rhnsd.service └─2453 rhnsd Nov 06 03:13:31 mbialjpj rhnsd[2453]: /etc/sysconfig/rhn/systemid does not exist or is unreadable Nov 06 07:13:31 mbialjpj rhnsd[2453]: /etc/sysconfig/rhn/systemid does not exist or is unreadable Nov 06 11:13:31 mbialjpj rhnsd[2453]: /etc/sysconfig/rhn/systemid does not exist or i
Re: [SGE-discuss] Error at the time of Distribution staging
Thanks William and Love, Now I had downloaded gridengine-8.1.9-1.el6.src and performed rpm -Uvh gridengine-8.1.9-1.el6.src in mu /opt/sge folder as a super user warning: gridengine-8.1.9-1.el6.src.rpm: Header V3 RSA/SHA1 Signature, key ID 92258035: NOKEY Updating / installing... 1:gridengine-8.1.9-1.el6 # [100%] During the process of installation through ./inst_sge -m -x command I got the following error qmaster startup script -- We can install the startup script that will start qmaster at machine boot (y/n) [y] >> *after hitting Return the following error came* cp /opt/sge/default/common/sgemaster /etc/init.d/sgemaster.mbialjpj_cluster /usr/lib/lsb/install_initd /etc/init.d/sgemaster.mbialjpj_cluster Command failed: /usr/lib/lsb/install_initd /etc/init.d/sgemaster.mbialjpj_cluster Probably a permission problem. Please check file access permissions. Check root read/write permission. Check if SGE daemons are running. P.S. I had selected user as "root" . Installing Grid Engine as user >root< Hit to continue >> And I have given cluster name as = "mbialjpj_cluster" Looking forward to hear from the experts Regards On Wed, Oct 19, 2016 at 8:08 PM, Dave Love <d.l...@liverpool.ac.uk> wrote: > Himanshu Joshi <anshuhi...@gmail.com> writes: > > > Dear William, > > Apologies, I am new to the setup or I might be wrong in interpreting the > > suggested solution. > > Can you just help me in making the packages available for RHEL 7 because > > the link you sent (http://copr.fedoraproject.org/coprs/loveshack/SGE/) > does > > not have any package or repositories.for successful installation of SGE, > > unlike the link for RHEL5/RHEL6 or a Debianish version. > > It has links to the .repo files and another about enabling copr > repositories, i.e. what to do with the .repo files to that you can do > "yum install gridengine ...". > -- Himanshu Joshi M.Tech. Cognitive & Neuroscience. Ph.D Scholar, Department of Psychiatry NIMHANS, Bangalore Publications <https://scholar.google.co.in/citations?hl=en=OspDsGUJ_op=list_works=AJsN-F4EvpCnES94r26jSpcDQFnN_-rSpEtp0PNdwObxCjniNpjkL55yPooOzK6epx6bHLvPuwJ2LIL3Wgkvxn4xeZXy5Wh0NpiR4E_Ebq88a1jaCS4r5q14b_4jCaeeDct8aeK15Bxr> Multimodal Brain Image Analysis Laboratory <http://mbial.weebly.com/himanshu-joshi.html> ___ SGE-discuss mailing list SGE-discuss@liv.ac.uk https://arc.liv.ac.uk/mailman/listinfo/sge-discuss
