1. Feb 13, 2017

joshmccraney

Hi PF!

Any help would be awesome!

Attached Files:

• auto-installation-mac.pdf
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2. Feb 13, 2017

Staff: Mentor

Downloading them doesn't mean they're installed. It would be best to follow the instructions for Xcode to get them and install them. If you used an apple cd to install them that would work too.

3. Feb 13, 2017

joshmccraney

Where would I find this?
Yes, it was a dmg file.

4. Feb 13, 2017

Staff: Mentor

Did you click on it to install the tools?

5. Feb 13, 2017

joshmccraney

Are you asking if I clicked on the dmg file: gfortran-5.2-Yosemite.dmg

6. Feb 13, 2017

Staff: Mentor

You said in your post you downloaded the command line tools a different way that's why I asked if you used the dmg to install them.

7. Feb 13, 2017

Staff: Mentor

What command is failing?

So looking at your instruction steps you had to build auto. Did it build okay?

8. Feb 13, 2017

joshmccraney

Oh, no I did not. I used this link:

http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/

When I try to enter command lines into the terminal it prompts me that I already have the command tools installed.

9. Feb 13, 2017

joshmccraney

Yes, this is correct.

10. Feb 15, 2017

joshmccraney

I don't know how I missed this before. How could I tell if it built okay? (Sorry, I'm not too great with computers)

11. Feb 15, 2017

Staff: Mentor

The steps 3 thru 8 in step 7'did you get the message AUTO has been configured with support for OpenMP?

-----------------------------------------------------------------------------------------

4. Download AUTO07p (version 0.9) from: http://sourceforge.net/projects/auto-07p/files/auto07p/ and in Finder place the /auto/ directory in your home directory.

6. Download the auto.env.sh file and save it in the directory ~/auto/07p/cmds/

Now open the Terminal Application in /Applications/Utilities and type at the command line > source ~/auto/07p/cmds/auto.env.sh

7. You are now ready to install AUTO. In the terminal window now type > cd ~/auto/07p/ > ./configure

(the last line of the output should be
***************************************************
AUTO has been configured with support for OpenMP
*************************************************** )

then type in the terminal window > make all

8. Testing that AUTO works.

In a terminal window, type > mkdir ~/Desktop/test_auto/ > cd ~/Desktop/test_auto > auto

(you should now get a new prompt: AUTO> )

at the new prompt type AUTO> copydemo(‘abc') AUTO> load(equation=‘abc') AUTO> load(constants=‘abc') AUTO> run AUTO> save(‘abc') AUTO> plot(‘abc')

12. Feb 15, 2017

Staff: Mentor

One thing to be aware is that when it asks you to open a terminal window you should open it and not reuse an already opened one because each time you open a new one it initialized its environment with the latest values.

These values may have set because of earlier steps you took to install it.

As an example, say one of your steps added a path to the path variable in the .bashrc or .profile file you won't see it there until you open a new terminal which reads the .bashrc and/or .profile files

13. Feb 15, 2017

Staff: Mentor

also notice in step 7 the make all command that builds what you're going to run in step 8

14. Feb 15, 2017

joshmccraney

I did everything but go stuck at step 8. To confirm, I got the message AUTO has been configured with support for OpenMP . I am able to make the directory, but then when I go in and type > auto it says -bash: auto: command not found
When I look into the folder test_auto i notice it is empty. Any help?

15. Feb 15, 2017

Staff: Mentor

open a new terminal window and try the which command

which auto

if its in the path then it should find it and report on where it found it

As an example, which auto says nothing ie I don't have it but which python says:

Code (Bash):

~:~ $which auto ~:~$ which python

/usr/bin/python

~:~ \$
{/code]

16. Feb 15, 2017

joshmccraney

Shoot mine says nothing too! But I made it to this point; what do you suppose the issue is?

17. Feb 15, 2017

Staff: Mentor

The only thing I can think of is try it again step by step.

Are you on OSX Lion or some other MacOS variant?

The instructions say for Lion other os variants may have modified steps.

I found some bug reports but they were too old. Also looking at sourceforge the last update was October 2015 so it may no longer be maintained and not work for later MacOS variants.

You might have to use sudo on some of your commands to get them to do stuff correctly. I've seen problems like this on my linux box where an install actually admin privileges to install in some directory.

So what this install is doing is first requiring Xcode to get Mac developer tools which aren't normally installed then getting a version of Python, the GNU for Lion compilers for Fortran and gcc and then using them to build a version of AUTO for your machine. There's a lot of dependencies here. You probably need to check if gcc is there and gfortran is there via the which command.

Do you need AUTO or would something like Freemat do for your work?

Freemat is a MATLAB clone thats freely available and is pretty easy to use for plots and such.

Alternatively, there's Julia which is also similar to matlab and has quite a few plotting plugins to make pdf quality plots.

Here's some info on Python and Julia using the Juypter notebook interface

https://lectures.quantecon.org/

Last edited: Feb 15, 2017
18. Feb 15, 2017

Staff: Mentor

19. Feb 15, 2017

joshmccraney

Thanks for all your help! Some people in my research group got this working for Sierra, so maybe I'll update and follow their steps again (which looks like it's what you were taking me through). So weird though that this isn't working? I'll keep you posted on results if you care.

20. Feb 15, 2017

joshmccraney

Sorry, answering your recommendations, I'm unsure if other programs will do what AUTO does. The professor seems to think AUTO can do stuff that most programs cannot regarding bifurcations and such.