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Nothing works....HELP!!

HELP!! I'm trying to complete the tutorial, but absolutely nothing is working working properly!!!

Here is a list of the modifications I've made to my shell.
1. Copied over a ".tcshrc" file from someone else.
2. Maked sure that "usr/local/bin" is under "set path = (..."
3. Changed "setenv TMPDIR /ptmp/$LOGNAME"
to "setenv TMPDIR /glade/scratch/$LOGNAME"

Every time I create a new case I need to make the following modifications,
1. In env_build.xml change the root directory from "/ptmp/..." to "/glade/scratch/..."
2. In env_run.xml change "/ptmp/..." to "/glade/scratch/..."

I am still having the following issues,
1. I get a message telling me that several files were not found, build continues anyway.
2. After several failed attempts at doing the branch run example I managed to get my xml files to look almost exactly (minus the ptmp files) like my colleague who completely the tutorial except hers runs and mine exits before completing.
3. When trying to do a continuation run for b.day2.2, the run exits before completion.
4. Regularly the system becomes extremely slow, almost to the point of being non-responsive (might be my internet connection?).
5. I tried to copy the source code to my home directory the copy failed, but there were some files that copied that I can’t get rid of.
6. Once a run completed with a different job ID then it started with…this never happened again, but it was odd.​

Please help, I've been at this for almost a week now and I'm not halfway through day 2! I'm still learning all of this and I have no idea what to do any more, every solution I come up with seems to lead to another, larger, problem. Help!!!
 
things got so bad I decided to give up and start from scratch and wrote out all the modifications I need to make that I got from members of my research group and CISL. So far everything is working relatively smoothly.

I think part of the issue might have been an error I didn't catch in the first model that carried over when I cloned from it and tried to branch from it.
 
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