How do I download AUTO Hi PF on a Mac?

[member 428835]

Hi PF!

I'm trying to run AUTO07p on a mac OSX Yosemite. Attached are the instructions for downloading I was given. I downloaded Command Line Tools (step 1) a different way, but I have downloaded them. Once I arrive at step 8, after typing auto, I am prompted "command not found"

Any help would be awesome!

 

[jedishrfu]

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.

Was your download a dmg file?

 

[member 428835]

Downloading them doesn't mean they're installed. It would be best to follow the instructions for Xcode to get them and install them.

Where would I find this?

Was your download a dmg file?

Yes, it was a dmg file.

 

[jedishrfu]

Did you click on it to install the tools?

 

[member 428835]

Did you click on it to install the tools?

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

 

[jedishrfu]

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.

 

[jedishrfu]

What command is failing?

Oh I see you typed auto and got command not found.

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

 

[member 428835]

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.

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.

 

[member 428835]

What command is failing?

Oh I see you typed auto and got command not found.

Yes, this is correct.

 

[member 428835]

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

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)

 

[jedishrfu]

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

-----------------------------------------------------------------------------------------
3. Download the gcc-lion.tar.gz and gfortran-lion.tar.gz binaries from: ! http://hpc.sourceforge.net/ These will either be downloaded to your downloads folder in ~/Downloads or onto your Desktop. Open the Terminal application in your applications/utilities/ folder and type > cd ~/Downloads or > cd ~/Desktop depending on where the binaries have been downloaded. Next type in the terminal window > sudo tar -xvf gcc-lion.tar -C /. and enter your password. Then type > sudo tar -xvf gfortran-lion.tar -C /.

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')

 

[jedishrfu]

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

 

[jedishrfu]

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

 

[member 428835]

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')

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?

 

[jedishrfu]

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:

~:~ $ which auto

~:~ $ which python

/usr/bin/python

~:~ $
{/code]

 

[member 428835]

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

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

 

[jedishrfu]

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 that's 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/

 

[jedishrfu]

Okay I looked at OSX Lion 10.7 and its four releases older than Yosemite 10.10 so I'm sure the instructions won't work. You might need to hack it somehow by getting later versions of each of the xcode tools for yosemite and gcc and gfortran for yosemite

https://en.wikipedia.org/wiki/MacOS

https://en.wikipedia.org/wiki/MacOS#/media/File:Mac_OS_X_Timeline_of_Versions.png

 

[member 428835]

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.

 

[member 428835]

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.

 

[jedishrfu]

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.

Its not weird its Apple being Apple. I've had this happen with homebrew stuff. It seems they like to break compatibility from time to time.

One of my biggest beefs with Apple is why they don't follow the filesystem organization that Linux and other Unixes follow. The store programs in /Applications
vs /usr/bin ... I suppose its got to do with making things uninstallable by installing them in a single place so that its easily removable.

 

[member 428835]

Its not weird its Apple being Apple. I've had this happen with homebrew stuff. It seems they like to break compatibility from time to time.

One of my biggest beefs with Apple is why they don't follow the filesystem organization that Linux and other Unixes follow. The store programs in /Applications
vs /usr/bin ... I suppose its got to do with making things uninstallable by installing them in a single place so that its easily removable.

Yea, I don't know much about computers but this is really starting to get annoying. Perhaps I'll switch to a PC on my next purchase, though that'll be a while considering 3 years ago I had to take out a second mortgage to pay for this Mac

 

[jedishrfu]

Yea, I don't know much about computers but this is really starting to get annoying. Perhaps I'll switch to a PC on my next purchase, though that'll be a while considering 3 years ago I had to take out a second mortgage to pay for this Mac

You'll hate the PC once you start programming it and wish you had the unix command line back at least that's been my experience. You can get software on Windows to mimic Unix but its on windows and has a quirky nature.

https://www.cygwin.com/

and this article on getting Unix capability on windows:

https://www.howtogeek.com/170870/5-ways-to-run-linux-software-on-windows/

 

[fog]

Hello everyone,
maybe somebody can help me?
I just installed AUTO on my Mac and everything is fine... the test in the end of the instruction works.
However, as soon as I reboot my Mac, it forgets that I installed AUTO (command not found). Then I have to reinstall (following the instruction starting at point 6) and it works again. Does anybody know why my Mac always forgets the installation and how I can prevent this?
Thanks in advance.

 

[S.G. Janssens]

I'm not on a Mac, but since there are some similarities between MacOS and unix OSes, could it be that you need to set a path to a directory containing the AUTO command in .bashrc or .bash_profile?

 

[fog]

Yes thank you... this tip helped me to localize the problem. It is the line "source ~/auto/07p/cmds/auto.env.sh " which somehow makes AUTO just available for this terminal window (even without restart, a new terminal window can not open AUTO afterwards). So I don't know how to change it/solve the problem, but at least I know now what I have to google. :)

 

[fog]

Ok found it.
echo "source ~/auto/07p/cmds/auto.env.sh" >> .bash_profile
I don't know what it does but it works. :D

 

[jedishrfu]

The echo just prints the quoted text the >> means to a append the printed text to the end of the bash_profile file in your home directory.

Each time you open a command window the bash_profile will be run meaning it will run that line too.

The source command when run will add parameter values to your environment (use env command to see them)

Unix programs look to the environment for these values to know how your system is configured i.e. Where you've stored data for that program or where key libraries and commands are located ( see the PATH and LD_LIBRARY_PATH parameters as examples)

 

[fog]

Oh thank you for the explanation.