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Friday, May 24, 2013

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" "$@"

Thursday, May 23, 2013

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








Friday, May 17, 2013

fortran file append


This partial code is to open existing (OLD) file, DHD00000.xyz, and write (APPEND) additional information from the end of the file

open(unit=1,file='DHD00000.xyz',status='old',position='append')
 write(1,*) "Here we go!"
close(1)

stop
end




Tuesday, April 30, 2013

How to draw cylinders using VMD


 set pos1 { 0 0 0 }
 set pos2 { 1 1 1 }
 set pos3 { 2 2 2 }
 set pos4 { 3 3 3 }

 draw material Opaque

 draw color yellow
 draw cylinder $pos1 $pos2 radius 0.3


 draw color red
 draw cylinder $pos2 $pos3 radius 0.3


Sunday, April 28, 2013

How to install lapack and scalapack on CentOS 6


 yum -y install compat-libgfortran-41.x86_64 gcc-gfortran.x86_64 libgfortran.x86_64
 yum -y install openmpi.x86_64 openmpi-devel.x86_64
 yum -y install lapack-devel.x86_64 lapack.x86_64
 yum -y groupinstall development
 rpm  -ivh  http://archive.linux.duke.edu/pub/epel//6/x86_64/epel-release-6-8.noarch.rpm
 yum  update
 yum repolist
 yum -y install scalapack-common.x86_64 scalapack-openmpi.x86_64 scalapack-openmpi-devel.x86_64 scalapack-openmpi-static.x86_64

Friday, April 19, 2013

How to list only number directories


find . -maxdepth 1 -type d | grep -v './[.]' | cut -c 3- | grep -v '[a-z]?*' | grep -v '[A-Z]?*' | sort | sed ':a;N;$!ba;s/\n/ /g'

Saturday, April 13, 2013

How to setup system Login banner and Login message

edit the "/etc/issue" and "/etc/motd" files

Wednesday, April 10, 2013

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


Thursday, March 28, 2013

How to print a regular file to pdf from command line



http://askubuntu.com/questions/27097/how-to-print-a-regular-file-to-pdf-from-command-line

enscript my_text_file.txt -o - | ps2pdf - output.pdf

enscript -B -PPDF test.txt

unoconv -f pdf test.txt

Monday, March 11, 2013

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

Monday, February 25, 2013

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)

Sunday, February 24, 2013

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


Saturday, February 23, 2013

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


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

Wednesday, February 20, 2013

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

Tuesday, February 19, 2013

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

bash: /usr/bin/ssh: Permission denied

This message has been a headache, happening a couple of times when I upgrade or update packages.

albertsk@stokes:~$ ssh
bash: /usr/bin/ssh: Permission denied


root@stokes:ssh$ ll /usr/bin/wget
-rwxr-xr-x 1 root root 369848 Feb 10  2012 /usr/bin/wget*

root@stokes:ssh$ chmod og+x /usr/bin/ssh
chmod: changing permissions of `/usr/bin/ssh': Operation not permitted

root@stokes:ssh$ ll /usr/bin/ssh
-rwx------ 1 root root 650492 Feb 12 01:46 /usr/bin/ssh*

root@stokes:ssh$ chmod og+x /usr/bin/ssh
chmod: changing permissions of `/usr/bin/ssh': Operation not permitted

root@stokes:ssh$ lsattr /usr/bin/ssh
-u---a-------e- /usr/bin/ssh

root@stokes:ssh$ lsattr /usr/bin/wget
-------------e- /usr/bin/wget

root@stokes:ssh$ chattr -uai  /usr/bin/ssh

root@stokes:ssh$ lsattr /usr/bin/ssh
-------------e- /usr/bin/ssh

root@stokes:ssh$ chmod og+xr  /usr/bin/ssh
root@stokes:ssh$ ls /usr/bin/ssh
/usr/bin/ssh

albertsk@stokes:~$ ssh localhost
Last login: Tue Feb 19 15:10:25 2013 from localhost
Welcome to Ubuntu 12.04.2 LTS (GNU/Linux 3.2.0-37-generic x86_64)

 * Documentation:  https://help.ubuntu.com/

albertsk@stokes:~$ 

Monday, February 18, 2013

customized .bst file


/usr/share/texmf-texlive/bibtex/bst/natbib/

there are many .bst files, which one can modify.

After type/enter

$ texhash





Thursday, February 14, 2013

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

Saturday, January 26, 2013

How to install netcdf on Ubuntu



 apt-get install netcdf-bin  nco netcdf-doc libnetcdf-dev  libnetcdf6

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