problem to launch miRDeep2 by PBS

[unique379]

Hi all,

Here i am facing a small problem to launch miRDeep2 into my server by PBS. plz short-out anyone.

error:

mkdir mirdeep_runs/run_14_05_2013_t_11_53_28

Error: Perl PDF::API2 package not found
Check if the perl PDF::API2 package is correctly installed and all Pathes were set correctly, though right now its running in randfold phase correctly.

while by simple way (by terminal mode) its running quite well even with PDF::API2 package without any error.

Note: i also commented to PDF::API2 module inside miRDeep2.pl script to check if other things are ok however yes its okey all except this module.

i am asking to launch in PBS mode bcz after leaving system, my lab suppose to be off all system by remotely except my cluster server

please help me,

Thanks once again and waiting for your kind input.

[GenoMax]

I am no PSB expert but it appears the the "PDF::API2" package is not installed (or incorrectly installed) for system-wide access (i.e. from job execution nodes). Have you reported this error to your cluster administrators?

[unique379]

As i wrote, its properly working by terminal that means PDF::API2 package correctly installed on my system. but i really don't understand why its not working by PBS on server.
Unfortunately we don't have any maintainer for our cluster, we are only responsible. Its lifescope server by the way.

thanks anyway

[dpryan]

When you execute the program directly on the terminal, then the program is being run on whatever system that terminal is connected. When you execute it via PBS, it's being run on a worker node on the cluster. What GenoMax wrote means that there's likely a disconnect between the installation on the head node and the worker/job execution nodes. This will often be the case if you've installed PDF::API2 yourself on the head node and whatever mount point that's on doesn't exist on the execution nodes.