Phylogenetics

Hi Jim,

I am having trouble submitting PAUP jobs to the Moab. I am not certain where PAUP is located (the correct directory and path), and my analysis is getting hung up at the submit file. Below is a copy of my submit file:

#!/bin/bash

#MOAB -l nodes=1
#MOAB -j oe
#MOAB -m abe
#MOAB -N paup
#MOAB -l walltime=8:90:00:00

/opt/Bio/paup/paup -n TEST1.1.nex

Thanks,

John

Thursday, 11 April 2013 07:48

James Wilgenbusch,

Yes. That's exactly what's wrong. You need to execute this from the general access log in node. You can check to make sure that your script will work by typing:

"ls /opt/Bio/mrbayes/mb"

If the file is not there you will get this message:

ls: /opt/Bio/mrbayes/mb: No such file or directory

or something like it. Also to check for where an appropriate binary is located you can type the following command:

"which mb"

On submit this will give you:

/usr/common/i686-linux/bin/mb

Hope this helps.

Monday, 28 March 2011 16:07

John Schenk,

Thanks for you help Jim! I changed the Executable, but now I am getting the following error: ERROR: Executable file /opt/Bio/mrbayes/mb does not exist

I have a suspicion that it is due to me connecting to the @submit.scs.fsu.edu node via pamd. Is there a different node that I should connect to?

Thanks again,

John

Monday, 28 March 2011 15:50

James Wilgenbusch,

Hi John,

The application MrBayes will likely use as much memory as is on the system that Condor gives it. MrBayes often uses lots of memory, especially for long running jobs so this can be a problem. To be sure that your job is paired with a system that has lots of memory, I suggest using the requirements statement. For example:

Requirements = Memory >= 2000

will only let your jobs run on systems with 2GB of memory or more.

You can figure out what memory is available to condor systems by typing in the command:

condor_status

The seventh column in the output from this command is memory available per job. I would also suggest being a little more explicit with your requirements statement to include the OS and the cpu architecture. For example:

Requirements = Memory >= 2000 && OpSys == "LINUX" && Arch =="X86_64"

Lastly, this job was submitted from submit, which is a node in the Department of SC. Not everyone has access to these nodes. To run this from HPC I recommend that you replace:

Executable = /usr/common/i686-linux/bin/condor_mb

with this

Executable = /opt/Bio/mrbayes/mb

and then you can delete this:

InitialDir = /panfs/panasas1/users/jschenk/mb/300project/BI/

Hope this helps,
Jim

Thursday, 10 March 2011 15:22

John Schenk,

I am trying to run an MPI MrBayes job, however, I am receiving an error message (in my *.output file) that says MrBayes has run out of memory:
The program ran out of memory while trying to allocate
the conditional likelihoods for the chain. Please try
allocating more memory to the program, or running the
data on a computer with more memory.
Error in command "Mcmc"

Any ideas on how to allocate more memory to MrBayes?

Below is my submit file, if it helps diagnose the problem:
Universe = Vanilla
Executable = /usr/common/i686-linux/bin/condor_mb

output = ConcatBI_Gene.output
error = ConcatBI.error
log = ConcatBI.log
machine_count = 4
InitialDir = /panfs/panasas1/users/jschenk/mb/300project/BI/
Arguments = Concat300BI_genePart.nex Concat_Gene.txt1
Queue

~John

Wednesday, 09 March 2011 13:42

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