Terminal: missing command line, bash in endless loop - linux

Since this morning Terminal has been acting strangely. It runs login and bash (the shell), but the ID keeps running up (it should equal the ID of login and remain constant) and opens additional processes like sort, cat, env and then closing them. This prevented me from entering any commands.
In trying to solve the problem I did a Shell -> Send Reset and Shell -> Send Hard Reset, which didn't solve the problem and now my command line is gone. I can still enter commands via Shell -> New commands.
I've created another admin user and tested terminal and that works.
I'm looking to stop the endless loop and restore my command line.
My OS is OSX 10.9.5

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Linux how to launch visible terminal with script file automatically at startup

I have seen many ways to launch a script like putting it in profile.D, rc.local, or creating a auto start file but none of those launch the file in a visible window if at all. I need it to be in a visible window in Ubuntu. I need to do this because I am using several emulators to stream to different services, and I don't want to have to start the script on each manually.
I am using visual box for the emulator. The sh file is on a removable drive because it is an external file. I also need it to run as sudo.
Edit: I don't actually need it to run at startup. I just need to have the script run. I can probably just sleep really long for graphic to load.
Edit 2: So I created a service that launched a sh file in /usr/bin/ which was supposed to create a gnome-terminal window that ran my script. It ran, however It didn't create a visible window for some reason. I then tried to specify a display which caused gnome to freak out. Dbus was not launching correctly. another question stated that gnome would not work because of how it was designed and stated to use konsole instead. Konsole also stated that it could not connect to a display, giving a QXcbConnection error. Konsole does not have an option to specify display. I don't know what else to try
Edit 3: So I did the thing in the comment. And the service works. However it only works after I run the file that the service runs in usr/bin manually after every restart. The important parts of the file:
#!/bin/bash
sleep 60
ufw disable
ssh nateguana#$(hostname) -X
xhost +
*launch Gnome**only works after file ran manually*
I have also tried exporting DISPLAY, and changing users with su. I have not tried importing SSHD, as another question said to do, as I think that is only for non local connections. I have also tried every single arrangement of commands possible. Xhost errors stating that it is unable to open display "".
You can use gnome-terminal -e <command> to spawn a new bash terminal which runs the command.
You could use something like
gnome-terminal -e /path/to/bashfile
Bear in mind, this will end the terminal after the bash scipt is done executing.
To avoid this,in a newline add $SHELL to the end of your bash script.
PS: the -e argument is deprecated and might be removed in later versions

Windows command prompt capture output of bash script in one step

I trigger a bash script from Windows command prompt.
postCloneSetup.sh
It opens another window and then returns. The window it spawned stays open and logs output text.
I want to capture the output from the spawned window and return that to the Windows command prompt.
I would prefer to use something like
$(postCloneSetup.sh) // Linux for capturing output to current context
for the Windows command prompt.
I'd prefer not to modify postCloneSetup.sh. I know I could have it write out to a file with
exec &> postCloneSetupLog.log
but then I must wait and manually run
type postCloneSetupLog.log
to see the output in the console. This is not possible for integrating into a CI engine, which is my goal.
How can I capture the output from the spawned console in one command?

subprocess problems with sudo,ctrl+c and pipes

I need to run an external C_program using subprocess from a python script.
Here is the tricky parts:
the external program needs to run with super user privileges, and thus I need to ask the user to input his password to make sure he is allowed to run the program.
The external program might run for extremely long time (sometimes days) and the user might need to terminate it manually using CTRL+C
The output of the C_program should be printed to the screen thus the stdout should be piped to the subprocess.
this is what I've tried doing:
try:
proc = subprocess.Popen(c_program, shell=True, stdin=subprocess.PIPE, stderr=subprocess.STDOUT)
#needs sudo password to run this program
proc.communicate(getpass.getpass())
except KeyboardInterrupt:
print "you stopped c_program, script will now go on..."
#do other things
unfortunately, this will cause two problems which I cannot seem to be able to fix:
pressing CTRL+C while c_program is being executed will do absolutly nothing (not only won't it stop the execution of c_program or even the python script itself, it is just ignored...)
In case the script does finish its run, the terminal starts behaving... it will not display what the user is typing in but it does respond to it (for example, typing ls -l will not be displayed on the screen, but, after pressing enter, the output of the command will be printed to the screen)
I'm using Python 2.7 on Ubuntu
Please help :)

How can I revert my last choice on terminal if it shows > symbol?

I'll be glad if someone can fix the title to be more appropriate since I'm pretty new to terminal.
I have an issue with terminal. Once I execute a command, if it goes to the next line, I can't close it or revert it. I assume it starts the executable or asks for more parameters using >
For example:
//Windows Machine
vagrant up
//Vagrant Instance Unix Machine
$ git
>
>
>
> ... it goes on like this, I can't close > so I can't execute other commands
The only solution on fixing is restarting the terminal (which means I need to restart Vagrant instance)
It happens on some commands only - not all, so I don't know what makes a difference.
For example, executing composer, I get information about Composer and terminal goes back to main state. However, if I execute things like php, git, mysql, > symbol appears and I can't return from there.
So, two basic questions;
What causes this?
How can I terminate the current command to go back main state?
Any help would be greatly appreciated.
Ps. I use both windows terminal and unix terminal and this issue happens on both.
Normally you'll see a > prompt if you've entered a command that's syntactically incomplete, for example if there's a unterminated string literal:
$ echo 'hello
> '
hello
$
It means that the shell is waiting for you to type the rest of the command, or at least enough of it to make for something that's not a syntax error.
In this example, the default prompt, $PS1, is '$ ', and the secondary prompt, $PS2, is '> '. Read the documentation for your shell (probably bash) for more information.
You can cancel the current command and get back to your primary prompt for a new command by typing Control-C.
This is all about the behavior of your shell; it has nothing to do with your terminal (almost certainly a terminal emulator), which merely provides a GUI for your shell to run in.

Linux: using the tee command via ssh

I have written a Fortran program (let's call it program.exe) with does some simulation for me. Via ssh I'm logging ino some far away computers to start runs there whose results I collect after a few days. To be up-to-date how the program proceeds I want to write the shell output into a text file output.txt also (since I can't be logged in the far away computers all the time). The command should be something like
nohup program.exe | tee output.txt > /dev/null &
This enables me to have a look at output.txt to see the current status even though the program hasn't ended its run yet. The above command works fine on my local machine. I tried first with the command '>' but here the problem was that nothing was written into the text file until the whole program had finish (maybe related to the pipe buffer?). So I used the workaround with 'tee'.
The problem is now that when I log into the computer via ssh (ssh -X user#machine), execute the above command and look at output.txt with the VI editor nothing appears until the program has finished. If I omit the 'nohup' and '&' I will not even get any shell output until it has finished. My thought was that it might have to do something with data being buffered by ssh but I'm rather a Linux newbie. For any ideas or workaround I would be very grateful!
I would use screen utility http://www.oreillynet.com/linux/cmd/cmd.csp?path=s/screen instead of nohup. Thus I would be able to set my program to detached state (^A^D) reconnect to the host, retrieve my screen session (screen -r)
and monitor my output as if I never logged out.

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