Byte:xsede hqin$ ssh hongqin@login.xsede.org
hongqin@login.xsede.org's password:
Last login: Wed Aug 13 17:38:55 2014 from spelman-fw.spelman.edu
Welcome to the XSEDE Single Sign-On (SSO) Hub!
Your storage on this machine is limited to 100MB.
You may connect from here to any XSEDE resource on which you have an account.
To view a list of sites where you actually have an account, visit:
https://portal.xsede.org/group/xup/accounts
Here are the login commands for common XSEDE resources:
Blacklight: gsissh blacklight.psc.xsede.org
Darter: gsissh gsissh.darter.nics.xsede.org
Gordon Compute Cluster: gsissh gordon.sdsc.xsede.org
Gordon ION: gsissh gordon.sdsc.xsede.org
Keeneland: gsissh gsissh.keeneland.gatech.xsede.org
Mason: gsissh mason.iu.xsede.org
Maverick: gsissh -p 2222 maverick.tacc.xsede.org
Nautilus: gsissh gsissh.nautilus.nics.xsede.org
Open Science Grid: gsissh submit-1.osg.xsede.org
Stampede: gsissh -p 2222 stampede.tacc.xsede.org
SuperMIC: gsissh -p 2222 supermic.cct-lsu.xsede.org
Trestles: gsissh trestles.sdsc.xsede.org
Contact help@xsede.org for any assistance that may be needed.
[hongqin@gw69 ~]$ gsissh blacklight.psc.xsede.org
Last login: Thu Aug 14 21:14:38 2014 from 184.77.11.206
Pittsburgh Supercomputing Center
This system is for the use of authorized users only. Unauthorized use may
be monitored and recorded. In the course of such monitoring or through
system maintenance, the activities of authorized users may be monitored.
By using this system you expressly consent to such monitoring.
Blacklight is unique, for optimal performance see http://www.psc.edu/index.php/computing-resources/blackligh
hqin2@tg-login1:~> module load R
hqin2@tg-login1:~> R -f test.R
#nano -w job1.sh
hqin2@tg-login1:~> module load R
hqin2@tg-login1:~> R -f test.R
hqin2@tg-login1:~> sh job1.sh
job1.sh: line 1: module: command not found
R version 2.15.3 (2013-03-01) -- "Security Blanket"
Copyright (C) 2013 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> x = 4*5
> write(x, "x.txt")
>
hqin2@tg-login1:~> qsub job1.sh
418479.tg-login1.blacklight.psc.teragrid.org
#in the queue as show by qstat
___________________
Note On 2015Jan13Tue,
I logged to blacklight and found the job was executed correctly
hqin2@tg-login1:~> cat job1.sh.e418479
/var/spool/torque/mom_priv/jobs/418479.tg-login1.blacklight.psc.teragrid.org.SC: line 1: module: command not found
/var/spool/torque/mom_priv/jobs/418479.tg-login1.blacklight.psc.teragrid.org.SC: line 2: R: command not found
__________________
hqin2@tg-login1:~> exit
logout
Connection to blacklight.psc.xsede.org closed.
[hongqin@gw69 ~]$ gsissh submit-1.osg.xsede.org
You have 1 active projects you can charge jobs to.
Project Name Balance (CPU Hours) End Date
-------------------------------- ------------------- ------------
TG-MCB140211 100000 08/08/2015
Note that you can still charge to a project with a negative balance, as
long as the project has not reached its end date. A project with a
negative balance may result in jobs being given lower priority.
When submitting jobs, please specify what project to charge to with a
+ProjectName line in your HTCondor submit file. For example:
+ProjectName = "TG-MCB140211"
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Your current filesystem usages and quotas are:
/home 0% used (28.0 KB of 20.0 GB)
/local-scratch 0% used (0.0 B of 2.0 TB)
NOTE: The /local-scratch filesystem automatically deletes files older than
90 days.
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
2015-01-12 03:27:40 UTC [hongqin@xd-login:~]$
2015-01-12 03:43:03 UTC [hongqin@xd-login:~]$ cat testOSH.sub
universe = vanilla
+ProjectName = "TG-MCB140211"
executable = testOSH.sh
output = job.out
error = job.err
log = job.log
notification = NEVER
queue
[hongqin@gw69 ~]$ pwd
/home/hongqin
[hongqin@gw69 ~]$ gsissh blacklight.psc.xsede.org
Last login: Sun Jan 11 22:04:05 2015 from gw69.iu.xsede.org
Pittsburgh Supercomputing Center
This system is for the use of authorized users only. Unauthorized use may
be monitored and recorded. In the course of such monitoring or through
system maintenance, the activities of authorized users may be monitored.
By using this system you expressly consent to such monitoring.
Blacklight is unique, for optimal performance see http://www.psc.edu/index.php/computing-resources/blacklight
hqin2@tg-login1:~> ls
job1.sh job2.pbs test.R test.txt x.txt
hqin2@tg-login1:~> ll
total 20
-rw-r--r-- 1 hqin2 mc48o9p 26 2015-01-11 22:13 job1.sh
-rw-r--r-- 1 hqin2 mc48o9p 38 2015-01-11 22:23 job2.pbs
-rw-r--r-- 1 hqin2 mc48o9p 26 2014-08-13 17:42 test.R
-rw-r--r-- 1 hqin2 mc48o9p 12 2014-08-13 17:41 test.txt
-rw-r--r-- 1 hqin2 mc48o9p 3 2015-01-11 22:13 x.txt
hqin2@tg-login1:~> qstat | grep qin
418479.tg-login1 job1.sh hqin2 0 Q batch_r
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