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