Hi all,

I am facing an issue with qsub command, when a script is issued with qsub as shown below:-

time qsub test.sh Your job 12973 ("test.sh") has been submitted

real 0m59.665s user 0m0.126s sys 0m39.754s

It took 59 sec to generate the job id. Initially there is no delay. Since a week, we are facing this issue.

Kindly suggest how to resolve the issue.

Step to reproduce the bugs:

yum install -y wget tar wget ​http://arc.liv.ac.uk/downloads/SGE/releases/8.1.9/sge-8.1.9.tar.gz tar -xvf sge-8.1.9.tar.gz cd sge-8.1.9 mkdir /opt/sge export SGE_ROOT=/opt/sge yum install -y java-1.8.0-openjdk.x86_64 csh make gcc ant man-1.6f-32.el6 cd source/ sh scripts/bootstrap.sh ./aimk -man -htmlman -with-munge -pam -spool-classic echo y | scripts/distinst -nobdb -local -noexit -allall lx-amd64

I tried this on centos6/amd64 and ubuntu16.04/amd64 (replacing

yum with apt java-1.8.0-openjdk.x86_64 with openjdk-8-jdk man-1.6f-32.el6 with man2html

), and I have the same error. Some binaries are not produced. I am using the last release, the 8.1.9.

The error:

&<--------------------------------------------&< GUI installer part done

sgeinspect dir "../nbgui" does not exist Checking and creating binary directories Installing binaries for lx-amd64 from /root/sge-8.1.9/source/LINUXAMD64 -->

--> /opt/sge/bin/lx-amd64

Installing sge_qmaster cp: cannot stat `sge_qmaster': No such file or directory

... Installing ../3rdparty/remote/LINUXAMD64/rlogin cp: cannot stat `../3rdparty/remote/LINUXAMD64/rlogin': No such file or directory

This command failed: cp ../3rdparty/remote/LINUXAMD64/rlogin /opt/sge/utilbin/lx-amd64/rlogin

chown: cannot access `/opt/sge/utilbin/lx-amd64/rlogin': No such file or directory

This command failed: chown 0 /opt/sge/utilbin/lx-amd64/rlogin

chgrp: cannot access `/opt/sge/utilbin/lx-amd64/rlogin': No such file or directory

This command failed: chgrp 0 /opt/sge/utilbin/lx-amd64/rlogin

chmod: cannot access `/opt/sge/utilbin/lx-amd64/rlogin': No such file or directory

This command failed: chmod 4755 /opt/sge/utilbin/lx-amd64/rlogin

Installing job binaries

Installing work cp: cannot stat `work': No such file or directory

This command failed: cp work /opt/sge/utilbin/lx-amd64/work

chown: cannot access `/opt/sge/utilbin/lx-amd64/work': No such file or directory

This command failed: chown 0 /opt/sge/utilbin/lx-amd64/work

chgrp: cannot access `/opt/sge/utilbin/lx-amd64/work': No such file or directory

This command failed: chgrp 0 /opt/sge/utilbin/lx-amd64/work

chmod: cannot access `/opt/sge/utilbin/lx-amd64/work': No such file or directory

This command failed: chmod 755 /opt/sge/utilbin/lx-amd64/work

Installing shared libraries

&<--------------------------------------------&<

Hello SGE Experts,

I have unzipped sge 8.1.9.tar file and coppied into my /home went to ...../source folder done ./scripts/bootstrap.sh Status: "Build successful.....Run ./aimk" after ./aimk warning [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 with multiple errors like 1.error: package junit.framework does not exist

2. error: cannot find symbol [java] [javac] public static Test

suite() { 3.fail("Unable to modify user qtask file") 4.fail("Unable to create job script"); ...etc.

Kindly advise the needful

Looking forward to hear from you

Regards

-- Himanshu Joshi M.Tech. Cognitive & Neuroscience. Ph.D Scholar, Department of Psychiatry NIMHANS, Bangalore Publications <​https://scholar.google.co.in/citations?hl=en&user=OspDsGUAAAAJ&view_op=list_works&gmla=AJsN-F4EvpCnES94r26jSpcDQFnN_-rSpEtp0PNdwObxCjniNpjkL55yPooOzK6epx6bHLvPuwJ2LIL3Wgkvxn4xeZXy5Wh0NpiR4E_Ebq88a1jaCS4r5q14b_4jCaeeDct8aeK15Bxr> Multimodal Brain Image Analysis Laboratory <​http://mbial.weebly.com/himanshu-joshi.html>