How to directly generate a STL file from netgen

# This is a Makefile

georoot=hfvmd001
geofile=$(georoot).geo
stlfile=$(georoot)_000.stl


netgenSTL:
netgen -batchmode -geofile=$(geofile)  -meshfile=$(stlfile) -meshfiletype="STL Format"

How to add and remove path

# in ~/bin/bashfun file
# add the following line in .bashrc
# . ~/bin/bashfun

add-intel ()
{
export PATH=/opt/intel/bin/:/opt/intel/compilers_and_libraries_2017.0.098/linux/mpi/intel64/bin/:$PATH
}

rm-intel ()
{
newpath=`echo $PATH | sed -e "s/\/opt\/intel\/bin\/://" | sed -e 's/\/opt\/intel\/compilers_and_libraries_2017.0.098\/linux\/mpi\/intel64\/bin\/://' `
# echo $newpath
export PATH=$newpath
}

How to open google chrome with incognito mode as default

1. Open /usr/share/applications/google-chrome.desktop 
• sudo vi  /usr/share/applications/google-chrome.desktop 
2. Find lines beginning with Exec and change
• /usr/bin/google-chrome-stable  
• to
• /usr/bin/google-chrome-stable  --incognito  

How to install OpenFOAM3+ on Ubuntu 16

1. Compilers (default): gcc and openmpi
2. Go to home directory and make "OpenFOAM" directory
   • cd
   • mkdir -p OpenFOAM
   • cd OpenFOAM
3. Download: OpenFOAM-v3.0+.tgz HERE
4. Unzip
   • tar -xzf OpenFOAM-v3.0+.tgz
   • cd OpenFOAM-v3.0+
5. Disable graphics compiling part
   1. Open
      • vi src/postProcessing/functionObjects/Allwmake
   2. Comment out the last line
      • # ./graphics/Allwmake
6. Take care of conflict due to flex++ version
   1. Open the following files
      1. $WM_PROJECT_DIR/src/triSurface/triSurface/interfaces/STL/readSTLASCII.L
      2. $WM_PROJECT_DIR/applications/utilities/mesh/conversion/gambitToFoam/gambitToFoam.L
      3. $WM_PROJECT_DIR/applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L
      4. $WM_PROJECT_DIR/applications/utilities/mesh/conversion/fluentMeshToFoam/fluentMeshToFoam.L
      5. $WM_PROJECT_DIR/applications/utilities/mesh/conversion/ansysToFoam/ansysToFoam.L
   2. Make change
      • from
        • #if YY_FLEX_SUBMINOR_VERSION < 34
        • extern "C" int yywrap()
        • #else
        • int yyFlexLexer::yywrap()
        • #endif
      • to
        • // #if YY_FLEX_SUBMINOR_VERSION < 34
        • // extern "C" int yywrap()
        • // #else
        • int yyFlexLexer::yywrap()
        • // #endif
7. Set up compiling environment
   • source OpenFOAM/OpenFOAM-v3.0+/etc/bashrc
   • echo " alias of30plus='source OpenFOAM/OpenFOAM-v3.0+/etc/bashrc'" >> $HOME/.bahsrc
8. Compile
   • ./Allwmake

to reset KDE screen

cp -a ~/.kde/share/apps/kscreen ~/.kde/share/apps/kscreen.bak

rm -f ~/.kde/share/apps/kscreen/*

sudo update-grub

shutdown -r now

Emacs short-cut

M-x
org-emphasize
org-mode
 

You can make words *bold*, /italic/, _underlined_, =verbatim= and ~code~, and, if you must, ‘+strike-through+’. Text in the code and verbatim string is not processed for Org mode specific syntax, it is exported verbatim.

Adding latex template in Ubuntu

Make a new directory for

Class files under
/usr/share/texlive/texmf-dist/tex/latex/

BST files under
/usr/share/texlive/texmf-dist/bibtex/bst/


STY files under
/usr/share/texlive/texmf-dist/tex/latex/

SLURM

http://slurm.schedmd.com/quickstart.html

pdfcrop with margins

http://askubuntu.com/questions/124692/command-line-tool-to-crop-pdf-files

If you wish to crop a pdf with left, top, right and bottom margins of 5, 10, 20, and 30 pt (points), then run

pdfcrop --margins '5 10 20 30' input.pdf output.pdf

in terminal. To actually crop something away, use negative values in the argument for crop. For example,

pdfcrop --margins '-50 -50 -50 -50' input.pdf output.pdf

crops 50 pts from the left, top, right, bottom (in this order).

If you run only the command pdfcrop input, it will output a file titled input-crop.pdf with zero margins. I find this very handy when including pdf illustrations in documents.

Cropping multiple files

Unfortunately, pdfcrop cannot crop multiple files at the time. It is however easy to write a script that will crop all pdfs in the folder the script is located in.

Create a new empty file, and call it something.sh. Open it with a text editor and insert the following:

#!/bin/bash

for FILE in ./*.pdf; do
  pdfcrop "${FILE}"
done

Save it, and close. Then right click the file, go to Properties > Permissions and check the field Allow executing file as program. Now close the dialog. Run the script by double clicking it and choosingRun in Terminal. And new, zero-margin cropped version of all pdfs with suffix -crop will now be printed in the folder. If you want margins or other things, you can of course just open the script and add arguments after pdfcrop.

linear regression matlab script

function [p,Rsq] = LinearRegression (Xin,Yin)
% LinearRegression example
% x=0:1:9;
% y=3.0 * x + 7 + rand(1,length(x)) ;
% [p,Rsq] = LinearRegression (x,y) ;
% yfit = p(1)*x + p(2) ;
% plot(x,y,"o",x,yfit) ;
p = polyfit(Xin,Yin,1);
Yfit =  p(1) * Xin + p(2);
Yresid = Yin - Yfit;
SSresid = sum(Yresid.^2);
SStotal = (length(Yin)-1) * var(Yin);
Rsq = 1 - SSresid/SStotal;

lyx shortcuts

https://pepebioinformatics.wordpress.com/2014/03/06/lyx-keyboard-shortcuts/

LyX Keyboard Shortcuts

1. ⇧ + ⌘ + L -> Insert Label (label-insert);
2. ⌘ + L -> Insert ERT (ert-insert);
3. ⇧ + ⌘ + G -> Insert Graphic (dialog-show-new-inset graphics);
4. ⇧ + ⌘ + FF -> Insert FloatFigure (float-insert figure);
5. ⇧ + ⌘ + FT -> Insert FloatTable (float-insert table);
6. ⇧ + ⌘ + P -> Typewriter font;
7. ⇧ + ⌘ + C -> Insert Cross-reference (dialog-show-new-inset ref);
8. ^ + A + [C, L or R] -> paragraph-params \align Center, Left or Right;
9. ⌘ + E -> Italic (font-emph);
10. ⌘ + B -> Bold (font-bold);
11. ⌘ + M -> Insert Math (math-mode);
12. ⌘ + ⇧ + R -> Refresh Run
13. ⌘ + R -> Run
14. ^ + P + [*] + [234]; layout [without numbers] [S/SubS/SubSubS]

Netgen on Mac

Netgen installation on Mac is hopeless.
It is better to use Ubuntu virtual machine or Windows laptop.

Netgen command line approach

This works for version 4.9 but does not for 5.3.1 (only GUI mode).

$  netgen -batchmode  -geofile=cone.geo -meshfile=cone.ng -coarse

$  netgen -batchmode  -geofile=cone.geo -meshfile=cone.ngn  -meshfiletype="Neutral Format"

The possible mesh size options are
-verycoarse
-coarse
-moderate
-fine
-veryfine

Compilation with NETGEN Ubuntu 14.04

Compilation with NETGEN Ubuntu 14.04

http://forum.freecadweb.org/viewtopic.php?t=6702


=== Mon Aug 17 22:47:36 HST 2015
OpenGL library is located in /usr/lib/x86_64-linux-gnu/
The netgen compilation did not give any error after installing libxmu-dev library. This will also install Togl1.7 library so that no separate installation of Togl 1.7 is necessary.
 
$ apt-get install libxmu-dev 

After installation, execution of 'netgen' in ng directory gave:
 
symbol lookup error: /usr/lib/libTogl.so: undefined symbol: tkStubsPtr
 
-ltcl8.6 -ltk8.6  -ltkstub8.5


=== Mon Aug 17 10:00:36 HST 2015 ===
The next error came out of 'netgen' compiling. Togl cannot call XmuLookupStandardColormap function in OpenGL, which need to be fixed.

### error message ### 
/bin/bash ../libtool --tag=CXX   --mode=link g++  -g -O2 -fopenmp -export-dynamic  -o netgen demoview.o ngappinit.o onetcl.o parallelfunc.o ngpkg.o ../libsrc/visualization/libvisual.la ../libsrc/csg/libcsgvis.la ../libsrc/csg/libcsg.la ../libsrc/interface/libinterface.la ../libsrc/meshing/libmesh.la -L/usr/lib/Togl1.7  -lTogl -lGLU -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6    -lGL -lXmu -lX11   

libtool: link: g++ -g -O2 -fopenmp -o .libs/netgen \
demoview.o ngappinit.o onetcl.o parallelfunc.o ngpkg.o \
-Wl,--export-dynamic  \
../libsrc/visualization/.libs/libvisual.a \
../libsrc/csg/.libs/libcsgvis.so \
../libsrc/csg/.libs/libcsg.so \
../libsrc/interface/.libs/libinterface.so \
../libsrc/meshing/.libs/libmesh.so \
-L/usr/lib/Togl1.7 -lTogl -lGLU \
-L/usr/lib/x86_64-linux-gnu -ltk8.6 -ltcl8.6 -lGL -lXmu -lX11 \
-fopenmp -Wl,-rpath -Wl,/opt/netgen/lib

/usr/lib/Togl1.7/libTogl.so: undefined reference to `XmuLookupStandardColormap'

collect2: error: ld returned 1 exit status
make: *** [netgen] Error 1

=== Sun Aug 16 23:37:50 HST 2015
Difficulties of compiling netgen source package is purely from Togl library.
In "configure" file of netgen, Togl version is specified as 1.7, but it does require functions included in Togl 2.0.


To overcome this issue, install Togl1.7 in
/opt/Togl1.7
make a link to it in /usr/lib
$ cd /usr/lib
ln -s /opt/Togl-1.7  /usr/lib/Togl1.7

Go do /opt/Togl-1.7 and make a link of Togl library:
$ ln  -s  libTogl1.7.so  libTogl.so

Then the next is OpenGL:
http://xed.ch/help/opengl.html#check

 

How to directly launch Lyx on Mac

This tip is originally to work around the bug of Mac Yosemite that BASH environment is not inherited to child applications.

In terminal, type and enter

$  /Applications/LyX.app/Contents/MacOS/lyx &

If necessary, reconfigure and restart.

Compiliing openmpi using Intel compiler

# Download the source code from  http://www.open-mpi.org/software/

# configuring 
./configure --prefix=/opt/openmpi-1.8.1-Intel CC=icc CXX=icpc F77=ifort FC=ifort

# parallel make using 4 cores
 make -j 4 all

# installation with sudo permission
 sudo bash
 make install

# "sudo make install" does not work due to environment settings.

Other source: https://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-open-mpi-with-the-intel-compilers

Installation/Linux/OpenFOAM-2.3.0/Ubuntu

sudo apt-get install build-essential cmake flex bison zlib1g-dev qt4-dev-tools libqt4-dev \ 

gnuplot libreadline-dev libncurses-dev libxt-dev libopenmpi-dev openmpi-bin \ 

libboost-system-dev libboost-thread-dev libgmp-dev libmpfr-dev

cd ~
mkdir OpenFOAM
cd OpenFOAM
wget "http://downloads.sourceforge.net/foam/OpenFOAM-2.3.0.tgz?use_mirror=mesh" -O OpenFOAM-2.3.0.tgz
wget "http://downloads.sourceforge.net/foam/ThirdParty-2.3.0.tgz?use_mirror=mesh" -O ThirdParty-2.3.0.tgz
 
tar -xzf OpenFOAM-2.3.0.tgz 
tar -xzf ThirdParty-2.3.0.tgz

source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc WM_NCOMPPROCS=4 WM_MPLIB=SYSTEMOPENMPI

echo "alias of230='source \$HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc $FOAM_SETTINGS'" \

>> $HOME/.bashrc

source  $HOME/.bashrc

of230

cd $WM_THIRD_PARTY_DIR
# This next command will take a while... somewhere between 5 minutes to 30 minutes.
./Allwmake > make.log 2>&1
#update the shell environment
wmSET $FOAM_SETTINGS

#Go into OpenFOAM's main source folder
cd $WM_PROJECT_DIR
# This next command will take a while... somewhere between 30 minutes to 3-6 hours.
./Allwmake > make.log 2>&1
#Run it a second time for getting a summary of the installation
./Allwmake > make.log 2>&1

cd $WM_THIRD_PARTY_DIR
./makeParaView4 -qmake $(which qmake-qt4)
 
cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers 
wmSET $FOAM_SETTINGS
./Allwclean 
./Allwmake

http://openfoamwiki.net/index.php/Installation/Linux/OpenFOAM-2.3.0/Ubuntu#Ubuntu_14.04

How to install openlava in Ubuntu

1) prerequisite:
    sudo apt-get install python-software-properties         
   
2) add ppa
    sudo add-apt-repository ppa:cansmith/ol

3) update repository
    sudo apt-get update

4) install openlava
    sudo apt-get install --yes openlava

5) edit /etc/hosts: the first line
from
    127.0.0.1       localhost
to
    127.0.0.1       myhostname  localhost

6) setup configuration
- Go to openlava directory
    cd /etc/openlava/
- open openlava.sh
    sudo vi openlava.sh
- change
    LSF_ENVDIR=/usr/etc
  to
      LSF_ENVDIR=/etc/openlava
- source it
    . ./openlava.sh
- add it to ~/.bashrc
    echo ". /etc/openlava/openlava.sh " >> ~/.bashrc
     
7) check openlava status in /etc/openlava
    sudo ./openlava status
the output must look like
lim pid: <>
res pid: <>
sbatchd pid: <>
lim mbatchd: <>
(without any numbers in <>)

8) start openlava
    sudo ./openlava start
the output must look like
Starting daemons...
lim started
res started
sbatchd started

9) Check a couple of commands:
albertsk@heyum:openlava$ bhosts
HOST_NAME          STATUS       JL/U    MAX  NJOBS    RUN  SSUSP  USUSP    RSV
heyum              ok              -      8      0      0      0      0      0


albertsk@heyum:openlava$ bjobs
No unfinished job found

albertsk@heyum:~$ bhist
No matching job found

10) run the first job
- go to home directory
    cd
- make a test directory
    mkdir bsub
    cd bsub
- edit a job file job.bsub:
#BSUB-q normal                  # Job queue
#BSUB-J myfirstjob              # name of the job
#BSUB -o lava-%J.out
#BSUB -e lava-%J.err
hostname
pwd
ls -laF

- submit the job
    bsub < job.bsub
- try following commands: bjobs, bhist, bpeek   

   
   



 

how to use at command with output

at -m -f myscript.sh now > test.txt  2>&1

source: http://kb.iu.edu/data/aewo.html#examples

openssl installation on Mac

1. Download openssl:  openssl-1.0.1f.tar.gz
2.
./configure darwin64-x86_64-cc --prefix=/usr/local/openssl-1.0.1f
make make install


http://mac-dev-env.patrickbougie.com/openssl/