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

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!

shell script with options

http://www.mkssoftware.com/docs/man1/getopts.1.asp


EXAMPLE
This is an example of using getopts in a shell script. Compare it to the getopt example.

# Example illustrating use of getopts builtin. This
# shell script would implement the paste command,
# using getopts to process options, if the underlying
# functionality was embedded in hypothetical utilities
# hpaste and vpaste, which perform horizontal and
# vertical pasting respectively.
#
paste=vpaste # default is vertical pasting
seplist="\t" # default separator is tab

while getopts d:s o
do case "$o" in
d) seplist="$OPTARG";;
s) paste=hpaste;;
[?]) print >&2 "Usage: $0 [-s] [-d seplist] file ..."
exit 1;;
esac
done
shift $OPTIND-1

# perform actual paste command
$paste -d "$seplist" "$@"

How to make DHDall.xyz

#!/bin/bash

DHDfile=($(ls -1 DHD?????.xyz))  # Read all files of DHD?????.xyz
interval=$1        # Interval is the first argument.
: ${interval:=1}   # If there is no argument, default value is 1.


if [ -f DHDall.xyz ] # If DHDall.xyz exist
then
   rm DHDall.xyz     # then delete it.
fi
touch DHDall.xyz     # As DHDall.xyz is absent, touch it.

for (( i=0; i < ${#DHDfile[@]} ; i=i+$interval )) do
   cat  ${DHDfile[$i]} >> DHDall.xyz
done
exit

iptables setting

 # Basic setup
 iptables --flush
 iptables -P FORWARD DROP
 iptables -P OUTPUT ACCEPT
 iptables -P INPUT DROP
# Allow SSH
 iptables -A INPUT  -i eth0 -p tcp --dport 22  -j ACCEPT
 iptables -A OUTPUT -o eth0 -p tcp --sport 22  -j ACCEPT
# Allow local loopback
 iptables -A INPUT -i lo -j ACCEPT
 iptables -A OUTPUT -o lo -j ACCEPT
# Allow DNS
 iptables -A OUTPUT -p udp -o eth0 --dport 53 -j ACCEPT
 iptables -A INPUT  -p udp -i eth0 --sport 53 -j ACCEPT
# Allow ping
 iptables -A OUTPUT -p icmp --icmp-type echo-request -j ACCEPT
 iptables -A INPUT  -p icmp --icmp-type echo-reply -j ACCEPT
# Allow http
 iptables -A INPUT  -i eth0 -p tcp --sport 80 -m state --state ESTABLISHED -j ACCEPT
 iptables -A OUTPUT -o eth0 -p tcp --dport 80 -m state --state NEW,ESTABLISHED -j ACCEPT
# Allow https
 iptables -A INPUT  -i eth0 -p tcp --sport 443 -m state --state ESTABLISHED -j ACCEPT
 iptables -A OUTPUT -o eth0 -p tcp --dport 443 -m state --state NEW,ESTABLISHED -j ACCEPT
# Printer (ipp=631, cups=515)
 iptables -A OUTPUT -p tcp -d 192.168.60.157  --dport 515 -j ACCEPT
 iptables -A INPUT  -p tcp -s 192.168.60.157  --sport 515 -j ACCEPT

how to install qt5 + phone app devel tool

http://developer.ubuntu.com/get-started/gomobile/

How to build Goto blas using Intel compilers

Download GotoBlas http://www.tacc.utexas.edu/tacc-projects/gotoblas2

make  FC=ifort   CC=icc  BINARY=64   USE_THREAD=0

The last option is to build without thread.  Output message:

 GotoBLAS build complete.

  OS               ... Linux             

  Architecture     ... x86_64               

  BINARY           ... 64bit                 

  C compiler       ... INTEL  (command line : icc)

  Fortran compiler ... INTEL  (command line : ifort)

  Library Name     ... libgoto2_prescott-r1.13.a (Single threaded)  

how to disable touch pad

Login as root.

$ xinput list
 You will see results similar to

⎡ Virtual core pointer                          id=2    [master pointer  (3)]
⎜   ↳ Virtual core XTEST pointer                id=4    [slave  pointer  (2)]
⎜   ↳ SynPS/2 Synaptics TouchPad                id=15   [slave  pointer  (2)]
⎜   ↳ Logitech USB Receiver                     id=11   [slave  pointer  (2)]
⎜   ↳ Logitech USB Receiver                     id=12   [slave  pointer  (2)]
⎣ Virtual core keyboard                         id=3    [master keyboard (2)]
    ↳ Virtual core XTEST keyboard               id=5    [slave  keyboard (3)]
    ↳ Power Button                              id=6    [slave  keyboard (3)]
    ↳ Video Bus                                 id=7    [slave  keyboard (3)]
    ↳ Video Bus                                 id=8    [slave  keyboard (3)]
    ↳ Sleep Button                              id=9    [slave  keyboard (3)]
    ↳ USB 2.0 UVC VGA WebCam                    id=10   [slave  keyboard (3)]
    ↳ Asus WMI hotkeys                          id=13   [slave  keyboard (3)]
    ↳ AT Translated Set 2 keyboard              id=14   [slave  keyboard (3)]

The touchpad id is 15. To disable it:

$ xinput set-prop 15 "Device Enabled" 0

to re-enable it

$ xinput set-prop 15 "Device Enabled" 1

image convert in Linux

convert -colorspace RGB -interlace none -density 300x300 -quality 100 mycode_pbs-crop.pdf mycode_pbs-crop.png

pbsnodes

To see the status of all nodes:
$ pbsnodes -a 

To see down nodes only
$ pbsnodes -l 

====================

pbsnodes(8B)                          PBS                         pbsnodes(8B)

NAME
       pbsnodes - pbs node manipulation

SYNOPSIS
       pbsnodes [-{a|x}] [-q] [-s server] [node|:property]
       pbsnodes -l [-q] [-s server] [state] [nodename|:property ...]
       pbsnodes [-{c|d|o|r}] [-q] [-s server] [-n] [-N "note"] [node|:property]

DESCRIPTION
       The  pbsnodes command is used to mark nodes down, free or offline.  It can
       also be used to list nodes and their state.  Node information is  obtained
       by sending a request to the PBS job server.  Sets of nodes can be operated
       on at once by specifying a node property prefixed by a colon.
       Nodes do not exist in a single state, but actually have a set  of  states.
       For  example,  a  node  can  be  simultaneously "busy" and "offline".  The
       "free" state is the absence of all other states and so is  never  combined
       with other states.

       In  order  to  execute  pbsnodes with other than the -a or -l options, the
       user must have PBS Manager or Operator privilege.

OPTIONS
       -a             All attributes of a node or all nodes are listed.  This  is
                      the default if no flag is given.

       -x             Same as -a, but the output has an XML-like format.

       -c             Clear OFFLINE from listed nodes.

       -d             Print  MOM  diagnosis  on the listed nodes.  Not yet imple-
                      mented.  Use momctl instead.

       -o             Add the OFFLINE state.  This is different from being marked
                      DOWN.  OFFLINE prevents new jobs from running on the speci-
                      fied nodes.  This gives the administrator a tool to hold  a
                      node  out  of  service without changing anything else.  The
                      OFFLINE state will never be set or cleared automatically by
                      pbs_server; it is purely for the manager or operator.

       -p             Purge  the  node  record  from  pbs_server.  Not yet imple-
                      mented.

       -r             Reset the listed nodes by clearing OFFLINE and adding  DOWN
                      state.  pbs_server will ping the node and, if they communi-
                      cate correctly, free the node.

       -l             List node names and their state.  If no state is specified,
                      only  nodes  in  the  DOWN,  OFFLINE, or UNKNOWN states are
                      listed.  Specifying a state string acts as an  output  fil-
                      ter.   Valid  state  strings are "free", "offline", "down",
                      "reserve", "job-exclusive", "job-sharing",  "busy",  "time-
                      shared", or "state-unknown".

       -N             Specify  a  "note" attribute.  This allows an administrator
                      to add an arbitrary annotation to  the  listed  nodes.   To
                      clear a note, use -N "" or -N n.

       -n             Show the "note" attribute for nodes that are DOWN, OFFLINE,
                      or UNKNOWN.  This option requires -l.

       -q             Supress all error messages.

       -s             Specify the PBS server’s hostname or IP address.

SEE ALSO
       pbs_server(8B) and the PBS External Reference Specification

Local                                                             pbsnodes(8B)

Efficient yum installation

1. Make a directory such as /etc/yum/Group, which is shared to all the nodes using NFS.
2. Download package files:
• yum groupinstall -y 'Development Tools' --downloadonly --downloaddir=/opt/yum/Group
• yum update   --downloadonly --downloaddir=/opt/yum/  openmpi openmpi-devel openmpi-devel.x86_64 qt-devel cc gcc-c++ bison ncurses-devel tix.x86_64 glibc-devel flex zlib-devel libXt-devel binutils-devel gcc44 gcc44-c++ zlib-devel
1. If "--downloadonly" option does not work, then
• yum install  -y  yum-downloadonly
3. To install downloaded package at the master as well as compute nodes:
• yum  localinstall -y /opt/yum/Group/*.rpm 
4. If you get errors regarding yum execution, try
• yum clean dbcache

yum download

Type the following command to install plugin, enter:

# yum install yum-downloadonly

To download http only:

# yum  update httpd  -y  --downloadonly

How to install OpenFOAM on CentOS

1. Package Installation
• sudo yum groupinstall -y 'Development Tools'
• sudo yum install  -y openmpi openmpi-devel openmpi-devel.x86_64 qt-devel
• sudo yum install  -y  cc gcc-c++ bison ncurses-devel tix.x86_64 glibc-devel flex zlib-devel libXt-devel binutils-devel
• sudo yum install -y gcc44 gcc44-c++ zlib-devel
• yum upgrade -y 
2. Check your OS architecture to forcefully load Open-MPI into the environment
• uname -m
1. If 32 bit:
• mpi-selector --system --set openmpi-1.4-gcc-i386
2. If 64 bit:
• mpi-selector --system --set openmpi-1.4-gcc-x86_64
• In my case, "openmpi-1.4-gcc-x86_64" is not listed by executing "mpi-selector --list". To register openmpi-1.4-gcc-x86_64:
• mpi-selector  --register openmpi-1.4-gcc-x86_64  --source-dir  /usr/lib64/openmpi/1.4-gcc/etc
3. Log out and log in again.  If you did step 1 and 2 as root, at this time log in as a regular user.
4. Download and unpack
• cd ~
• mkdir OpenFOAM
• cd OpenFOAM
• wget "http://downloads.sourceforge.net/foam/OpenFOAM-2.1.1.tgz?use_mirror=mesh" -O OpenFOAM-2.1.1.tgz
• wget "http://downloads.sourceforge.net/foam/ThirdParty-2.1.1.tgz?use_mirror=mesh" -O ThirdParty-2.1.1.tgz
• tar xzf OpenFOAM-2.1.1.tgz 
• tar xzf ThirdParty-2.1.1.tgz
5. For X86 #here you can change 4 to the number of cores you've got
• source $HOME/OpenFOAM/OpenFOAM-2.1.1/etc/bashrc WM_NCOMPPROCS=4 WM_COMPILER=Gcc44 WM_MPLIB=SYSTEMOPENMPI
• export WM_CC='gcc44'
• export WM_CXX='g++44'
• echo "source $HOME/OpenFOAM/OpenFOAM-2.1.1/etc/bashrc $FOAM_SETTINGS" >> $HOME/.bashrc
• echo "export WM_CC='gcc44'; export WM_CXX='g++44'" >> $HOME/.bashrc
• sed -i -e 's=gcc=$(WM_CC)=' OpenFOAM-2.1.1/wmake/rules/linux64Gcc44/c
• sed -i -e 's=g++=$(WM_CXX)=' OpenFOAM-2.1.1/wmake/rules/linux64Gcc44/c++
6. Now let's build OpenFOAM. It usually takes 30 minutes to 6 hours.
•  #Go into OpenFOAM's main source folder
  • cd OpenFOAM-2.1.1
• # 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
7. 
   

Preliminary
OpenFOAM uses libmpi.so.1.  If this is not found in   /usr/lib64/openmpi/1.4-gcc/lib, then do followings

• Log in as root
• cd /usr/lib64/openmpi/1.4-gcc/lib
• ln  -s  libmpi.so  libmpi.so.1

This is to make a symbolic link from libmpi.so to libmpi.so.1, which should be done all the nodes if OpenFoam will be run in parallel. 

Related links:

http://wiki.hpc.ufl.edu/doc/From_mpi-selector_to_environment_modules
http://na-inet.jp/na/pccluster/centos_x86_64-en.html

UseDNS no in sshd_config

"It turns out there is a setting in OpenSSH that controls whether SSHd should not only resolve remote host names but also check whether the resolved host names map back to remote IPs. Apparently, that setting is enabled by default in OpenSSH. The directive UseDNS controls this particular behaviour of OpenSSH, and while it is commented in sshd_config (which is the default configuration file for the OpenSSH daemon in most enviornments), as per the man page for sshd_config, the default for UseDNS is set to enabled. Uncommenting the line carrying the UseDNS directive and setting it to “no” disables the feature."

http://ayaz.wordpress.com/2008/02/03/usedns-resolution-and-openssh/

So to speed up connection speed of OpenSSH, in /etc/ssh/sshd_config file, put


UseDNS no

PBS scripts for mpirun

#!/bin/bash
#PBS -l walltime=00:30:00
#PBS -l nodes=3:ppn=2
#PBS -N mypi
#PBS -V
cd $PBS_O_WORKDIR
/opt/openmpi-1.6.3-intel-pbs/bin/mpirun -mca btl_tcp_if_include eth0 -mca btl tcp,self -mca plm tm -np 6 fpi.x

How to install Openmpi using ifort and icc

$ ./configure --with-tm=/usr/include/torque/  --prefix=/opt/openmpi-1.6.3-intel-pbs CC=icc   CXX=icpc   F77=ifort    FC=ifort

$ make all install

openssh reinstallation

sudo apt-get remove --purge openssh-server 

sudo apt-get install openssh-server

resolve memtest86+ (4.20-1.1ubuntu1) hangs

Quick workaround:

Append the following to /etc/default/grub:

GRUB_DISABLE_OS_PROBER=true

Run 

$ sudo update-grub2

This will disable os-prober so grub doesn't see the other disks (this way it won't fail with an error).
Run sudo dpkg --configure -a to complete the configuration (should be successful this time).
The side-effect of this workaround is that you will loose all other boot entries in GRUB, so if you have a Windows dual boot or other distro's, you should remove or comment the line in /etc/default/grub and then run sudo update-grub2 once more to fully populate the GRUB menu.

How to resolve “Could not get lock /var/lib/dpkg/lock” problem.

Delete two "lock" files.

sudo rm /var/lib/dpkg/lock

sudo rm /var/cache/apt/archives/lock