Having an understanding of the hardware layout of the HPCC enables you to understand where your files are, what disks you should use for your data and how your program will run. Below is a schematic of the HPC layout.
Everyone logs into the “login node”. From there you submit your job using a PBS job submission script. The “head node” manages all the jobs distributed over all the “compute nodes”. The PBS scheduler running on the head node will assign your job to one of the compute nodes.
Your home directory under
/shared/homes/ is on the Isilon storage system.
It is mounted over the network by the login node and all the compute nodes.
Thus your home directory
/shared/homes/XXXXXX (where XXXXXX is your
staff/student ID) is common across all nodes.
Each compute node has a local SSD disk with a directory
Your program running on a compute node can read and write to that nodes local SSD disk (the /scratch/ directory) much faster than over the network to the /shared/homes/ directory which comes from the Isilon storage appliance.
This is why within your PBS submission script you should copy your input files to the
/scratch/XXXXXX directory before your program runs. Your program should read or
write to that local directory. When your program has ended your PBS script should
copy your output data back from
/shared/homes/XXXXXXis on the Isilon storage system. Each node has a has a local SSD disk with a directory
/scratch/. A node can read and write to its local SSD disk much faster than over the network.
Why do you need to to use
/scratch/ for your data reading and writing?