Ross Mounce

Building upon the instructions given
[here](http://tnt.insectmuseum.org/index.php/Running_tnt_in_parallel)
and [here](http://www.zmuc.dk/public/phylogeny/tnt/) I thought I'd write
up one of the many useful things Pablo Goloboff kindly taught us at the
TNT scripting workshop after the Hennig XXXI meeting.

[![](http://rossmounce.co.uk/wp-content/uploads/2012/07/workshop.jpg "Riverside TNT workshop 2012"){.size-full
.wp-image-270 loading="lazy" decoding="async" width="507" height="380"
srcset="https://rossmounce.co.uk/wp-content/uploads/2012/07/workshop.jpg 507w, https://rossmounce.co.uk/wp-content/uploads/2012/07/workshop-300x224.jpg 300w"
sizes="(max-width: 507px) 100vw, 507px"}](http://rossmounce.co.uk/wp-content/uploads/2012/07/workshop.jpg)

It's actually not the easiest thing to setup if you're using
[Ubuntu](http://www.ubuntu.com/)... Pablo had to help me do it -- I
would never have got it up and running on my own.

THE FOLLOWING INSTRUCTIONS ASSUME YOU'RE USING UBUNTU ON A MULTICORE
MACHINE

You'll need to install the *pvm* package either from the repositories
with

`sudo apt get install pvm`

or download and compile [from
source](http://www.netlib.org/pvm3/index.html)

It's actually better to compile from source because the pvm package in
the Ubuntu repositories is out of date -- they provide only version
3.4.5, whilst the latest version of pvm, released way back in 2009 is
3.4.6 ! I guess the packaging team have other priorities...

Then you'll need to configure pvm on your machine:

- edit your bashrc file  `nano ~/.bashrc`  and insert this line:

export PVM_ROOT=/usr/lib/pvm3

save & close the bashrc file. Now  `source ~/.bashrc` and then test the
path with `echo $PVM_ROOT` this should now return

/usr/lib/pvm3

- in your user home directory (for me this is /home/ross/ ) create a
  plaintext file called hostlist (the exact name doesn't matter but
  remember it) and write one line within this file:

rossnetbook ep=/usr/bin/

(replace 'rossnetbook' with your computer hostname -- if you're not sure
what this is then `nano /etc/hostname` will tell you) save and close
this file.

- now start pvm from your user home directory with `pvm hostlist`  this
  tells pvm your hostname and the path. Unfortunately you'll need to
  start-up pvm this way every time you restart your computer. Perhaps
  there's a better way? Let me know if so...

Finally, make sure you've copied the 64-bit TNT binary to both /usr/bin/
& to your user home directory and make sure that they're executable.

Now you should be ready to go...

if you get an error message like this from TNT:

> tnt\*\>ptnt begin ajob2 2 = mult 5; return ; ptnt wait . ;  
> Macro language is ON  
> Macros: 50.5 Kb in use, 51.8 Kb free  
> libpvm \[pid7539\] /tmp/pvmd.1000: No such file or directory  
> libpvm \[pid7539\] /tmp/pvmd.1000: No such file or directory  
> libpvm \[pid7539\] /tmp/pvmd.1000: No such file or directory  
> libpvm \[pid7539\]: pvm_config(): Can't contact local daemon
>
> Can't enter parallel interface (make sure PVM is running)

you've probably forgotten to start pvm with `pvm hostlist`

see the video I uploaded below for demonstration of the speed-up
possible by performing tasks in parallel:

the video shows me performing a simple search on the zilla dataset of
Chase et al. (1993) using traditional heuristic settings (60 reps)
performed first in serial, then in parallel (starting after 2:00) 20
reps x 3 slaves.

100 seconds for search 1, down to just 48 seconds for search 2 (in
parallel). YMMV

Neither of these searches found the shortest length trees btw!

Commands:  
`mxram 100;` /\* increase memory \*/  
`p zilla.tnt;` /\* read in the data \*/  
`hold 20000;` /\* increase the maximum number of trees held \*/  
`mult 60;` /\* perform a traditional search with 60 replications \*/  
`le;` /\* tree lengths \*/

/\* parallel tnt job, called 'ajob' using 3 slaves performing 'mult 20'
on each slave \*/  
`ptnt begin ajob 3 = mult 20; return ; ptnt wait . ;`

basically just insert what you want your slaves to do in between the '='
and the return; commands.

`ptnt get ajob;` /\* get data back from slaves to master \*/

This was just the tip of the iceberg of the course. I can't even begin
to write-up the rest of the course in this much detail! But I hope this
helps...

<figure id="attachment_285" class="wp-caption aligncenter"
aria-describedby="caption-attachment-285" style="width: 444px">
<a
href="http://rossmounce.co.uk/wp-content/uploads/2012/07/workshop2.jpg"><img
src="http://rossmounce.co.uk/wp-content/uploads/2012/07/workshop2.jpg"
class="size-full wp-image-285" loading="lazy" decoding="async"
srcset="https://rossmounce.co.uk/wp-content/uploads/2012/07/workshop2.jpg 444w, https://rossmounce.co.uk/wp-content/uploads/2012/07/workshop2-300x225.jpg 300w"
sizes="(max-width: 444px) 100vw, 444px" width="444" height="333" /></a>
<figcaption>many many thanks Pablo, and all the organisers of this
workshop AND the conference – it was *much* appreciated</figcaption>
</figure>


Building upon the instructions given here and here I thought I’d write up one of the many useful things Pablo Goloboff kindly taught us at the TNT scripting workshop after the Hennig XXXI meeting. It’s actually not the easiest thing to setup if you’re using Ubuntu… Pablo had to help me do it – I would never have got it up and running on my own.


Rogue Scholar Beiträge

Running TNT in parallel