2013 Homework 1

Warning

This is a 2013 homework assignment.

Due Wednesday, April 10, 2013, by 11:00pm PDT.

The goals of this homework are to:

• Make sure you are familiar with basic Unix commands (see Unix, Linux, and OS X) and an editor, (see Text editors),
• Start using git (Git) to download course materials,
• Create your own bitbucket repository to keep your coursework and post homeworks to be graded.
• Make sure you have some necessary software installed.

Start early on this assignment so that you can get help from the TAs and/or discussion board if you have trouble with software or with using git.

Before tackling this homework, you should read some of the class notes and links they point to. In particular, the following sections are relevant:

• Unix, Linux, and OS X
• Downloading and installing software for this class
• Text editors
• Git
• Bitbucket repositories: viewing changesets, issue tracking
• Bibliography and further reading

By doing this homework you create a bitbucket repository containing some files that we can view to grade.

See also the Bitbucket 101 instructions that for more tips on setting up bitbucket accounts and using git.

1. First, if you have not already completed the survey on your background and computing needs, please do so now. You can find it here. [Available as of Friday, April 5]

2. Make sure you have access to git on the computer you plan to use (see Downloading and installing software for this class). Read the section Git and the documentation linked from there in order to get a sense of how it works.

3. Clone the class repository following the Instructions for cloning the class repository.

   Make sure you have set the environment variable UWHPSC since this is used below.

4. Set up your own personal repository on Bitbucket, by carefully following all of the instructions at Creating your own Bitbucket repository. By following these instructions you will also create a clone of the repository and add some files to it.

   Make sure you have set the environment variable MYHPSC since this is used below.

5. In the clone of your repository, create a subdirectory homework1:

   $ cd $MYHPSC
   $ mkdir homework1
   

   You should now be able to cd into this directory:

   $ cd homework1
   

   or later you can get there from anywhere via:

   $ cd $MYHPSC/homework1
   

6. Copy some files from the class repository to your own repository by:

   $ cp $UWHPSC/codes/homework1/*  $MYHPSC/homework1
   

   This should create the files

   • test1.py
   • test2.sh
   • test3.f90

   in the directory $MYHPSC/homework1.

7. Use git add and git commit to add these three files and commit a snapshot.

8. Modify test1.py as instructed in the docstring at the top of the file. Try running it via:

   $ python test1.py
   

   It should give results like the following:

   Code run by Your Name
   Environment variable UWHPSC is /somepath/uwhpsc
   Environment variable MYHPSC is /somepath/myhpsc
   Imported numpy ok
   Imported matplotlib ok
   Imported pylab ok
   

   Following the instructions, you will add and commit to files, a modified version of test1.py and the output file test1output.txt.

9. Modify test2.sh as instructed in the comments at the top of the file.

10. Run this bash shell script via:

    $ bash test2.sh
    

    This should give output something like the following:

    Environment variable UWHPSC is /somepath/uwhpsc
    Environment variable MYHPSC is /somepath/myhpsc
    
    which ipython returns...
    /somepath/ipython
    
    which gfortran returns...
    /usr/local/bin/gfortran
    
    gfortran --version returns...
    GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
    
    [more stuff]
    
    Compiling and running a Fortran code...
     Code run by Your Name
     Successfully ran Fortran 90 program
    

    Now run it again and redirect the output to a file:

    $ bash test2.sh > test2output.txt
    

    Add and commit the modified test2.sh and the output files to your repository.

    Note: At the end you should have the following files committed to your repository:

    • $MYHPSC/testfile.txt
    • $MYHPSC/homework1/test1.py
    • $MYHPSC/homework1/test1output.txt
    • $MYHPSC/homework1/test2.sh
    • $MYHPSC/homework1/test2output.txt
    • $MYHPSC/homework1/test3.f90

    Do not check in the file a.out, which was created when the Fortran code was compiled.

    Make sure the copies you want graded have been committed, and then push them to bitbucket via:

    $ git push
    

    These files should then also be visible from your bitbucket webpage, by clicking on the “Source” tab, see Bitbucket repositories: viewing changesets, issue tracking.

11. You created a private repository, so you will have to give us permission to view or clone it. Do so by clicking on the Gear tab at the top of your Bitbucket page for this repository, then on “Access Management”, and then add the following three users with Read access: rjleveque and the TAs smoe and ssusie.

12. Finally, let us know where your Bitbucket repository is so that we can clone it and/or view your source files online in order to grade it. If you are registered in the class, you should be able access the Canvas course webpage. Go to that page and follow instructions under Homework 1 to send us this information.

    You will also have to submit the SHA-1 hash of the commit that you want graded. This is the 40-digit hexadecimal string that shows up when you type:

    $ git log
    

    in your repository.

If you discover you made a mistake in what you turned in you may resubmit this survey with a different SHA-1 hash code. Full credit will be received only if you make your final submission before the due date/time.