having a problem installing the OCSSW data processors

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devon.mckinnon
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having a problem installing the OCSSW data processors

by devon.mckinnon » Mon Apr 10, 2017 11:46 pm America/New_York

Hi guys,

I am having a problem installing the OCSSW data processors on my mac. I keep getting this error message from using the GUI in SeaDAS;

Execution log for
[/var/folders/vd/nw2z96ld4nnfht8snkmr0zym0000gn/T/install_ocssw.py, --install-dir=/Applications/seadas-7.4/ocssw, --aquarius, --aqua, --terra, --seawifs, --git-branch=v7.4]
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Error - git is either not installed or not in the PATH.

I have OS Sierra 10.12.3, I have downloaded anaconda, and I use IDLE intermittently. I have downloaded GitHub Desktop, but don't really know anything about it or what git is.
I am not savvy at coding, but I'm assuming I need to change the path in the Install OC Processors GUI?

I really appreciate any help! Thanks!

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having a problem installing the OCSSW data processors

by OB.DAAC - SeanBailey » Tue Apr 11, 2017 7:27 am America/New_York

"Error - git is either not installed or not in the PATH" explains the issue quite plainly.  The requirements for OCSSW include Git.
You don't need to know anything about Git to install the processors, but your machine does need it for that process to work, as the installation uses Git.  The easiest way to do that is to download the installer from the Git website.

You will also find that the version of python that comes installed with the Mac doesn't play nice with the HTTPS connections on oceancolor websites, so you'll also probably want to install an alternate version. One we've found works is from Anaconda .  You'll want python2, as the SeaDAS scripts have not been updated to python3 yet.

Sean

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having a problem installing the OCSSW data processors

by OB SeaDAS - knowles » Tue Apr 11, 2017 9:05 am America/New_York


devon.mckinnon
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having a problem installing the OCSSW data processors

by devon.mckinnon » Wed Apr 12, 2017 11:11 pm America/New_York

Danny and Sean,

Thank you so much for your help, I downloaded Git as suggested, do I also need to download a git GUI or is there anything else I need to do besides downloading it?
I corrected the issue of having the incorrect python version installed, I now have "Python 2.7.13 :: Anaconda 4.3.1 (x86_64)", however I am still not able to update the $PATH environment variable.

I am getting this error message when I try to update the $PATH environment variable:

Devons-MBP:~ Devon$ bash Anaconda2-4.3.1-MacOSX-x86_64.sh
bash: Anaconda2-4.3.1-MacOSX-x86_64.sh: No such file or directory

However I see the answer in the FAQ was using "Python 2.7.13 :: Anaconda 4.3.0 (x86_64)" does that matter?
When I download the command line installer for python 2.7, it just gives me a text file of python code, do I run that code with Anaconda, Terminal or IDLE?
Also I am sure I have that previous failed OCSSW directory, where would I find that exactly?

I do really greatly appreciate your help, I'm more of a chemist than coder, and am really excited to start using SeaDAS.

DWM

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having a problem installing the OCSSW data processors

by gnwiii » Thu Apr 13, 2017 7:26 am America/New_York

You don't need a git GUI.  I'm not sure what you mean by "not able to update the $PATH environment variable".   The command to run the Anaconda installer needs to be run in the directory that contains the downloaded file "Anaconda2-4.3.1-MacOSX-x86_64.sh".   Usually, this will be the Downloads folder, in which case you would run:
Devons-MBP:~ Devon$ cd Downloads
Devons-MBP:~/Downloads Devon$ bash Anaconda2-4.3.1-MacOSX-x86_64.sh

When you install Anaconda Python it should offer to set the PATH variable for you.  Git installs to /usr/local/git and then creates a symbolic link in /usr/local/bin, which should already be in your PATH.  There are some simple commands you can run in a terminal to check that these installs have worked.   Below I show both the command you type in a terminal (the stuff on the first line after the "[...]$ " prompt).

1. check that your python is the anaconda 2.7.13 version from Continuum Analytics:
[...]$ python --version
Python 2.7.13 :: Continuum Analytics, Inc.


2. check your git installation:
[...]$ which git
/usr/local/bin/git
[...]$ git --version
git version 2.10.1


It is worth mentioning that you can install git using the "conda" command:
[...]$ conda search git
Fetching package metadata .........
git                          2.6.4                         0  defaults       
                             2.9.3                         0  defaults       
                             2.11.1                        0  defaults       
[...]
[...]$ conda install git
Fetching package metadata .........
Solving package specifications: .

Package plan for installation in environment [your python location]:

The following NEW packages will be INSTALLED:

    curl:  7.52.1-0
    expat: 2.1.0-0
    git:   2.11.1-0

Proceed ([y]/n)? y

expat-2.1.0-0. 100% |################################| Time: 0:00:00 346.11 kB/s
curl-7.52.1-0. 100% |################################| Time: 0:00:00 732.11 kB/s
git-2.11.1-0.t 100% |################################| Time: 0:00:07   1.50 MB/s



[...]$ which git
[your python location]/bin/git
[...]$ git --version
git version 2.11.1

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having a problem installing the OCSSW data processors

by OB SeaDAS - knowles » Thu Apr 13, 2017 9:55 am America/New_York

Devon,

From the command line run:
% cd ~/Downloads  (or wherever you have the Anaconda script)

then (in case the directory is not in your path) run:
% bash ./Anaconda2-4.3.1-MacOSX-x86_64.sh

It'll ask some questions, stay with it until it finishes.

The script will automatically update your PATH with the Anaconda version placed up front.  It does this by adding some lines to this file: ~/.bash_profile

Your ocssw directory is wherever you installed it :)  Assuming you went with the default directory, open the SeaDAS GUI, go under Menu: OCSSW -> Install OC Processors  or Menu: OCSSW -> Update OC Processors, and you will see exactly where the ocssw directory is (or wants to be).

After installing Anaconda python, you will need to open a new window in order to have the new version of python loaded.

To have the new python path accessible via the SeaDAS GUI you will likely have to restart your computer.

Danny

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having a problem installing the OCSSW data processors

by devon.mckinnon » Thu Apr 13, 2017 10:08 pm America/New_York

I ran the Continuum Analytics script and installed everything I believe, I still am not getting the right python version results
ie
Devons-MBP:Downloads Devon$ python --version
Python 2.7.13 :: Anaconda 4.3.1 (x86_64)

and I am still getting the same error message in the SeaDAS OCSSW install prompt that git is not in the path?
Do I have to change the Local Install Directory in the SeaDAS GUI?

I did the conda command and now have

Devons-MBP:~ Devon$ git --version
git version 2.11.1

I am sorry for being so ignorant of terminal commands and pathways... And I appreciate your help! It's starting to get frustrating...

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having a problem installing the OCSSW data processors

by OB SeaDAS - knowles » Fri Apr 14, 2017 7:06 am America/New_York

Why don't you just install OCSSW via the GUI?  Delete the current ocssw directory and then go to Menu -> OCSSW and install from there.

Your python and git versions are now correct so this should work from the GUI.

If you are doing this from the command line then please show the command which you are running along with the error message which it sent out.

Danny

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having a problem installing the OCSSW data processors

by gnwiii » Fri Apr 14, 2017 2:57 pm America/New_York

Many of my colleagues share your frustration.   I think you are very close to having things working, so please don't give up.  I'm sure there are many users encountering similar problems, so it is very useful when someone steps up to point out gaps in the documentation and persists until everything is working properly.

In past I have done a number of hands-on practicals sessions for Ocean Colour workshops.  We found it important to devote the first afternoon to an introduction to the bash command-line and expected students to spend some time in the evenings with the references.  I know it is difficult for most people to dedicate an afternoon and evening to intensive study of topics that seem distantly related to their priorities, but the reality is that scientific software is often "high maintenance" so unless you are fortunate enough to work in group that has "UNIX" (which includes linux and macOS) experts, you will need to learn some basic command line skills.  SeaDAS 7 needs to be usable in the most common Windows, linux, and MacOS configurations.  This requires some compromises, and means that the documentation tends to be "generic" and assumes that the reader can fill in  the gaps for their platform.  As you have discovered, the command line is often needed to sort out problems.  It is much more effective  to past fragments from the command-line into a forum post than to collect screen snapshots from a GUI interface.

To complicate matter further, the switch from http to https  by the US government left users of all sorts of services scrambling to reconfigure systems. 

One bit of confusion:
You say" I still am not getting the right python version results
ie
Devons-MBP:Downloads Devon$ python --version
Python 2.7.13 :: Anaconda 4.3.1 (x86_64)"

Since this matches the version in SeaDAS 7 FAQ: Installing the OCSSW Processors on a Mac I assume yo meant to say you are now getting the right Python version.

devon.mckinnon
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having a problem installing the OCSSW data processors

by devon.mckinnon » Fri Apr 14, 2017 9:15 pm America/New_York

FIGURED IT OUT!!!!

I just needed to run "xcode -select --install" after installing git and the correct python version and it updated the developer path with git.

I remember trying this initially, but I had the incorrect python version installed so nothing happened..

Thank you everyone for your help, now onto learning SeaDAS!! : )

DWM

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