[Mne_analysis] static executables?

Tue Oct 7 15:25:04 EDT 2014

Dear Eric,

I got it to work by adding the environmental command in the bash form (export LD_LIBRARY_PATH=`pwd`) inside the os.system() call.
Of course you’re right about doing that with subprocess() and you’re right too about just doing it all in mne-python.

It was very helpful to kick it around with you – thank you.
I understand about generating static executables since it doesn’t seem like your group is actively supporting that version of mne.

Best Regards,

Don

From: mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Eric Larson
Sent: Tuesday, October 07, 2014 3:10 PM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] static executables?

If you're going to call system processes from Python, you're better off using the `subprocess` module than `os.system`. mne-python has a convenience wrapper `mne.utils.run_subprocess` that might be easier for you. If you want to use subprocess directly, the keyword argument for subprocess.Popen (which is the function wrapped by run_subprocess that you'd want to use) has a keyword argument "env" where you can set your own environment variables for it to pass to the subprocess.

It might be possible to compile static executables, but I'm not sure how much work it would be (possibly non-trivial)...

Eric

On Tue, Oct 7, 2014 at 12:02 PM, Krieger, Donald N. <kriegerd at upmc.edu<mailto:kriegerd at upmc.edu>> wrote:
Hi Eric,

It doesn’t work but I think I know why.
I am using a csh wrapper which executes a python script.
And within the python script I run the mne_ executables with  os.system(cmd)
I think that the python script doesn’t pass the value I’ve set for LD_LIBRARY_PATH to mne_forward_solution unless I explicitly tell it to do so.
I’ll see about getting that to  work.

But is there any way that you  could produce static executables?

Thanks.

Regards,

Don

[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654<tel:%28412%29648-9654> Office
(412)521-4431<tel:%28412%29521-4431> Cell/Text

From: mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu> [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu>] On Behalf Of Eric Larson
Sent: Tuesday, October 07, 2014 2:30 PM

To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] static executables?

FYI I originally got the libs from the Ubuntu repos, in case you're curious (or in case I eventually delete the libs from my site):

https://launchpad.net/ubuntu/hardy/i386/libgfortran1
https://launchpad.net/ubuntu/hardy/amd64/libgfortran1

Yes, you should be able to set the LD_LIBRARY_PATH environment variable. In fact this is one of the things that the mne_setup_sh script does to ensure that things like "libquicktime.so" can be found in the mne/lib directory, which is why I typically just put libgfortran.so.1 in there. I don't think you'll need to do anything else, but if it doesn't work you should be able to work out from the mne_setup_sh script if anything else is necessary.

Eric

On Tue, Oct 7, 2014 at 11:15 AM, Krieger, Donald N. <kriegerd at upmc.edu<mailto:kriegerd at upmc.edu>> wrote:
Hi Eric,

Thanks for posting back so quickly.

I would be happy to upload the library with each copy of the job and I do have it.
How do I get the executables to find it in a local directory I create?
Is there an environmental variable, something like LD_LIBRARY_PATH that I can set.

Regards,

Don

From: mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu> [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu>] On Behalf Of Eric Larson
Sent: Tuesday, October 07, 2014 1:59 PM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] static executables?

Actually, I forgot I uploaded them to my website for convenience at one point:

http://faculty.washington.edu/larsoner/libgfortran.so.1s.zip

Just rename the appropriate libgfortran.so.1.i686 or libgfortran.so.1.x86_64 to libgfortran.so.1, put it in e.g. mne/lib (same place that libquicktime.so lives) and you should be good to go.

Eric

On Tue, Oct 7, 2014 at 10:55 AM, Eric Larson <larson.eric.d at gmail.com<mailto:larson.eric.d at gmail.com>> wrote:
If it's easy for you to use Python, equivalent (and in some cases faster or more capable) functionality for setting up volume source spaces and computing forward solutions exists in mne-python.

If it's only the Fortran libraries (specifically libgfortran.so.1) that you need, shoot me an email and I can give you a copy of the x86_64 and i686 versions that other people have used with success (and I have used over many versions of Ubuntu). I recently set up an Ubuntu 12.04 server VM for testing recently, and all I needed to run the MNE command-line tools was a copy of libgfortran.so.1 (which I put in the mne/libs dir), and some of the X libraries which were accessible via apt-get -- I imagine a similar solution would work for you.

Eric

On Tue, Oct 7, 2014 at 10:43 AM, Krieger, Donald N. <kriegerd at upmc.edu<mailto:kriegerd at upmc.edu>> wrote:
Dear MNE team:

I need static executables for mne_volume_source_space and mne_forward_solution .
I am using these in a processing stream which is deployed to the open science grid and am encountering many machines which lack the shared fortran libraries on which the executables in your standard distribution rely.

Is it easy to create relink them to create static versions?
Are there some out there to which you could point me?

I am using version 2.9 of mne_forward_solution (compiled 1Feb2013)
and version 1.11 of mne_volume_source_space (also compiled 1Feb2013).

Thanks for any help you can provide.

Regards,

Don

Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

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