how_to_config_sge.md

How to configure SGE for pipeline

1. List all parallel environments (PE) on your SGE.

   $ qconf -spl

2. If you don't have one then ask your system admin to add a new one with name shm.

   $ sudo qconf -ap shm

3. Give a large number to slots for your PE.

   $ sudo qconf -mp shm
     pe_name            shm
     slots              999
     ...

4. List all queues on your SGE.

   $ qconf -sql

5. Ask your system admin to connect PE to your queue.

   $ sudo qconf -mq [QUEUE_NAME]
     ...
     pe_list               make shm
     ...