[Eeglablist] getting started with AMICA

[Jason Palmer]

Hi Joseph,

 

It seems to be getting confused in trying to automatically set up the binary
filename (full path) and the MPI bin directory location .  referencing
"dreamio4 ." when it tries to run the run the binary, seeming missing a
beginning "/".  First off, have you verified that the binary runs on the
command line with one of the sample input.param and datafiles?

 

If the binary runs standalone (see amica webpage), then you might try
bypassing the beginning section of runamica12.m and setting:

 

                MPI_BIN  =  <full path of your mpich2 bin directory>

                AMBIN = <amica binary file name with full path>

 

And for running on the cluster, it's best use a filename, and specify the
number of channels with 'num_chans', and output directory with 'outdir'.

 

It also seems to be finding a "make" parallel environment and trying to use
openmpi. Make is not really a supported parallel environment-it was added as
a workaround for a cluster at UCLA and I thought it was unique to that
cluster. You should be able to query sge to tell you the available parallel
environments with:

 

                $ qconf -spl

 

Ideally you would have mpich2 installed, and a parallel environment called
"mpich", or  <pe_name> set up to use it. You can check the pe setup with
"qconf -sp <pe_name>". If you have a valid parallel environment set up and
named, you can add the matlab command line keyword:

 

                >> runamica12( '/home/me/mydata.fdt', 'num_chans',
EEG.nbchan, 'outdir', '/home/me/myoutput/'., 'use_pe', '<pe_name>', .);

 

It has also worked on openmpi installations (orte, as opposed to mpich), but
may not work on all openmpi.

 

Besides the parallel environment, and the path names being set up correctly,
you need to have a queue set up. You should be able to see a list of queues
(and available slots) with:

 

                $ qstat -g c

 

Or just a list of queues with "qconf -sql". Then with a queue name, you can
add the matlab command line keyword,

 

                >> runamica12( '/home/me/mydata.fdt', 'num_chans',
EEG.nbchan, 'outdir', '/home/me/myoutput/' ., 'use_queue', '<queue_name>',
.);

 

To set the number of processors to use (your queue must have this number of
slots available to run the job), use the keyword,

 

                >> runamica12( .., 'numprocs', 16, .);

 

To get 16 slots/cores for example.

 

If it successfully submits a job, it will give you a job id number in the
immediate matlab output. You can use "qstat" to check the job status, either
"qw" for queue wait, or "r" for running. It should put a file in your home
directory called qsub.sh.o<jobid>, which contains all the output, and a
similar file containing any error output, in addition to the output saved in
the output directory specified by the 'outdir' keyword.

 

Let me know if none of that helps.

 

Best,

Jason

 

 

From: Makoto Miyakoshi [mailto:mmiyakoshi at ucsd.edu] 
Sent: Tuesday, December 04, 2012 7:40 PM
To: Joseph Orr; Jason Palmer
Cc: eeglablist at sccn.ucsd.edu
Subject: Re: [Eeglablist] getting started with AMICA

 

Dear Jason,

 

Could you help him please?

 

Makoto

---------- Forwarded message ----------
From: Joseph Orr <oricon at umich.edu>
Date: 2012/12/4
Subject: [Eeglablist] getting started with AMICA
To: eeglablist at sccn.ucsd.edu


I am trying to run AMICA for the first time and am running in to some
trouble. I am using a cluster running Kubuntu 64-bit with SGE installed.

 

I downloaded the amica12lnx64 binary and have runamica12.m in my path. I
loaded a .set file and executed "[ EEG.icaweights, EEG.icasphere, mods ] =
runamica12( EEG.data(:,:) )"

 

I received the following on the command line:

mpich is not a parallel environment
orte is not a parallel environment
Using make parallel environment.
Writing data file:
/dreamio2/banichlab/studies/VTS/eeg/VTS_ERP2/tmpdata91338.fdt
bash: dreamio4: command not found
Please disregard any Warnings about X11 forwarding.
qsub id = 
You can watch the last 25 lines of the output with:
   $ watch tail -n 25 qsub.sh.o
or in Matlab:
   >> system('watch tail -n 25 qsub.sh.o')
You can load the output as it's running by typing:
   >> mods =
loadmodout12('/dreamio2/banichlab/studies/VTS/eeg/VTS_ERP2/amicaouttmp/')
Error in ==> runamica12 at 101
binfile = 'amica12lnx64';

??? Output argument "weights" (and maybe others) not assigned during
call to
"/dreamio2/banichlab/studies/VTS/eeg/toolboxes/runamica12.m>runamica12".

 
Do I need to set up additional files to get AMICA to run?

Thanks in advance,
Joe


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-- 
Makoto Miyakoshi
JSPS Postdoctral Fellow for Research Abroad
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego

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