Post Job File Processing Error Unable To Copy File
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your password (which it never has, so it always fails). You'll
Unable To Copy File /var/spool/torque/spool/
get an email similar to the one below. PBS Job Id: script is written in dos/windows text format 26 Job Name: myJOB Exec host: comp028/38+comp028/37+comp028/36+comp028/35+comp028/34+comp028/33+comp028/32+comp028/31+comp028/30+comp028/29+comp028/28+comp028/27+comp028/10+comp028/9+comp028/8 An error has occurred processing your job, see below. Post
Dos2unix
job file processing error; job 26 on host comp028/38+comp028/37+comp028/36+comp028/35+comp028/34+comp028/33+comp028/32+comp028/31+comp028/30+comp028/29+comp028/28+comp028/27+comp028/10+comp028/9+comp028/8 Unable to copy file /var/spool/torque/spool/26.OU to username@launch:/export/home/username/out *** error from copy Permission denied (publickey,keyboard-interactive). lost connection *** end dos2unix command error output Output retained on that host in: /var/spool/torque/undelivered/26.OU Unable to copy file /var/spool/torque/spool/26.ER to username@launch:/export/home/username/err *** error from copy Permission denied (publickey,keyboard-interactive). lost connection *** end error output Output retained on that host in: /var/spool/torque/undelivered/26.ER To fix this, create a set of SSH keys. $ ssh-keygen -t dsa Accept all defaults, they're fine. Then, have your own account trust your own keys. This will allow you to SSH from yourself to yourself without a password, no matter which node you're on. $ cat ~/.ssh/id_dsa.pub > ~/.ssh/authorized_keys Each machine you then want to SSH to without a password then has to be added to the ~/.ssh/known_hosts file by connecting to it manually. $ ssh launch $ ssh launch.hpc Submit script format Files created on Windows machines usually contain unprintable end-of-line characters which may be misinterpreted by Linux command interpreters (shells). If your submit script is Windows formatted, you will get the following error when trying to submit it: qsub: script is written in DOS/Windows text format If this happens, there is a utility called dos2unix that you can use to convert the text file from DOS/Windows formatting to Linux formatting. $ dos2unix myscript.sub dos2unix: converting file myscript.sub to UNIX format ... Retrieved from "https://www0.sun.ac.za/hpc/index.php?title=Common_errors&oldid=302" Navigation menu Views Page Discussion View source History Personal tools Create account Log in Navigation
to be copied Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi, I'm having an issue with the torque output and error files on our ROCKS cluster. For some reason, they fail to be copied to the proper place after https://www0.sun.ac.za/hpc/index.php?title=Common_errors the job has finished executing and the user gets an email similar to the one attached below. Has anyone experienced anything similar? Any ideas on how to solve? Thanks in advance! -J -- Jason Greenbaum Manager, Bioinformatics Core | jgbaum at https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2011-November/055419.html liai.org La Jolla Institute for Allergy and Immunology PBS Job Id: 571.herman.liai.org Job Name: cufflinks Exec host: compute-0-3/23+compute-0-3/22+compute-0-3/21+compute-0-3/20+compute-0-3/19+compute-0-3/18+compute-0-3/17+compute-0-3/16+compute-0-3/15+compute-0-3/14+compute-0-3/13+compute-0-3/12+compute-0-3/11+compute-0-3/10+compute-0-3/9+compute-0-3/8+compute-0-3/7+compute-0-3/6+compute-0-3/5+compute-0-3/4+compute-0-3/3+compute-0-3/2+compute-0-3/1+compute-0-3/0 An error has occurred processing your job, see below. Post job file processing error; job 571.herman.liai.org on host compute-0-3/23+compute-0-3/22+compute-0-3/21+compute-0-3/20+compute-0-3/19+compute-0-3/18+compute-0-3/17+compute-0-3/16+compute-0-3/15+compute-0-3/14+compute-0-3/13+compute-0-3/12+compute-0-3/11+compute-0-3/10+compute-0-3/9+compute-0-3/8+compute-0-3/7+compute-0-3/6+compute-0-3/5+compute-0-3/4+compute-0-3/3+compute-0-3/2+compute-0-3/1+compute-0-3/0 Unable to copy file /opt/torque/spool/571.herman.liai.org.OU to jgbaum at herman.liai.org :/home/jgbaum/projects/cufflinks/cufflinks_resting.out *** error from copy scp: /home/jgbaum/projects/cufflinks/cufflinks_resting.out: No such file or directory *** end error output Output retained on that host in: /opt/torque/undelivered/571.herman.liai.org.OU Unable to copy file /opt/torque/spool/571.herman.liai.org.ER to jgbaum at herman.liai.org :/home/jgbaum/projects/cufflinks/cufflinks_resting.err *** error from copy scp: /home/jgbaum/projects/cufflinks/cufflinks_resting.err: No such file or directory *** end error output Output retained on that host in: /opt/torque/undelivered/571.herman.liai.org.ER -------------- next part -------------- An HTML attachment was scrubbed... URL: https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/attachments/20111103/81a6db7e/attachment.html Previous message: [Rocks-Discuss] snmp and rocks Next message: [Rocks-Discuss] torque
does the PBS jobmanager handle job dir clean-ups? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi, I have a tricky problem with the PBS jobmanager. Every Sat->Sun midnight, my submit host loses all connectivity to its http://lists.globus.org/pipermail/gt-user/2006-June/000890.html remote jobs. I am using Condor-G and its grid manager. The PBS job manager creates a directory $HOME/.globus/job/