Specifically, Cray requires a special command (aprun) embedded within the qsub request to execute the job on a batch node (Cray defaults to running on login/compute nodes without the aprun syntax). When hand-keying a qsub request to Cray Linux supercomputers, the directed syntax is:
qsub <qsub parameters> -V
aprun -n #CPUS /executable.exe param1 param2 ...
Ctrl-D
Where the user provides 'return' after the -V (denoting passage of parameters in the qsub statement) and after the executable/parameter set. Ctrl-D terminates the input and executes the qsub/aprun command.
The problem is, there are a variety of ways described on the net for inputting the Ctrl-D (which simply means EOF) in a BASH script, but none of them work in the context of the qsub-embedded aprun command.
What I need to do is execute this same syntax for multiple qsub/aprun commands in a single script. How do I code this in BASH?
The solution syntax is:
qsub <qsub parameters> -V <<EOF
cd
aprun -n #CPUS /executable.exe param1 param2 ...
EOF
qsub <qsub parameters> -V <<EOF
cd
aprun -n #CPUS /executable.exe param1 param2 ...
EOF
Note the location of the <<EOF (no space between << and EOF), the cd is on a new line and followed by a newline with the aprun syntax and the final EOF in the set is without the leading <<, followed by a newline.
This syntax will execute each qsub/aprun command into a new batch node job submission. Output from the script will be the series of job IDs requested.