...
This
...
is
...
all
...
about
...
how
...
to
...
compute
...
on
...
coyote.
...
There's
...
another
...
site
...
with
...
other
...
information
...
at:
...
https://wikis-mit-edu.ezproxyberklee.flo.org/confluence/display/ParsonsLabMSG/Coyote
...
Gaining access:
| Wiki Markup |
|---|
I'm pretty sure that \[greg\] still helps out with this, you would probably need to ask him for access. Also, if you are working off campus, you need to log into your on-campus account first then ssh onto coyote. If you have questions about this, just ask me. Also, put yourself on the mailing list by checking out the other link above. |
...
What is available:
modules
module add python/2.7.3
...
module
...
add
...
atlas/3.8.3
...
module
...
add
...
suitesparse/20110224
...
module
...
add
...
numpy/1.5.1
...
module
...
add
...
scipy/0.11.0
...
module
...
add
...
biopython
...
module
...
add
...
matplotlib/1.1.0
...
module
...
add
...
matlab
...
(matlab
...
above
...
one
...
above
...
is
...
2009)
...
module
...
add
...
matlab/2012b
...
Not
...
QIIME
...
as
...
far
...
as
...
I
...
can
...
tell.
...
Interactive computing:
I've
...
was
...
able
...
to
...
get
...
onto
...
a
...
node
...
with:
...
qsub
...
-I
...
-l
...
nodes=1
...
But
...
when
...
I
...
tried
...
to
...
use
...
matlab
...
with
...
(module
...
add
...
matlab)
...
it
...
didn't
...
work
...
(although
...
it
...
did
...
work
...
upon
...
ssh'ing)
...
To
...
run
...
matlab
...
with
...
the
...
window,
...
first
...
log
...
in
...
with
...
X11:
...
ssh
...
-X
...
user@coyote.mit.edu
...
ssh
...
-X
...
super-genius
...
module
...
add
...
matlab/2012b
...
matlab
Submitting multiple jobs:
Before running the program below, make sure to load the following modules (I tried without and I got an error loading argparse):
module add python/2.7.3
...
module
...
add
...
atlas/3.8.3
...
module
...
add
...
suitesparse/20110224
...
module
...
add
...
biopython
...
module
...
add
...
java/1.6.0_21
...
You
...
can
...
also
...
just
...
source
...
csmillie's
...
.bashrc
...
to
...
make
...
sure
...
it
...
works
...
(if
...
you
...
didn't
...
do
...
anything
...
else
...
to
...
yours
...
that
...
you
...
need).
...
Also,
...
there
...
are
...
different
...
timed
...
queues,
...
so
...
make
...
sure
...
if
...
you
...
get
...
this
...
working
...
that
...
it
...
submits
...
to
...
the
...
right
...
queue.
...
From
...
what
...
I
...
can
...
tell
...
there
...
is
...
short,
...
long
...
and
...
ultra.
...
Not
...
sure
...
what
...
the
...
exact
...
compute
...
times
...
are
...
for
...
each.
...
From
...
Mark
...
and
...
Chris
...
-
...
I've
...
been
...
using
...
a
...
script
...
chris
...
wrote
...
which
...
works
...
pretty
...
well:
...
/home/csmillie/bin/
...
ssub
What it does
It streamlines job submission. If you give it a list of commands, it will (1) create scripts for them, and (2) submit them as a job array. You can give it the list of commands as command line arguments or through a pipe.
Quick examples
1. Submit a single command to the cluster ssub "python /path/to/script.py
...
>
...
/path/to/output.txt"
...
2.
...
Submit
...
multiple
...
commands
...
to
...
the
...
cluster
...
(use
...
semicolon
...
separator)
...
ssub "python
...
/path/to/script1.py;
...
python
...
/path/to/script2.py"
...
3.
...
Submit
...
a
...
list
...
of
...
commands
...
to
...
the
...
cluster
...
(newline
...
separator)
...
cat
...
/list/of/commands.txt
...
| ssub
Detailed example /home/csmillie/alm/mammals/aln/95/
...
In
...
this
...
directory,
...
I
...
have
...
12,352
...
fasta
...
files
...
I
...
want
...
to
...
align.
...
I
...
can
...
do
...
this
...
on
...
100
...
nodes
...
quite
...
easily:
...
1.
...
First,
...
I
...
create
...
a
...
list
...
of
...
commands
...
:
...
for
...
x
...
in
...
`ls
...
*fst`;
...
do
...
y=${color}{x%.*}
...
;
...
echo
...
muscle
...
-in
...
$x
...
-out
...
$y.aln;
...
done
...
>
...
commands.txt
...
The
...
output
...
looks
...
like
...
this:
...
...
...
muscle
...
-in
...
O95_9990.fst
...
-out
...
O95_9990.aln
...
muscle
...
-in
...
O95_9991.fst
...
-out
...
O95_9991.aln
...
muscle
...
-in
...
O95_9992.fst
...
-out
...
O95_9992.aln
...
muscle
...
-in
...
O95_9993.fst
...
-out
...
O95_9993.aln
...
...
...
2.
...
Then
...
I
...
submit
...
these
...
commands
...
as
...
a
...
job
...
array:
...
cat
...
commands.txt
...
| ssub
How to configure it
Copy it to your ~/bin (or wherever). Then edit the top of the script:uname = your username tmpdir = directory where scripts are created max_size = number of nodes you want to use
Other things
It automatically creates random filenames for your scripts and job arrays. These files are created in the directory specified by "tmpdir" It can also submit individual scripts instead of a job array.