HowTo install AliEn from source

Manual

HowTo upgrade to a new AliEn version

Manual

HowTo get debug output

Add "-- debug 5" at the end of the alien call e.g.

"alien login --debug 5"

HowTo add a post install file

This has to be done before the package is added

  • Create a proxy
    • alien proxy-init
  • Login to alien
    • alien login
    • The user is defined . $HOME?.alien/Environment
  • Goto directory where you want to add the file. If the directory don't exist create the directory
    • e.g. mkdir -p packages/panda_extern/0.1
    • e.g. cd packages/panda_extern/0.1
  • Add the file to the file catalog
    • add [filename] [file location on local computer]
    • e.g. add post_install /misc/uhlig/post_install

HowTo add a package

This add the new package to the file catalog

  • Define the package you want to install
    • packman define [name] [version] [file location on local computer] post_install=[location of postinstall file] -platform source -se [SE] -dependencies="list of dependencies"
    • e.g. packman define panda_extern 0.1 /misc/uhlig/cbmsoft_devel_021107.tar.gz post_install=/panda/user/p/pbarprod/packages/panda_extern/0.1/post_install
    • packman define pandaroot 0.4 /misc/uhlig/SVN/ctest/test/pandaroot_r1727.tar.gz dependencies=panda_extern::0.1 post_install=/panda/user/p/pbarprod/packages/pandaroot/0.4/postinstall
    • packman define cbmroot jun09 /misc/cbmgrid/alien_packages/cbmroot/cbmroot_jun09.tar.gz dependencies=cbm_extern::jul08 post_install=/cbm/user/c/cbmgrid/packages/cbmroot/jun09/cbmroot_postinstall_jun09 -platform source -se CBM::GSI::xrdlustre
In the directory there now should be two files post_install and Linux-i686. If there is no difference between i686 and x86_64 copy Linux-i686 to Linux-x86_64. This is normaly correct if you deal with source packages which are compiled on the grid computers. After this step you should be prepared for everything.

HowTo remove a package

  • packman undefine [name] [version] -platform [source][i686][x86_64]

Normally this is done automatically when you submit a job which depends on some packages. But for testing it can be done in a manual fassion

  • Install the package on a dedicate site (CE Computing Element)
    • packman install [package]::[version] [site]
    • e.g. packman install panda_extern::0.1 PANDA::GSI::grid8

HowTo get information about a package

  • packman list -force
  • packman test package
    • packman test cbmroot::dec10
  • packman listInstalled -name [packman instance of this site]
    • packman listInstalled -name CBM::GSI::lxi020_packman

Short tutorial for using Alien

  • Login on lxi027.gsi.de as user cbmgrid
  • Check certificate and if expired create new one
    • alien proxy-info
    • alien proxy-init
  • Login to the alien system
    • alien login
  • Move to jdl directory
    • cd jdl
  • View and describe date1.jdl and date2.jdl
    • cat date1.jdl
  • Submit a job to the grid
    • submit date1.jdl
  • Check job status
    • top (to show all processes)
    • ps trace id (show complete info about process id)
    • ps trace id all (show more verbose output about the job)
    • masterJob id (show status of all subjobs of the masterjob)
    • masterjob id -status status resubmit (resubmit all subjobs which ended in status)
  • Check the output of job with id
    • cat /proc/cbmgrid//job-output/stdout
  • Submit a job with parameters (5)
    • submit dat1.jdl 5
  • Check what the job is doing while execution. The first command shows the files in the workdir. The second command shows the last of the standard output.
    • spy <id> workdir
    • spy <id> stdout tail <nr_of_lines> 

HowTo update/change a host certificate

  • Download the certificate from your CA authority
  • Export the certificate from the browser (Browser dependent)
  • Extract the certificate (public key) into PEM-format. The requested password is the password you defined during the export from the browser.
    • openssl pkcs12 -clcerts -nokeys -in mycert.p12 -out usercert.pem
  • Extract the certificate (private key) into PEM-format. The requested password is the password you defined during the export from the browser. It is important that no passphrase is defined because of the machine certificate.
    • openssl pkcs12 -in mykey.pem -nocerts -nodes -out hostkey.pem
  • Copy the newly created certificates into the right directories
  • Central services
    • hostkey.pem -> ~/.alien/globus/userkey.pem
    • hostkey.pem -> ~/.alien/etc/aliend/ldap/certs/host.key.pem
    • hostkey.pem -> /etc/aliend/ldap/certs/hostkey.pem
    • usercert.pem -> ~/.alien/globus/usercert.pem
    • usercert.pem -> ~/.alien/etc/aliend/ldap/certs/host.cert.pem
    • usercert.pem -> /etc/aliend/ldap/certs/hostcert.pem
  • Site services
    • hostkey.pem -> ~/.alien/globus/userkey.pem
    • usercert.pem -> ~/.alien/globus/usercert.pem

Problems with file quotas

If you see a error message like below it could be that the user exceeds the file quotas.

 Job 1982 inserted from cbmgrid@lxcbm.jinr.ru 
 Job state transition from INSERTING to WAITING
 Job state transition to STARTED    |=|  procinfotime: 1292241432 site: CBM::GSI::lxcbmgrid001_ce started: 1292241432
                                         node: lxb435.gsi.de 
 Job state transition from STARTED    to RUNNING    |=|  procinfotime: 1292241432 site: CBM::GSI::lxcbmgrid001_ce 
                                        started: 1292241432 spyurl: lxb435.gsi.de:8085 node: lxb435.gsi.de 
 Job state transition from RUNNING    to SAVING     |=|  procinfotime: 1292241432 site: CBM::GSI::lxcbmgrid001_ce 
                                         error:  
 Job state transition to ERROR_SV   |=|  procinfotime: 1292241442 site: CBM::GSI::lxcbmgrid001_ce 
                                     spyurl:  finished: 1292241442 
 ENVELOPE ERROR: Uploading file for user (cbmgrid) is denied, file size (727) - total file size quota exceeded.
 Authen has thrown an access exception: [quotaexception]
 Could not store the file /tmp/cbmgrid-work/alien-job-1982/log_archive on any SE. This file is lost!
 THERE WAS AT LEAST ONE FILE, THAT WE COULDN'T STORE ON ANY SE.
 The job finished on the worker node with status ERROR_SV

The file quotas can be changed by the admin. The command to see the quotas is

fquota list -unit G

The command to set the quotas is

fquota set <user> maxTotalSize <size in Bytes>

to set the maximum number of bytes to be used by the user. To set the maximum number of files the command is

fquota set <user> maxNbFiles <number of files>

-- FlorianUhlig - 05 Nov 2007
Topic revision: r19 - 08 Jun 2011, FlorianUhlig
 
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