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/

Cross compiling between FORTRAN and C to use memset.

Makefile

===
FC=ifort
CC=icc
foo: mainf.o fmemset.o
        $(FC) mainf.o fmemset.o -o foo

mainf.o: mainf.f90
        $(FC) -c mainf.f90 -o mainf.o

fmemset.o: fmemset.c
        $(CC)  -c fmemset.c -o fmemset.o
run:
        ./foo

clean:
        /bin/rm -f *.o ./foo
===


FORTRAN code: mainf.f90
===
program Albert
    integer  :: x,y
    real :: a(4,4)
    do 20 i=1,4
        do 10 j=1,4
            a(i,j) = 4
            write (*,*) a(i,j)
10      continue
20  continue
    ! zeroing out 4*4 elements, each of 4 bytes
    call fmemset(a,4*4*4)
    write (*,*) "UPDATED ARRAY:"
    do 40 i=1,4
        do 30 j=1,4
            write (*,*) a(i,j)
30      continue
40  continue
    write(*,*) size(a)
end program Albert
===




C code: fmemset.c
===
#include
void fmemset_(void *a, int *n)  {
         memset(a,0,*n);
}
===


Developed by Prof. Henri Casanova at UHM.  Thanks!

bash script default input values

#!/bin/sh
dir1=$1
dir2=$2
: ${dir1:="TxtInOut-serial"}
: ${dir2:="TxtInOut-omp-02"}