Using PETSc under Cygwin

Question

I'm trying to get PETSc running under Cygwin on my Windows machine to test parallel code. Unfortunately there's a problem where Cygwin is importing elements from my Windows path of the form:

C:\Program Files (x86)\...

And the problem is that the PETSc and MPI compilers are falling on their faces because they don't invoke cygpath to fix the " " characters. So, I need help with one of three things:

1. How to get Cygwin to not load the Windows path

   • I put it on its own partition and am trying to use only native Cygwin compilers so it could, hopefully, live without knowing much about Windows.

2. Rewrite my PATH variable to escape all the " " characters by replacing them with "\ "

I know this:

       echo $PATH | sed 's/ /\\ /g'

Does exactly what I need, but I can't get it to execute as an "export PATH=" command in .bashrc. I've tried:

export PATH='echo $PATH | sed '"'"'s/ /\\ /g'"'"' '

Which just breaks my Cygwin session to the point that I need to repair .bashrc in Notepad++ to boot again

export PATH="echo $PATH | sed 's/ /\\ /g'"

Which just prepends "echo " and appends " | sed 's/\ /g" to PATH.

export PATH='echo $PATH | sed "s/ /\\ /g"'

Which replaces my entire path with just "echo $PATH | sed "/\ /g"

3. Something I haven't thought of at all.

Any help would be greatly appreciated.

Answer 1

How to get Cygwin to not load the Windows path

For the bash shell this can be done by making some small changes to ~/.bash_profile.

I like to have complete control over the PATH in Cygwin bash, so I added the following code to my ~/.bash_profile

# Build up the path using the directories in ~/.path_elements
unset PATH
while read line; do 
  PATH="${PATH}$line"; 
done < ~/.path_elements

# Add current directory to path
export PATH=".:${PATH}"

Notes:

• unset PATH removes any PATH already configured by the Cygwin startup code.

• The while loop reads in path elements from a file in my home directory (~/.path_elements) to build up my preferred PATH

• Finally we add the current directory . to the PATH and export it.

• Adding the current directory to the PATH could be considered as a security risk since built in commands could be replaced by commands located in the current directory. Please bear that in mind if you choose to use my code.

The contents of my ~/.path_elements are as follows. Modify and season to your taste to add extra elements to the path.

/home/DavidPostill/bin:
/usr/local/bin:
/usr/bin:
/c/Windows/system32:
/c/Windows

Result:

DavidPostill@Hal /f/test
$ echo $PATH
.:/home/DavidPostill/bin:/usr/local/bin:/usr/bin:/c/Windows/system32:/c/Windows