WMSX examples

Note1: There is an installed copy of WMSX software on the KFKI AFS. To activate it, follow the instructions of that homepage.

Note2: The WMSX can work without the User Interface environment. For this, you only need an installed copy of WMSX on your computer, the usual ~/.globus/usercert.pem, ~/.globus/userkey.pem files and the ~/.glite directory as on any User Interface machine, plus you need to provide the ~/.globus/certificates directory, which can be obtained from any User Interface machine from /etc/grid-security/certificates. These files and directories can also be relocated by the X509_USER_CERT, X509_USER_KEY, GLITE_USER_HOME and X509_CERT_DIR environmental variables.

Note3: If your home directory is located on AFS, it is advised to source the following shell script before logging on to the Grid:

## Make new .globus directory and export it:
chmod  -R  755  /tmp/$USER/globus  >&/dev/null
rm  -rf  /tmp/$USER/globus
mkdir  -p  /tmp/$USER/globus
cp  $HOME/.globus/usercert.pem  /tmp/$USER/globus/
cp  $HOME/.globus/userkey.pem  /tmp/$USER/globus/
cp  $HOME/.globus/certificates  /tmp/$USER/globus/
export  X509_USER_CER=/tmp/$USER/globus/usercert.pem
export  X509_USER_KEY=/tmp/$USER/globus/userkey.pem
export  X509_CERT_DIR=/tmp/$USER/globus/certificates
## Make new .glite directory and export it:
chmod  -R  755  /tmp/$USER/glite  >&/dev/null
rm  -rf  /tmp/$USER/glite
mkdir  -p  /tmp/$USER/glite
cp  -rd  $HOME/.glite/* /tmp/$USER/glite/
export  GLITE_USER_HOME=/tmp/$USER/glite
(for bash), or
## Make new .globus directory and export it:
chmod  -R  755  /tmp/$USER/globus  >&/dev/null
rm  -rf  /tmp/$USER/globus
mkdir  -p  /tmp/$USER/globus
cp  $HOME/.globus/usercert.pem  /tmp/$USER/globus/
cp  $HOME/.globus/userkey.pem  /tmp/$USER/globus/
cp  $HOME/.globus/certificates  /tmp/$USER/globus/
setenv  X509_USER_CER  /tmp/$USER/globus/usercert.pem
setenv  X509_USER_KEY  /tmp/$USER/globus/userkey.pem
setenv  X509_CERT_DIR  /tmp/$USER/globus/certificates
## Make new .glite directory and export it:
chmod  -R  755  /tmp/$USER/glite  >&/dev/null
rm  -rf  /tmp/$USER/glite
mkdir  -p  /tmp/$USER/glite
cp  -rd  $HOME/.glite/* /tmp/$USER/glite/
setenv  GLITE_USER_HOME  /tmp/$USER/glite
(for tcsh). This ensures that the necessary files are accessible even after your AFS tickets expire (as they are copied to some local directory). You could also put these inside a shell function or alias in your .bashrc or .tcshrc, like:
### Function to export the grid stuff in $HOME to the /tmp/$USER:
exportlocal()
{
    # ... the above stuff comes here ...
}
(for bash), or
### Alias to export the grid stuff in $HOME to the /tmp/$USER:
alias  exportlocal  \
# ... the above stuff comes here, but put ' ; \' instead of new line, and continue in next line ...
(for tcsh).

If your home is on AFS, it is also advised to move also your working directory under /tmp/$USER, together with all the necessary files and directories, described in the following sections. To prevent that the regular cleanup cron job deletes some of your files from /tmp/$USER when they are too old, run the command

find  /tmp/$USER  -print  -exec touch {} \;
after unpacking the below tarballs into /tmp/$USER.

Simple job submission with traditional JDL files

Job submission with glite-wms-job-submit is not very straightforward, as the generated job identifier has to be stored, and then the job output retrieval directory has to be resolved by this identifier. To save you from this typing exercise, the WMSX is capable of managing the output retrieval directory for simple jobs.

You can find a prepared example for this task here: simplejob.tar.gz. To submit the example job, type the following commands.

Get the tarball:

> tar  -xzf  simplejob.tar.gz
> rm  -f  simplejob.tar.gz
> cd  simplejob

Log onto the Grid:

> glite-voms-proxy-init  -voms your_vo
# If your job is expected to be long, also get long term authentication:
> myproxy-init  -d  -n

Submit the job:

> wmsx-provider.sh  workdir
> wmsx-requestor.sh  -vo your_vo
# If your job is expected to be long, also make the WMSX remember your grid password:
> wmsx-requestor.sh  -remembergrid
# If your job is expected to be long and you are working on AFS, also make the WMSX remember your AFS password:
> wmsx-requestor.sh  -rememberafs
> wmsx-requestor.sh  -j simplejob.jdl  -r workdir/out/resultdir
# Or, if JobType = "Interactive" was set in the JDL file, say instead:
> wmsx-requestor.sh  -j simplejob.jdl  -r workdir/out/resultdir  -o workdir/out/StdOutFile

Your results shall be retrieved into the directory workdir/out/resultdir. If your job was interactive ( JobType = "Interactive" was set in the JDL file), the file containting StdOut / StdErr shall be workdir/out/StdOutFile, which shall be updated on the fly. Remark: if the JobType = "Interactive" was set, the fields StdInput, StdOutput and StdError cannot be set in the JDL file.

If you are finished, you can stop WMSX, and destroy your Grid authentications:

> wmsx-requestor.sh  -k
# If myproxy-init was used, i.e. for long term jobs:
> myproxy-destroy  -d
> glite-voms-proxy-destroy

An educative example for simple interactive job submission may be found here: interactive.tar.gz. This works in a similar way as the simplejob.tar.gz example.

Mass submission of independent jobs: parameter scan with short calculations

WMSX is a very convenient tool for mass submission of short, e.g. of about maximum 1 day lifetime, independent jobs. Possible application: parameter scan studies with relatively short calculations. (The job lifetime is limited by the typical allowed maximal job lifetimes, assigned by the Grid sites. A limit of 3 day running time is typical, so a maximum 1 day job is fine.) WMSX automatically manages output retrieval issues and the limiting of the number of concurrently running jobs. For this purpose, the jobs are described with a slightly extended JDL language, which is preprocessed by WMSX. If JobType = "Interactive" is set, the file containing StdOut / StdErr is updated on the fly, so you can see what your job is actually doing. A pre-execution script helps to prepare inputs, and a post-execution script helps to process outputs of the job.

You can find a prepared example for this task here: sample.tar.gz. To submit the example job, type the following commands.

Get the tarball:

> tar  -xzf  sample.tar.gz
> rm  -f  sample.tar.gz
> cd  sample

Log onto the Grid:

> glite-voms-proxy-init  -voms your_vo
# If your jobs are expected to be long, also get long term authentication:
> myproxy-init  -d  -n

Submit the jobs:

> wmsx-provider.sh  workdir
> wmsx-requestor.sh  -vo your_vo
# If your jobs are expected to be long, also make the WMSX remember your grid password:
> wmsx-requestor.sh  -remembergrid
# If your jobs are expected to be long and you are working on AFS, also make the WMSX remember your AFS password:
> wmsx-requestor.sh  -rememberafs
# If you want to submit many-many jobs, limit the number of concurrently running jobs e.g. to 100:
> wmsx-requestor.sh  -n 100
> wmsx-requestor.sh  -a arg.list

The file arg.list contains a list of jobs (together with its parameters) to be started. Your results shall be retrieved under the directory workdir/out. If your job was interactive ( JobType = "Interactive" was set in the JDL file), the file containting StdOut / StdErr shall be updated on the fly.

If you are finished, you can stop WMSX, and destroy your Grid authentications:

> wmsx-requestor.sh  -k
# If myproxy-init was used, i.e. for long term jobs:
> myproxy-destroy  -d
> glite-voms-proxy-destroy

Mass submission of chained jobs: parameter scan with long calculations

The mass submission has an important feature: each job can decide whether a launch of a further job is needed. This decision is done by the post-execution script: if it returns with exitcode 1, the chain script is invoked. The lines of the standard output of the chain script is interpreted by WMSX as lines in the arg.list file (see previous example), so new jobs are launched. In this way, jobs can be chained (and the chains can also fork, as a job can also launch multiple jobs). In this way, a parameter study with long term calculations can be performed. The long term calculations are preformed by the job chains. A good example is numerical solution of partial differential equations: multiple chains are launched (possibly with different initial conditions), and each chain is imitating a long term job (the solution of the partial differential equation with a given initial condition), split up into subsequent shorter term jobs.

You can find a prepared example for this task here: chainsample.tar.gz. To submit the example job, type the following commands. (Similar to the previous example.)

Get the tarball:

> tar  -xzf  chainsample.tar.gz
> rm  -f  chainsample.tar.gz
> cd  chainsample

Log onto the Grid:

> glite-voms-proxy-init  -voms your_vo
# If your jobs are expected to be long, also get long term authentication:
> myproxy-init  -d  -n

Submit the jobs:

> wmsx-provider.sh  workdir
> wmsx-requestor.sh  -vo your_vo
# If your jobs are expected to be long, also make the WMSX remember your grid password:
> wmsx-requestor.sh  -remembergrid
# If your jobs are expected to be long and you are working on AFS, also make the WMSX remember your AFS password:
> wmsx-requestor.sh  -rememberafs
# If you want to submit many-many jobs, limit the number of concurrently running jobs e.g. to 100:
> wmsx-requestor.sh  -n 100
> wmsx-requestor.sh  -a arg.list

The file arg.list contains a list of jobs (together with its parameters) to be started. Your results shall be retrieved under the directory workdir/out. If your job was interactive ( JobType = "Interactive" was set in the JDL file), the file containting StdOut / StdErr shall be updated on the fly.

If you are finished, you can stop WMSX, and destroy your Grid authentications:

> wmsx-requestor.sh  -k
# If myproxy-init was used, i.e. for long term jobs:
> myproxy-destroy  -d
> glite-voms-proxy-destroy

-- AndrasLaszlo - 10 Jul 2009

Topic attachments
I Attachment History Action Size Date Who Comment
Gzgz chainsample.tar.gz r1 manage 1.6 K 2008-04-16 - 15:42 AndrasLaszlo Chainsample example
Gzgz interactive.tar.gz r1 manage 0.5 K 2008-04-16 - 15:41 AndrasLaszlo Interactive example
Gzgz sample.tar.gz r1 manage 1.3 K 2008-04-16 - 15:41 AndrasLaszlo Sample example
Gzgz simplejob.tar.gz r1 manage 0.5 K 2008-04-16 - 15:40 AndrasLaszlo Simplejob example
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Topic revision: r18 - 2010-01-27 - AndrasLaszlo
 
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