2.3 Using software through runtime environments

The FGCI environment contains a set of pre-installed software tools because installing complex software tools within the grid job can be difficult. The software installed on FGCI is used by accessing its Run Time Environment (RTE). The RTE concept is analogous to the environment modules used in the computing servers of CSC: the RTE adds the commands of the selected software to the command path and sets up the environment variables that the software uses. In addition, RTEs are used to tell the ARC middleware what software are available on the different clusters. The FGI clusters don't all contain the same RTE:s.

List and usage examples about RTEs that are available in FGCI can be found from the FGI Runtime Environments pages:

https://confluence.csc.fi/display/fgi/Runtime+Environments

An RTE is taken into use by adding the runtimeenvironment parameter to the job description file. For example, the RTE that is used for Bowtie2 software is referred to as APPS/BIO/BOWTIE-2.0.0. To use Bowtie2 commands in a grid job you should add following line to the job description file:

(runtimeenvironment="APPS/BIO/BOWTIE-2.0.0")

Bowtie2 can utilize OpenMP based parallelisation. For the case of programs which are capable of parallel computing, that is, running on more than one core, the runtime environment can define the number of computing cores to be used. This kind of arrangement allows the system to automatically set the suitable core number, which may be different in different clusters, for parallel processing. The core number defined by the RTE is typically stored to an environment variable which is then used to transport this information to the command to be executed.

Below is an example of a job description file (bowtie2.xrsl) that uses the Bowtie2 RTE:

&
(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" "chr_18.fa")
   ("reads.fq" "reads.fq")
)
(outputfiles=>
   ("output.sam" "output.sam")
)

In the command script file we use the environment variable $BOWTIE_NUM_CPUS, defined by the RTE with the bowtie2 command:

#!/bin/sh
echo "Hello Bowtie2"
bowtie2-build -p $BOWTIE_NUM_CPUS chr_18.fa chr_18
bowtie2 -p $BOWTIE_NUM_CPUS chr_18 reads.fq > output.sam
exitcode=$?
echo "Bye Bowtie2!"
exit $exitcode
Details about what parameters a certain RTE defines can be checked from the home page of the RTE. In the case of Bowtie2 the address of the page is:

https://confluence.csc.fi/display/fgi/Bowtie2+runtime+environment

 

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