Notes

Linux Notes

in Pine, to scroll to the top: w, then C-y
in Pine, to scroll to the end: w, then C-v
Pine's Pico Quick Refs
to send standard output to the screen and a file simultaneously:
```
cmd | tee file
```
to find files modified for the last 2 days: find . -mtime -2
to only list hidden/files directories: ls -d .*
use find with grep to find files that contain a word:
$ find ~ -name '*' -exec grep -l 'mystring' \{\} \;
chmod octal numeric codes:
- 700: only owner can read
- 755: everyone can read but not write
- 775: only group can read and write
- 770: noone but group can read
- 666: everyone can read and write
- 1777: everyone can read,write,execute
secure copy with ssh:
- to preserve time stamp : -p
- to scp to sdome: % scp filename userid@sdome:dir_name
- to scp from sdome % scp myid@sdome:dir/file file
to cp preserving rights: cp -p

to compare files with ssh:

ssh me@my.local.host cat myremote.file | diff - mylocal.file

to get the number of lines in a file: wc -l myfile
to create a new archive and copy file1 and file2 into it:
```
tar -cvf archive.tar dir_of_file1_and_2
```
to untar: tar -vxf archive.tar
to list file in archive.tar: tar -tvf archive.tar

tar option keys:

c = create new 
t = list the file names in archive
v = verbose mode
x = extract
u = add

to extract a file filename in a tar file filearch.tar:

tar -xvf filearch.tar `tar -tf filearch.tar |grep
filename`

to see a file type : file <filename>

to only list directories:

 ls -1F | grep / | sed 's/\///' | pr -t -4

to only list files:
```
 ls -1F | grep -v / | pr -t -3 
```
to check what's inside a ahared lib: nm mylib.so

Linux Notes

to enable delete with backspace for vi and xemacs in console, try set : stty erase ^?
to rename a group of files in Redhat:
```
rename foo barfiles*
```

to rename with sed:

  for old in *.c; do
    new=`echo $old | sed 's/.c/.cc/'`
    mv $old $new
  done

to reverse search a command in bash: ctrl-R, then type command
to export PATH variable in permanently, do in /etc/profile or profile.d
to check redhat version: % less /etc/redhat-release
to check system: % uname
to check cpu: % less /proc/cpuinfo
use screen to split screen: ctrl-a S
to create screen: ctrl-a c
to switch regions: ctrl-a tab
to get help: ctrl-a ?
to install new library path: edit entry in /etc/ld.so.conf; then login as root: % ldconfig

to loop through file names in a directory and execute commands

for variable in value1 value2 value3
do 
    echo $variable;
    # do something useful...
done

to update files across machines with rsync: rsync -Cavuzbtn userid@foo:src/bar /data/tmp
- C : exclude cvs-like
- a : archive mode --recurse; preserve
- v : verbose
- u : update only
- z : compress
- b : backup--preexisting files renamed with ~
- t : preserve time
- n : dry run; only testing transfer
to use ssh in rsync, set RSYNC_RSH to be ssh
quick refs to mc:
- to delete: F8
- to copy: F5
- to select by pattern: +
- to unselect: -
- to move: F6
- to soft link: C-x s
- to mkdir: F7
- to swap panels: C-u
- to toggle 1-2 panels: A-t
- to create hotlist: C-\
- to incrementally search: C-s
- to find:A-?
- to mark file: Ins
- to ftp with ssh: cd /#sh:user@host:C:/remote/dir/path
to maintain services in /etc/rc[0-6].d, use chkconfig
services and ports are in /etc/services
to kill ssh session: ~ .
using nohup to run long process in background causes ssh session to hang upon logout. use above to kill ssh while keeping bg process running

Latex Notes

to use < and > in text mode: \textless and \textgreater
to annotate in bibliography, use annotation.bst
to make sure letter/word is capped in bibtex, put {}
to set irregular last name, use {}
to include all items not cited: \nocite {*}

to print out all bibtex database items:

	    \documentstyle{amsart}
	    \begin{document}
	    \nocite{*}
	    \bibliographystyle{amsplain}
	    \bibliography{mybibliography}
	    \end{document}

to print ~ properly: use the url package: then \url{~/my/path/or/url}

to convert pages range from dvi to postcript:

dvips -p startpage -l endpage -o fileout.ps filein.dvi

use subfigure package with //// to have vertically align subfigures

Postscript Notes

to put two pages on one sheet (of A4 paper): psnup -2 input.ps output.ps
to convert a document on A4 size paper to letter size paper:
```
psresize -pA4 -pletter input.ps output.ps
```
to create a new PostScript file selecting the pages 2,3,4,6 from an existing PostScript file:
```
psselect 2-4,6 input.ps output.ps
```
to make sure paper size is correct, check the DocumentSize inside the file
A4 bounding box: 0 0 595 842 (210 x 297 mm)
Letter bounding box: 0 0 612 792 (215.9 x 279.4 mm)
check default size in config.ps for dvips
to print a file double-sided on capable printer, edit the PostScript file and add the following line immediately after the first block of lines that begin with '%': statusdict /setduplexmode known { statusdict begin true setduplexmode end } if

Emacs Notes

use M-^ to join lines
use AUCtex with outline mode
to add custom macros to have completion: add "mymacro" in latex.el in the group below the comment "This have no special .."
to make these variables have certain face (color), add in the file font-latex.el in the group defcustom font-latex-match-reference-keywords
Latest stable version is 11.53. Use with latest Xemacs base: 21.4.15
to work around the buggy overlays-at error; put (require 'overlay) before (require 'tex-site) in the init.el
to modify default auctex view: M-x customize-variable RET TeX-view-style RET; then change variables
to use forward-search: use xdvi-search.el and srcltx.sty packages; modify xdvi-search.el's xdvi-bin to have -expert and -s 5
to bind to keyboard keys: (add-hook 'LaTeX-mode-hook (lambda () (local-set-key "\C-c\C-a" 'xdvi-jump-to-line)))
to use inverse-search: use gnuserv; edit /etc/hosts if necessary; gnuserv-start in .init.el; in xdvi call with CTRL Mouse Button 1
to replace using regexp: M (alt)-C-%

to force Fortran 90 mode on *.F instead of Fortran 77:

(setq auto-mode-alist (cons '("\\.F" . f90-mode) auto-mode-alist))

AUCtex seems to disable smart quotes if babel is used
to search a complete word, use regexp :
```
	  M-C-s  \Wmyword\W 
```
this seems also to work: \< myword\>

Vi Notes

to move faster by one character (Left-Down-Up-Right):h j k l
to write to the file those changes made to the buffer that have not already been written and quit: ZZ
to open new line below cursor for text: o
to open new line above cursor for text: O
to join two lines, type J in the first line
to repeat the search command in the forward and backward direction: n / N
to delete n number of x (x is word/line/sentence/paragraph): ndx
to switch upper case/lower case :~
to get the line number of current cursor position in the buffer and modification status of the file: ^g
to repeat the action performed by the last command:.
to undo the effects of the last command: u
to restore the current line to its state prior to present changes: U
to clear and redraw the current window: ^l.
to delete all the lines from the current line to the last line: :.,$d
to insert the contents of the file filename under the current line of the buffer: :r filename
to replace the first instance of text on the current line with new_text: :s/text/new_text/
to replace every occurrence of text on the current line with new_text: :s/text/new_text/g
to hanges every occurrence of text in the buffer to new_text: :g/text/s//new_text/g
to set line numbers: :set nu

Windows Notes

to cycle back and forth in windows explorer: tab/ shift tab

Word Notes

use outline mode to save time
to convert text to table, go to Table, convert text to table
shortcuts for german word 2k:
- ctrl+B: symbol
- ctr+F: bold
- ctrl+K: italic
- ctl+# : subscript
- ctrl++: superscript
- ctrl+U: underline
a good way to insert fig with caption for x-referencing:
- make a regular text box and inser the graphics and caption.
- insert the caption with the "Caption ..." selection on the "Insert" menu.
- convert the text box to a frame by accessing the text box's properties.
- format the frame from the frame properties dialog box.
- a better way is using 2 row column. insert pic in first row, caption in second
- in paragraph format, in cell and line, check keep lines together

MAPLE Notes

complete Unix Maple shortcuts
Maple programming notes of Prof. Kraft
to list variables : anames( ) for assigned variables; unames() for unassigned; anames(user) for my assigned vars
good orientation=[55,30]
positive x-y plane orientation=[-90,0]
the arrow -> works like a procedure
CodeGenaration options
- declare=[declaration(s)]: specifies the types of variables. Form is varname::vartype; varname = variable name; vartype = Maple type name (see CodeGenerationDetails)
to print plot to postscript file for later insert into Latex:
plotsetup(postscript, plotoutput=`image.ps`, plotoptions=`color,portrait,height=300,width=300`);
linalg is obsolete: use LinearAlgebra instead. See migration in installation dir.
check out Kraft's worksheet 4.05.ws for good procedure examples
to browse types help: programming--data types--Type cheking--Types
to actually see maple sources: interface( verboseproc=2 ); then : print(maple function);
to see remember table in expand: op( 4, eval(expand) );
use trace to trace a procedure
use forget to erase remember table
Short forms in LinearAlgebra package:
- column vector: < x,y,z >
- row vector: < x | y | z >
- 2x3 matrix: < < x | y | z >, < z | y | x > >

GNUPLOT Notes

Gnuplot Not So FAQ

use: every I:J:K:L:M:N
I Line increment
J Data block increment
K The first line
L The first data block
M The last line
N The last data block
every 2 plot every 2 line
every ::3 skip the first 3 lines
every ::3::5 plot from the 4-th to 6-th lines
every ::0::0 plot the first line only
every 2::::6 plot the 1,3,5,7-th lines
every :2 plot every 2 data block
every :::5::8 plot from 5-th to 8-th data blocks

ANSYS Notes

to view plots directed to *.GRPH file: run Display from Tansys

MATLAB Notes

good paper position for exporting to latex:
```
set(gcf,'PaperPosition',[0 0 8.0 6.0]) 
```
to run Matlab in the background and to persist after logout:
```
 nohup matlab -display NO < matlabfile.m >& output.out&
```
Matlab cannot plot directly to a file, so disable all plot command.
as a workaround, instead of running MATLAB in the background, you can leave the DISPLAY defined and use "invisible figures":
```
figure('visible','off')
```
```
 plot(1:10) 
```
```
print -djpeg 
```
to check Matlab on Unix systems variables: matlab -n
to startup without splash screen: matlab -nosplash

FORTRAN90 Notes

commands to invoke compiler:
- Intel Fortran ifort is binary INCOMPATIBLE with g77/ gcc
- f90...F90 on Unix
- f77...F77 ,,
- df ...F90 Compaq compiler
- pgf90 ...Portland Group F90
file name after !include should be in INCLUDE dir
for ifc version 8: use ifort not ifc
Good Programming Practice:
- use free-source form in new Fortran programs
- use meaningful variable names
- always use IMPLICIT NONE
- create a data dictionary, declare and define each variable that you use
- name your constants, rather than use 3.141593 for p, use pi = 3.141593. Use as much precision as your computer will support , e.g. pi = 4.0*atan(1.0) is an alternative
- use integers only to specify discrete, integral quantities, use real for continuous quantities
- avoid mixed-mode arithmetic, use conversion intrinsic functions, real, int, nint
- pay attention to readability:
- use comments liberally
- pay attention to layout, indent do loops etc
- use extra parentheses
- echo variables entered from a keyboard (it is a good idea to echo all input variables)
- initialize ALL variables in a program prior to use. You may do this
- with assignment statements
- with READ statements
- in declaration statements
- Always print the physical units with out put variables. Make sure that your comments indicate the units used in a program.
useful Intel Fortran 90 libraries:
GNU g77 fortran
- g77 doesn't accent .f90, use .F instead
- necessary options:
  - -ffree-form

== : .EQ.
/= : .NE.
> : .GT.
>= : .GE.
< : .LT.
<= : .LE.

.AND.
.OR.
.EQV.
.NEQV.
.NOT.

GNU Make Notes

Some makefile tips
suffix rules are obsolete; use pattern rules which are more general and clearer

CVS Notes

to reset any sticky tags: cvs update -A *
to have default CVSROOT repository, put in .bashrc: CVSROOT=:ext:login_id@host.address.some.where:/path/to/cvsroot
to force ssh protocol: set CVS_RSH=ssh in .bashrc
to initialize repository: cvs -d /usr/local/cvsroot/ init
to checkout: cvs checkout modulename
to update: cvs update module/filename
to commit: cvs commit -m "your message" module/filename
U file: The file was brought up to date with respect to the repository. This is done for any file that exists in the repository but not in your source, and for files that you haven't changed but are not the most recent versions available in the repository.
P file: Like U, but the cvs server sends a patch instead of an entire file. This accomplishes the same thing as U using less bandwidth.
A file: The file has been added to your private copy of the sources, and will be added to the source repository when you run commit on the file. This is a reminder to you that the file needs to be committed.
R file: The file has been removed from your private copy of the sources, and will be removed from the source repository when you run commit on the file. This is a reminder to you that the file needs to be committed.
M file: The file is modified in your working directory. M can indicate one of two states for a file you're working on: either there were no modifications to the same file in the repository, so that your file remains as you last saw it; or there were modifications in the repository as well as in your copy, but they were merged successfully, without conflict, in your working directory. cvs will print some messages if it merges your work, and a backup copy of your working file (as it looked before you ran update) will be made. The exact name of that file is printed while update runs.
C file: A conflict was detected while trying to merge your changes to file with changes from the source repository. file (the copy in your working directory) is now the result of attempting to merge the two revisions; an unmodified copy of your file is also in your working directory, with the name .#file.revision where revision is the revision that your modified file started from.

Petsc Notes

Petsc useful options:
- Options for all PETSc programs:
  - mpi_return_on_error: MPI returns error code, rather than abort on internal error
  - trinfo: prints total memory usage
  - get_resident_set_size: print memory usage at end of run
  - log[_all _summary]: logging objects and events
  - log_trace [filename]: prints trace of all PETSc calls
  - log_info : print informative messages about the calculations
  - v: prints PETSc version number and release date
  - options_file : reads options from file
- Matrix Options
- Vector options
- Preconditioner (PC) Options
- Krylov Method (KSP) Options
- Matrix Options
complete PETSc options
complete SLEPc options

Linux Cluster Notes

to shutdown some nodes:

cshutdown -k cluster1: cluster2: -t 5 system going down for updates