A worldwide e-Infrastructure for NMR and structural biology

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Testing accessibility of all SE from all CE (for grid admin)

Storage Element (SE) should be accessible from any Computing Element (CE).

An SE is a grid nodes that allow users to store some data. A CE is a grid nodes on which users can run computational works that potentially would access some data stored on some SE. It is important to ensure that every CE in the world can access every SE in the world. If not, it could mean that some firewall settings, or grid configuration files are wrong. This script is there to test that.

How to use it:

1. Download and untar the archive SE.tgz

(file provided below)

2. Run the ./1.monitor-submit.sh from your local User Interface

Note that this script might take a few minute to complete

This script will first upload a file to every SE of WeNMR vo in the home of the user. The file has the name test_file.prod-se-01.pd.infn.it.20110504-192741 where the numbers at the end are the date and time it was sent, and the begining of the file is the name of the storage element.

Then it will automatically submit a job for every combinason of SE and CE. The job simply consist of retreiveing the file from the SE.

All JDL files are stored in the JDL directory. All bash file that is run on the CEs are stored in the SH directory, and the output of the submission command is stored in the SUB directory.

3. You can check the current status of the job with the script: 2.monitor-status.sh

This will update the directory STATUS that store the status of all jobs. You should run the script (maybe 24h after the submission) and inspect the directory to check for problems. You could have jobs that failed because they stayed too long in the queue, or for some other reasons.

4. You can retrieve the output of the jobs with 3.monitor-retrieve.sh

You should do so to check the the output files are correct: can you see the content of input_file ("Hello")  in the subdirectories of the OUT directory? If so everything is good. If not, something is wrong on the CE, on the SE, or maybe the CE can't communicate with the SE.


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Cite WeNMR/WestLife

Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
"The FP7 WeNMR (project# 261572), H2020 West-Life (project# 675858) and the EOSC-hub (project# 777536) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, Taiwan and the US Open Science Grid."
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.


The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858