Changes between Initial Version and Version 1 of Software/MigrateN

Timestamp:

Mar 1, 2012, 8:11:57 PM (13 years ago)

Author:

Mikael Brandström Durling

Comment:

--

Software/MigrateN

@@ +1 @@
+== Migrate-N ==
+
+The software and instructions can be found on: http://popgen.sc.fsu.edu/Migrate/Info.html
+
+=== Mykopat Grid specifics ===
+
+Since Migrate-N can utilise multiple cores/computers when calculating migration rates, there are some specifics to keep in mind when running it in parallel. The basic workflow will be something like this (completely untested by me/MBD):
+ 1. Start migrate-n by typing ```migrate-n my_params.txt```
+ 1. Using the menus in migrate and the manual, set all parameters for your run, but DO NOT start the run.
+ 1. Save the param file, theres a menu option for that.
+ 1. Create a batch file used to submit the job to the grid. An example can be found at the bottom of the page. Request a small amount of memory per slot (1GB should be enough), but enough runtime for finishing the run.
+ 1. Submit the job with ```qsub my_batch_file``` and wait for an email telling you first that the job started to run, and then yet another when the run is done.
+ 1. Check the log files (job_name.oNNN and job_name.eNNN) to ensure that everything went well.
+ 1. If you need to rerun, start over from the top of this list, but the batch file can be reused.
+
+{{{
+#!/bin/sh
+# Sample batch file for migrate. Put this in a plain text file calle, for example migrate_batch and call it with qsub migrate_batch
+
+# Ensure the environment is correct
+#$ -V
+#$ -cwd
+
+# Ask for a mail at beginning, end and if the job is aborted
+#$ -m bea
+
+# We want to run migrate on 6 slots/cores, this number should ideally be number of loci + 1. 
+# However, there is currently a system limit at 8. The more you ask for, the longer it usually
+# takes before your job is started.
+#$ -pe openmpi 6
+
+# We want the system to allocate 5 hours run time to migrate, and 1G of ram per slot
+#$ -l h_rt=5:0:0,h_vmem=1G
+
+
+# Change my_parm_file to the name of your param_file
+mpirun migrate-n-mpi my_parm_file -nomenu
+}}}
+