Handling inputs flies on PBS


Single Input File (Serial run)

If you requires to run your job(s) over different 1 set input files, you have to add the line script into your PBS. Suppose the single input file is data1.ini. The program above will take the input data1.ini and generates an output file data1.out. In your submission scripts

#!/bin/bash
.....
.....
## Use data1.ini as the input file for $file
cd $PBS_O_WORKDIR
mybinaryprogram < data1.ini 1> data1.out 2> data1.err
.....
.....

Multiple Input Files (Serial run)

IF you wish to use multiple input files , you should use the PBS job array parameters. This can be expressed with the -t parameters. The -t option allows many copies of the same script to be queued all at once. You can use the PBS_ARRAYID to differenciate between the different jobs in the array.

Assuming the data file

data1.ini
data2.ini
data3.ini
data4.ini
data5.ini
data6.ini
data7.ini
data8.ini
#!/bin/bash
.....
.....
#PBS -t 1-8
cd $PBS_O_WORKDIR
mybinaryprogram < data${PBS_ARRAYID}.in 1> data${PBS_ARRAYID}.out 2> data${PBS_ARRAYID}.err
.....
.....

For above information is obtained from

  1. Michigan State University HPCC “Advanced Scripting Using PBS Environment Variables”
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