2.6 Using storage elements for data transport in FGCI
Moving large datasets between the local computer and grid clusters is often one of the major bottlenecks in grid computing. The FGCI environment includes a centralised data repository that can be used to avoid copying the same file repetitively between the local computer and the FGCI environment. This system allows FGCI users to load data into a central repository that can be accessed form the computing nodes, and is commonly referred to as a storage element. The storage element system of ARC has a cache system that in many cases significantly reduces the network load and speeds up the job submission process.
To illustrate the benefits of storage elements, lets assume that we are submitting one hundred grid jobs, all of which need the same large input file called bigdb.txt. If the input file is copied using the normal input file definitions in the job description files, then the bigdb.txt file is transported from local machine to the computing clusters one hundred times. A more clever way in this case is to first upload the bigdb.txt to the grid storage element. Then we modify the job description file so that in the input file list we refer to the bigdb.txt file in the storage element rather than to the local copy. When we now launch the 100 grid jobs, the first job in each computing cluster copies the input file from the storage element to the cache disk area of the computing cluster. Subsequent jobs now can use the same file from the local data cache. Thus, if we send 100 jobs to ten computing clusters, the data only needs to be transported from the storage element to the remote clusters only ten times.
The storage element of FGCI is based on the SRM (Storage Resource Manager) protocol. The address of the storage element protocol is:
User specific directories are not automatically created in the FGCI storage element. Instead, users should create their own personal sub-directory when they use the FGCI storage element for the first time.
The storage element system is intended to support running computing tasks in the FGCI environment. It is not intended for storing data for longer periods. As the size of the storage element is rather limited users must remove their unused data from the storage element. When the storage element starts filling up, the oldest files will be automatically removed. It should also be noted that the security level of the storage element is very low: you should not use it for sensitive data.
The files stored on the storage element can't be modified. If you wish to modify a file in storage element, you must first download it to your computer, modify the local copy, remove the original file from the storage element and then copy the modified file back to the storage element.
The storage element can be used through a set of ARC commands arcls, arccp and arcrm. The command arccp can be used to copy data between the local computer and the storage element. For example, the file bidgb.txt can be copied to the storage element with the command:
arccp bidgb.txt srm://bombay.csc.fi/fgi/userdirs/my_username/bigdb.txt
Note that in the file path of storage element we have added one extra folder level: my_username. When the command above is executed two things happen: 1. a new directory called my_username is created (if it does not yet exist). 2. the file bigdb.txt is copied there. (Currently the ARC client does not have a separate command for creating new directories. To create a new directory you must use the arccp command as above)
Copying a file from the storage element is also done with the arccp command. For example, the command:
arccp srm://bombay.csc.fi/fgi/userdirs/my_username/bigdb.txt bigb_copy.txt
Would copy the file bigdb.txt to the local computer into the file bigb_copy.txt
The content of a directory in the storage element can be checked with the command arcls. For example, the content of the my_username directory can be checked with the commands:
arcls -l srm://bombay.csc.fi/fgi/userdirs/my_username/
The command arcrm is used to remove a file from the storage element. Fore example, to remove the file bigdb.txt from the storage element, you should use the command:
2.6.2 Using storage elements in grid jobs
For the actual grid jobs, the storage element files are used via the job description files. There you can set that a specified input file is read from the storage element (instead of the local computer) or that a certain output file is transported to the storage element. For example, in the Bowtie2 runtime environment example in chapter 2.3 a chromosome sequence file, chr_18.fa, is used as one of the input files. If we copy the file to the storage element with the command:
arccp chr_18.fa srm://bombay.csc.fi/fgi/userdirs/my_username/chr_18.faand then modify the input line defining the chr_18.fa file to:
The output file of this job, output.sam, could be automatically saved to the storage element in the same way by modifying the output definition to:
Thus a job description file using the storage element for both reading the input and storing the results, would look similar to the example below. Note that the command script (run_bowtie2.sh) needs no modifications.
&(executable=run_bowtie2.sh) (jobname=bowtie2) (stdout=std.out) (stderr=std.err) (cputime="6 hours") (memory=4000) (runtimeenvironment=APPS/BIO/BOWTIE-2.0.0) (inputfiles= ("chr_18.fa" "srm://bombay.csc.fi/fgi/userdirs/my_username/chr_18.fa") ("reads.fq" "reads.fq") ) (outputfiles= ("output.sam" "srm://bombay.csc.fi/fgi/userdirs/my_username/output.sam") )
When the job is finished the output can be retrieved with the command:
arccp srm://bombay.csc.fi/fgi/userdirs/my_username/output.sam ./output.sam
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