urdme-help — Primary URDME email list

Re: [Urdme-help] Windows install

[Brian D. <br...@dr...>]

Hi Adam,
It is theoretically possible to run URDME under window using Cygwin or similar setup.  The reason this is necessary is URDME uses GCC to compile the model and solver together for efficient simulation.  Our team doesn't have the setup to develop and test a windows install, but if you are able to get it working we would love to know how to do that.  Alternatively, you could install linux on a virtual machine software package (such as VirtualBox) and run URDME there.

I also want to take this opportunity to plug the new work we are doing, pyURDME.  PyURDME is a python+fenics interface to URDME instead of the Matlab+Comsol interface.  It "should" be release soon (we are hoping to get v1.0 out in March).  This doesn't eliminate this issues with the windows install, but does provide access to the software without any commercial package (as well as some other great features).

Thanks,
  Brian Drawert

On Mar 3, 2014, at 1:54 PM, Adam Noel <ad...@ec...> wrote:

> Hi,
> 
> I noticed that the URDME installation instructions specify that Linux or OSX is required. Is there any particular reason why attempting an installation on Windows would not work?
> 
> Thanks,
> Adam
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[Urdme-help] Windows install

[Adam N. <ad...@ec...>]

Hi,

I noticed that the URDME installation instructions specify that Linux or
OSX is required. Is there any particular reason why attempting an
installation on Windows would not work?

Thanks,
Adam

Re: [Urdme-help] attempting to install URDME

[charles c. <cha...@gm...>]

Thanks for your replies. Linking to /Applications/MATLAB_R2013a.app/bin/matlab
worked and I was able to install successfully. Sadly I have hit another
barrier, namely that I don't have comsol. Alas!

Thank you both again for your help.
Charlie


On Thu, Oct 17, 2013 at 1:25 PM, Andreas Hellander <
and...@it...> wrote:

> Hi,
>
> I have 2013a installed On OSX 10.8.5, and I have my symlink set up like
> this
>
> /usr/local/bin/matlab -> /Applications/MATLAB_R2013a.app/bin/matlab
>
> Best regards
> Andreas
> -------------------------------------------
> Andreas Hellander
> Ph.D. Scientific Computing
> Division of Scientific Computing
> Department of Information Technology
> Uppsala University
>
> On Oct 17, 2013, at 5:52 PM, Brian Drawert <br...@dr...> wrote:
>
> > Hi Charlie,
> >
> > Sorry for the long delay in responding, we have had trouble with our
> email list software.
> > Can you send us a little more information on what your error is.  You
> mention different matlab executables, but what exactly is the error you are
> seeing?
> > I don't have Matlab 2013 currently installed, but for the urdme_init
> script to work, you will need to be able to run matlab in a terminal window
> (without any GUI).  My guess is that the file
> "/Applications/MATLAB_R2013a.app/bin/matlab" is the correct one for that.
>  However, I am not sure what the solution is as I don't fully understand
> your problem.
> >
> > Always happy to help,
> >  Brian Drawet
> >
> >
> > On Sep 16, 2013, at 8:59 AM, charles cooper wrote:
> >
> >> Hi,
> >>
> >> This is already partially addressed by your FAQ, but I am afraid I need
> to ask for more detail. When I look through the contents of the MATLAB
> folder, I am finding a couple of files that open up MATLAB when I call them.
> >>
> >> /Applications/MATLAB_R2013a.app/bin/matlab
> >> /Applications/MATLAB_R2013a.app/bin/maci64/MATLAB
> >> /Applications/MATLAB_R2013a.app/Contents/MacOS/StartMatlab
> >> /Applications/MATLAB_R2013a.app/Contents/MacOS/MATLAB_maci (looks like
> it links to ../../maci64/MATLAB)
> >>
> >> I've tried making links to each of these with ln -s {pathtofile}
> {linkname} and then moving them to /usr/local/bin to no effect. I have also
> tried adding export
> PATH="${PATH}":$/Applications/MATLAB_R2013a.app/Contents/MAcOS/ lines to my
> bash_profile, and still nothing. I wonder if anyone can recommend something
> else I can try?
> >>
> >> Mac OS 10.7.5, in case it helps.
> >>
> >> Thanks,
> >> Charlie
> >>
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> >
> >
> >
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Re: [Urdme-help] attempting to install URDME

[Andreas H. <and...@it...>]

Hi, 

I have 2013a installed On OSX 10.8.5, and I have my symlink set up like this

/usr/local/bin/matlab -> /Applications/MATLAB_R2013a.app/bin/matlab

Best regards
Andreas 
-------------------------------------------
Andreas Hellander
Ph.D. Scientific Computing
Division of Scientific Computing
Department of Information Technology
Uppsala University

On Oct 17, 2013, at 5:52 PM, Brian Drawert <br...@dr...> wrote:

> Hi Charlie,
> 
> Sorry for the long delay in responding, we have had trouble with our email list software.
> Can you send us a little more information on what your error is.  You mention different matlab executables, but what exactly is the error you are seeing?
> I don't have Matlab 2013 currently installed, but for the urdme_init script to work, you will need to be able to run matlab in a terminal window (without any GUI).  My guess is that the file "/Applications/MATLAB_R2013a.app/bin/matlab" is the correct one for that.  However, I am not sure what the solution is as I don't fully understand your problem.
> 
> Always happy to help,
>  Brian Drawet
> 
> 
> On Sep 16, 2013, at 8:59 AM, charles cooper wrote:
> 
>> Hi,
>> 
>> This is already partially addressed by your FAQ, but I am afraid I need to ask for more detail. When I look through the contents of the MATLAB folder, I am finding a couple of files that open up MATLAB when I call them.
>> 
>> /Applications/MATLAB_R2013a.app/bin/matlab
>> /Applications/MATLAB_R2013a.app/bin/maci64/MATLAB
>> /Applications/MATLAB_R2013a.app/Contents/MacOS/StartMatlab
>> /Applications/MATLAB_R2013a.app/Contents/MacOS/MATLAB_maci (looks like it links to ../../maci64/MATLAB)
>> 
>> I've tried making links to each of these with ln -s {pathtofile} {linkname} and then moving them to /usr/local/bin to no effect. I have also tried adding export PATH="${PATH}":$/Applications/MATLAB_R2013a.app/Contents/MAcOS/ lines to my bash_profile, and still nothing. I wonder if anyone can recommend something else I can try?
>> 
>> Mac OS 10.7.5, in case it helps.
>> 
>> Thanks,
>> Charlie
>> ------------------------------------------------------------------------------
>> October Webinars: Code for Performance
>> Free Intel webinars can help you accelerate application performance.
>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
>> the latest Intel processors and coprocessors. See abstracts and register >
>> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk_______________________________________________
>> Urdme-help mailing list
>> Urd...@li...
>> https://lists.sourceforge.net/lists/listinfo/urdme-help
> 
> 
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk
> _______________________________________________
> Urdme-help mailing list
> Urd...@li...
> https://lists.sourceforge.net/lists/listinfo/urdme-help

Re: [Urdme-help] attempting to install URDME

[Brian D. <br...@dr...>]

Hi Charlie,

Sorry for the long delay in responding, we have had trouble with our email list software.
Can you send us a little more information on what your error is.  You mention different matlab executables, but what exactly is the error you are seeing?
I don't have Matlab 2013 currently installed, but for the urdme_init script to work, you will need to be able to run matlab in a terminal window (without any GUI).  My guess is that the file "/Applications/MATLAB_R2013a.app/bin/matlab" is the correct one for that.  However, I am not sure what the solution is as I don't fully understand your problem.

Always happy to help,
  Brian Drawet


On Sep 16, 2013, at 8:59 AM, charles cooper wrote:

> Hi,
> 
> This is already partially addressed by your FAQ, but I am afraid I need to ask for more detail. When I look through the contents of the MATLAB folder, I am finding a couple of files that open up MATLAB when I call them.
> 
> /Applications/MATLAB_R2013a.app/bin/matlab
> /Applications/MATLAB_R2013a.app/bin/maci64/MATLAB
> /Applications/MATLAB_R2013a.app/Contents/MacOS/StartMatlab
> /Applications/MATLAB_R2013a.app/Contents/MacOS/MATLAB_maci (looks like it links to ../../maci64/MATLAB)
> 
> I've tried making links to each of these with ln -s {pathtofile} {linkname} and then moving them to /usr/local/bin to no effect. I have also tried adding export PATH="${PATH}":$/Applications/MATLAB_R2013a.app/Contents/MAcOS/ lines to my bash_profile, and still nothing. I wonder if anyone can recommend something else I can try?
> 
> Mac OS 10.7.5, in case it helps.
> 
> Thanks,
> Charlie
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from 
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk_______________________________________________
> Urdme-help mailing list
> Urd...@li...
> https://lists.sourceforge.net/lists/listinfo/urdme-help

[Urdme-help] attempting to install URDME

[charles c. <cha...@gm...>]

Hi,

This is already partially addressed by your FAQ, but I am afraid I need to
ask for more detail. When I look through the contents of the MATLAB folder,
I am finding a couple of files that open up MATLAB when I call them.

/Applications/MATLAB_R2013a.app/bin/matlab
/Applications/MATLAB_R2013a.app/bin/maci64/MATLAB
/Applications/MATLAB_R2013a.app/Contents/MacOS/StartMatlab
/Applications/MATLAB_R2013a.app/Contents/MacOS/MATLAB_maci (looks like it
links to ../../maci64/MATLAB)

I've tried making links to each of these with ln -s {pathtofile} {linkname}
and then moving them to /usr/local/bin to no effect. I have also tried
adding export
PATH="${PATH}":$/Applications/MATLAB_R2013a.app/Contents/MAcOS/ lines to my
bash_profile, and still nothing. I wonder if anyone can recommend something
else I can try?

Mac OS 10.7.5, in case it helps.

Thanks,
Charlie

[Urdme-help] Queries

[MD S. K. <mk...@pu...>]

Dear Sir,

We are interested to simulate the variability of pattern formation in embryonic development. However, the geometry we consider is ellipsoidal and hollow, and unlike the E.Coli cylindrical geometry, it won't have any depth (to be precise a negligible). Could you please say if it was possible to use a mesh of hollow structure in the existing URDME set up? 

Moreover, what kind of modifications it might needed, given that the current set up of existing URDME is inadequate. 

Thanks,

Shahriar Karim
ECE 
Ag. and Biological Engineering
Purdue University

Re: [Urdme-help] Unable to write file error

[Brian D. <br...@dr...>]

Hi Marc,

It looks like you have an interesting and rare problem.  There are sporadic reports on the Ubuntu forums of programs not being able to write to the "/tmp" directory, which causes all sorts of problems.  I can not replicate your problem on our servers (though they are not the same version of Ubuntu), so I am hoping you can run a few commands to help us debug this problem remotely.

In a terminal, as your usual user (not root) please execute the following commands and email us back the output:
	 ls -ld /tmp
	 ls -l `mktemp -t urdmemodel.XXXXXXXXXX`
	touch /tmp/urdme_test; ls -l /tmp/urdme_test
	mount

Hopefully this will be enough for us to figure out the problem.  I apologize that our software does not work out of the box, but appreciate your efforts to make it a more robust software package.

Thanks,
  Brian Drawert

On Oct 31, 2010, at 12:43 PM, Marc Sturrock wrote:

> Greetings URDME Team,
> 
> I have a query regarding the E. Coli example. I have been working through the URDME manual v1.1 and it suggests solving the example files to ensure everything is working OK.  Although URDME appears to install perfectly fine, I hit a road block when typing the command 
> 
>> fem2 = urdme(fem,'fange')
> 
> I receive back
> 
>> Compiling solver.
>> ??? Error using ==> save
>> Unable to write file
>> /tmp/urdmemodel.WxPguATOWz.mat: No such file or directory.
>> 
>> Error in ==> rdme2mat at 10
>> save(filename, '-STRUCT', 'urdme');
>> 
>> Error in ==> urdme at 227
>> rdme2mat(fem,inputfile);
> 
> I have attempted to change the permissions of the /tmp/ folder to allow the writing of files and I have also logged in as the root user but I still receive the same error.
> 
> I am using Ubuntu 10.04 with Comsol 3.5a and Matlab 2007a. 
> 
> Cheers,
> 
> Marc
> 
> 
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[Urdme-help] Unable to write file error

[Marc S. <mst...@ma...>]

Greetings URDME Team,

I have a query regarding the E. Coli example. I have been working through the URDME manual v1.1 and it suggests solving the example files to ensure everything is working OK.  Although URDME appears to install perfectly fine, I hit a road block when typing the command 

> fem2 = urdme(fem,'fange')

I receive back

> Compiling solver.
> ??? Error using ==> save
> Unable to write file
> /tmp/urdmemodel.WxPguATOWz.mat: No such file or directory.
> 
> Error in ==> rdme2mat at 10
> save(filename, '-STRUCT', 'urdme');
> 
> Error in ==> urdme at 227
> rdme2mat(fem,inputfile);

I have attempted to change the permissions of the /tmp/ folder to allow the writing of files and I have also logged in as the root user but I still receive the same error.

I am using Ubuntu 10.04 with Comsol 3.5a and Matlab 2007a. 

Cheers,

Marc



The University of Dundee is a Scottish Registered Charity, No. SC015096.

Re: [Urdme-help] Problem....URDME

[<mk...@pu...>]

Hi Brian,

Thanks for your reply. I created a symlink to ./matlab in the directory where I
keep urdme. It shows as below--

drwxr-xr-x 9 umulislab umulislab  4096 2010-07-12 10:07 urdme
-rwxr-xr-x 1 umulislab umulislab   406 2010-07-12 10:07 set_matlab_path.pl
-rw-r--r-- 1 umulislab umulislab   751 2010-07-12 10:07 README
-rwxr-xr-x 1 umulislab umulislab  2289 2010-07-12 10:07 install.sh
-rw-r--r-- 1 umulislab umulislab 35147 2010-07-12 10:07 COPYING
-rw-r--r-- 1 umulislab umulislab    61 2010-07-12 10:07 AUTHORS
drwxr-xr-x 5 umulislab umulislab  4096 2010-07-12 17:23 examples
lrwxrwxrwx 1 umulislab umulislab    43 2010-07-12 17:28 matlab ->
/home/umulislab/Documents/Matlab/bin/matlab
lrwxrwxrwx 1 umulislab umulislab    46 2010-07-12 17:29 matlab.sh ->
/home/umulislab/Documents/Matlab/bin/matlab.sh


However, I still I get 

ERROR: Matlab executable not found in your PATH


I am not sure what did you mean by--"The easiest way to fix the problem is to
simply add the matlab "bin" directory to your path."


For your information: 

My Matlab is installed in Following Directory

/home/umulislab/Documents/Matlab/

And my URDME is kept at /home/umulislab/Documents/urdme-1.1_beta


Given these, do you think I need to modify the install.sh file to insert the
matlab location? 

Please clarify what could be done to solve such problems. Thanks in Advance,

Mohammad Shahriar Karim

[Urdme-help] URDME 1.1 (beta) released

[Brian D. <br...@dr...>]

We have just released the beta version of URDME 1.1, please download and install it.  Bug reports are much appreciated.

Thanks,
  The URDME team

[Urdme-help] Welcome to the URDME mailing list

[Brian D. <br...@dr...>]

This email list is designed to be the primary support tool for the URDME project.  Please send all questions on usage, development and feature requests to this list.

Thanks,
 The URDME team