GeneralTechNotes

qmon& :  look up job status on device machine

qsub mpirun_device:   submit job to run
P-Quatom, make in debug mode:
Make MEHOD=dbg
=======================about module==================
module purge // clean all modules
module ava <name>  // see available modules related to <name>
module load <name>  // load the corresponding module
module unload <name> // clean the module <name>
module list // see the list of modules

======================about shared library and binaries===============
Check the defined symbols of .so file:    nm <filename>
Check the rpath of .so or binary file:  
(1)	readelf –d <filename>
(2)	objdump –x <filename> | grep RPATH   //or grep RUNPATH

==========================gnu plot==================================
Set axis:
set xrange[1:10] 
set autoscale x
set xtics font "Times-Roman, 30" 

set line style: http://gnuplot.sourceforge.net/docs_4.2/node237.html
set style line 1 lt 2 lw 2 pt 3 ps 0.5 
// define a line style 1, with line type 2(green), linewith 2, point type 3, point  size 0.5

Plot f(x) ls 1 // plot f(x), use the above defined line style 1.

Set logscale  y  // set logscale to y axis

Set font:
set xtics font "Times-Roman, 30" 


======================vim tips===========================

Recover from ctrl+s:  using ctrl+q



==============================git command=====================================
gitk  // see git history
git ls-files   // check the files in current dir that are on git reposory
git status
git status –-untracked-files=no
git log
git log –-author=yang
git checkout < 5 digits of commit #>   // go back to certain snapshot
git checkout –f <commit #>  // checkout the snapshot by force
git checkout master/head   // go to top(newest) snapshot
git diff –status <commit #1>..< commit #2>    // compare all files
git diff –status <commit #1>..<commit #2>  <filename>   // compare specific file
git commit –am ‘comments…’
gitk <filename>:  see the change history. 
git rm --cached filename    // untrack file

example of git clone:
git clone ssh://git-pop@device01/~/POP.git

online tutorial of git: https://www.atlassian.com/git/



=============================git cheat sheet ============================
Force git to overwrite local files on pull
git fetch --all
git reset --hard origin/master
git fetch downloads the latest from remote without trying to merge or rebase anything. 
Then the git reset resets the master branch to what you just fetched.

http://stackoverflow.com/questions/1125968/force-git-to-overwrite-local-files-on-pull

undo a git mege:
http://stackoverflow.com/questions/2389361/undo-a-git-merge

http://www.gitguys.com/topics/merging-with-a-conflict-conflicts-and-resolutions/
git show test:README

git ls-files -u
•	1: The “common ancestor” of the file (the version of the file that both the current and other branch originated from).
•	2: The version from the current branch (the master branch in this case).
•	3: The version from the other branch (the test branch)

http://www.gitguys.com/topics/whats-the-deal-with-the-git-index/
git diff: Show differences between your working directory and the index.
git diff –cached: Show differences between the index and the most recent commit.
git diff HEAD: Show the differences between your working directory and the most recent commit.

git branch model:
git checkout -b branch-ngit merge --no-ff branch-name (no fast forward) 
git branch -d branch-name
git push 
http://nvie.com/posts/a-successful-git-branching-model/

checkout previous files with paths:
git checkout  7ab2747 -- ./include/simulations/KLMC/DiagProfile.h
(-- separates versions and paths:   version -- path)

Save unfinished work to temporary files: (http://git-scm.com/book/en/Git-Tools-Stashing)
git stash; do some other work; git stash apply
git stash list //list all stash lists
git stash apply stash@{2} 
git stash apply --index

git detached head:
http://stackoverflow.com/questions/5772192/git-how-can-i-reconcile-detached-head-with-master-origin

https://event.on24.com/eventRegistration/prereg/register.jsp?eventid=607903&sessionid=1&key=4BA57B73175EA0C0D1260502E820E969

checkout a single file:
git checkout [hash_id] filepath
checkout previous version (detached head)
git checkout [hash_id]
go back to master:
git checkout master

discard all changes:
For a specific file use:
git checkout path/to/file/to/revert
For all unstaged files use:
git checkout -- .
Make sure to include the period at the end.

Compare differences:
git diff 6015c7..1510b3 --stat

atlassian.com/git/tutorial/undoing-changes?_escaped_fragment_=checkout#!checkout

show previous versions git show  filename
git show HEAD:./Structure.tex   //current one
git show HEAD^:./Structure.tex  //previous one
http://stackoverflow.com/questions/610208/how-to-retrieve-a-single-file-from-specific-revision-in-git
git log --stat filename
alias: 
git config --global alias.st status 
git config --global alias.ci 'commit -v'

http://stackoverflow.com/questions/2553786/how-do-i-alias-commands-in-git

http://git-scm.com/book/ch1-5.html#Your-Editor
Now that your identity is set up, you can configure the default text editor that will be used when Git needs you to type in a message. By default, Git uses your system’s default editor, which is generally Vi or Vim. If you want to use a different text editor, such as Emacs, you can do the following:
$ git config --global core.editor emacs
http://stackoverflow.com/questions/115983/how-do-i-add-an-empty-directory-to-a-git-repository

Modify a file and then commit work to local repository:
git add filename
git commit -m “new work” 

Forgot to add file before last commit: 
git add filename
git commit --amend

git rm file but keep on disk
git rm --cached file  

git branching:  http://git-scm.com/book/en/Git-Branching-What-a-Branch-Is
creating a new branch:     git branch newbr
checkout a new branch:    git checkout newbr
return to master branch:  git checkout master
merge branch to master:  git checkout master;  merge newbr 
delete a branch:  git branch -d newbr
check last branch: git branch -v
Create a branch and switch to it at the same time: git checkout -b iss53
check whether branches are merged or not: git branch --merged / --no-merged
synchronizing with remote branch: git pull origin

git rebasing: http://git-scm.com/book/en/Git-Branching-Rebasing
git rebase and conflict handling: http://gitbook.liuhui998.com/4_2.html
resolve conflict: check conflicted files, work on conflicted sessions, remove <<<< ==== >>>>, and do git add filename
When you have resolved this problem run "git rebase --continue".
If you would prefer to skip this patch, instead run "git rebase --skip".
To check out the original branch and stop rebasing run "git rebase --abort".

git pull and git merge: http://www.lurklurk.org/gitpix/gitpix.html
git pull combines git fetch and git merge
after merge, check conflict files: git ls-files -u (unmerged files)

git log: http://gitready.com/advanced/2009/01/20/bend-logs-to-your-will.html
git log --stat
git log --name-status
git rm --cached -r somedir will stage the deletion of the directory, but doesn't touch anything on disk.


=============================gdb notes=========================================

Gdb wiki: https://sourceware.org/gdb/wiki/HomePage
Print a vector:   (Gdb)  print myVector
print *(myVector._M_impl._M_start)@myVector.size()
http://stackoverflow.com/questions/253099/how-do-i-print-the-elements-of-a-c-vector-in-gdb

see the content of array:
p *array@len


use gdb in the command line

$ gdb  Quatom
$ set args  foo.in
$ run
When error message shows,
$ bt
Then it will quickly locate the place where error happens 

Catch Silly mistakes with GCC  (should compile in debug mode)
http://codeforces.com/blog/entry/15547

GCC 4.9.3 does not work with default gdb usr/bin/gdb
Use gdb 7.10.1 installed by orgul


==========================codelite tips====================

Ctrl+mouse left:  can be used to show the value of variables
When print variable values in gdb, uncheck “Enable debugger full logging”,  it makes the showing much clear
Then, if want to show the value of a vector, simply “print vector”


====================use hotkeys efficiently (get rid of mouse)=======================
General windows hotkeys
Ctrl+tab  // switch window within a program
Alt+tab  //   switch window between programs

Win+left_arrow   // move current window to the left part of current monitor
Win+right_arrow  // …

Win+shift+left_arrow  // move current window to the left monitor
Win+shift+right_arrow   // move current window to the right monitor
Alt + LeftArrow (or backspace)  // go back to previous webpage

For gedit, how to swith between different tabs:
Ctr+alt+pageup/pagedown


================use valgrind for performance analysis
First compile in gdb mode,
Then run the following:  (valgrind available on nandsim03)
valgrind --tool=callgrind ../../bin/Quatom <yourinputfile>  
you could terminate any time during the running.
Then  run  kcachegrind
Load the .out file generated by valgrind then you could see the analysis

Note: make sure you turn off the compile option fsanitize=address which  
that conflicts with valgrind as both are essentially trying to do more 
or less the same thing.


================use valgrind for memory check==============
valgrind --leak-check=yes myprog arg1 arg2


============ use valgrind for array bound check==================
Valgrind --tool=exp-sgcheck
http://stackoverflow.com/questions/2291114/runtime-array-bounds-checking-with-g