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Installing and Configuring GIT on CentOS 5

Git is a free & open source, distributed version control system designed to handle everything from small to very large projects with speed and efficiency.

Every Git clone is a full-fledged repository with complete history and full revision tracking capabilities, not dependent on network access or a central server. Branching and merging are fast and easy to do.

Step 1: Installing Dependencies required by GIT

# yum -y install zlib-devel openssl-devel perl cpio expat-devel gettext-devel

Step 2: Compile and Installing CURL

What is CURL? curl is a command line tool for transferring data with URL syntax, supporting DICT, FILE, FTP, FTPS, GOPHER, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, TELNET and TFTP.

# wget http://curl.haxx.se/download/curl-7.18.2.tar.gz
# tar xzvf curl-7.18.2.tar.gz
# cd curl-7.18.2
# ./configure
# make
# make install

Step 3: ldconfig /usr/local/lib

# vim /etc/ld.so.conf.d/common.conf

 

/usr/local/lib

Step 4: Install GIT

# wget http://www.codemonkey.org.uk/projects/git-snapshots/git/git-latest.tar.gz
# tar xzvf git-latest.tar.gz
# cd git
# autoconf
#./configure –with-curl=/usr/local
# make
# make install

Horray it is done.

Credits: Much of the credit of the materials must go to http://turbolinux.org/tag/centos-git/

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Installing dokuwiki on CentOS 6

This writeup is a modification from Installing dokuwiki on CentOS

 

Step 1: Get the latest dokuwiki  from http://download.dokuwiki.org/

# wget http://download.dokuwiki.org/src/dokuwiki/dokuwiki-stable.tgz
# tar -xzvf dokuwiki-stable.tgz

Step 2: Move dokuwiki files to apache directory

# mv dokuwiki-stable /var/www/html/docuwiki

Step 3a: Set Ownership and Permission for dokuwiki

# chown -R apache:root /var/www/html/dokuwiki
# chmod -R 664 /var/www/html/dokuwiki/
# find /var/www/html/dokuwiki/ -type d -exec chmod 775 {} \;

Step 3b: Remember to modify your mod_security or disable your selinux

# setenforce 0

Step 4: Continue the installation http://192.168.1.1/docuwiki/install.php

Ignore the security warning, we can only move the data directory after installing.
fill out form and click save

Step 5: Delete install.php for security

# rm /var/www/html/dokuwiki/install.php

Step 6: Create and move data, bin (CLI) and cond directories out of apache directories for security

Assuming apache does not access /var/www, only /var/www/html and /var/cgi-bin secure dokuwiki (or use different directory):

# mkdir /var/www/dokudata
# mv /var/www/html/dokuwiki/data/ /var/www/dokudata/
# mv /var/www/html/dokuwiki/conf/ /var/www/dokudata/
# mv /var/www/html/dokuwiki/bin/ /var/www/dokudata/

 Step 7: Update dokuwiki where the conf directory

# vim /var/www/html/dokuwiki/inc/preload.php
<?php
// DO NOT use a closing php tag. This causes a problem with the feeds,
// among other things. For more information on this issue, please see:
// http://www.dokuwiki.org/devel:coding_style#php_closing_tags

define('DOKU_CONF','/var/www/dokudata/conf/');

* Note the comments why there is no closing php

Step 8: Update dokuwiki where the data directory is

# vim /var/www/dokudata/conf/local.php
$conf['savedir'] = '/var/www/dokudata/data/';

Step 9: Set permission for dokuwiki again for the new directory with same permissions

# chown -R apache:root /var/www/html/dokuwiki
# chmod -R 664 /var/www/html/dokuwiki/
# find /var/www/html/dokuwiki/ -type d -exec chmod 775 {} \;

# chown -R apache:root /var/www/dokudata
# chmod -R 664 /var/www/dokudata/
# find /var/www/dokudata/ -type d -exec chmod 775 {} \;

 

Step 10: Go to wiki http://192.168.1.1/docuwiki/install.php

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40Gb Ethernet – A Competitive Alternative to InfiniBand (White paper)

Chelsio

This paper supports this conclusion with three real application benchmarks running on IBM’s Rackswitch G8316, a 40Gb Ethernet aggregation switch, in conjunction with Chelsio Communications’ 40Gb Ethernet Unified Wire network adapter. This paper shows how iWARP offers comparable application level performance at 40Gbps with the latest InfiniBand FDR speeds.

40Gb Ethernet: A Competitive Alternative to InfiniBand – LAMMPS, WRF and Quantum ESRESSO Modeling with 40Gb iWARP Technology (pdf)

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Configuring OpenLDAP on CentOS 6 (Part 1)

Step 1″ Install OpenLDAP packages

# yum install openldap openldap-servers openldap-clients

Step 2: Generate a password hash to be used as the admin password. This password hash will be used when you create the root user for your LDAP installation. For example:

[root]# slappasswd
New password : p@ssw0rd
Re-enter new password : p@ssw0rd
{SSHA}5lPFVw19zeh7LT53hQH69znzj8TuBrLv

Step 3: At /etc/openldap/ldap.conf

#
# LDAP Defaults
#

# See ldap.conf(5) for details
# This file should be world readable but not world writable.

include         /etc/openldap/schema/core.schema
include         /etc/openldap/schema/cosine.schema
include         /etc/openldap/schema/inetorgperson.schema
include         /etc/openldap/schema/nis.schema

#BASE   dc=example,dc=com
#URI    ldap://ldap.example.com ldap://ldap-master.example.com:666

# Allow LDAPv2 client connections. This is not the default
allow bind_v2

# DO not enable referrals until AFTER you have workinf directory
# service AND an understanding of referrals
# referrals     ldap://root.openldap.org

pidfile         /var/run/openldap/slapd.pid
argsfile        /var/run/openldap/slapd.args

#######################################################################
# ldbm and/or bdb database definitions
#######################################################################
database        bdb
suffix          "dc=cluster,dc=spms,dc=ntu,dc=edu,dc=sg"
rootdn          "cn=manager,dc=cluster,dc=spms,dc=ntu,dc=edu,dc=sg"

# Cleartext Passwords, especially for the rootdn, shoud
# be avoided. See slappasswd and slapd.conf for details
# Use of strong authentication ecouraged
rootpw          {SSHA}5lPFVw19zeh7LT53hQH69znzj8TuBrLv

# The database directory MUST exist prior to running slapd AND
# should only be accessible by the slapd and slap tools.
# Mode 700 recommended.
directory       /var/lib/ldap

# indices to be maintain for this database
index ObjectClass                       eq,pres
index ou,cn,mail,surname,givenname      eq,pres,sub
index uidNumber,gidNumber,loginShell    eq,pres
index uid,memberUid                     eq,pres,sub
index nisMapName,nisMapEntry            eq,pres,sub


#SIZELIMIT      12
#TIMELIMIT      15
#DEREF          never

TLS_CACERTDIR   /etc/openldap/certs

Step 4: Start the Service

# service slapd start

Step 5: Check that the service is working.

[root@ldap init.d]# netstat -lnpt |grep 389
tcp        0      0 0.0.0.0:389                 0.0.0.0:*                   LISTEN      13513/slapd
tcp        0      0 :::389                      :::*                        LISTEN      13513/slapd

Step 6: Create LDIF file to add data

# vim /etc/openldap/base.ldif

# cluster.spms.ntu.edu.sg
dn:     dc=cluster,dc=spms,dc=ntu,dc=edu,dc=sg
dc:     cluster
objectClass: top
objectClass: domain

# People, cluster.spms.ntu.edu.sg
dn: ou=Users,dc=cluster,dc=spms,dc=ntu,dc=edu,dc=sg
ou: Users
objectClass: top
objectClass: organizationalUnit

# Groups, cluster.spms.ntu.edu.sg
dn: ou=Groups,dc=cluster,dc=spms,dc=ntu,dc=edu,dc=sg
ou: Groups
objectClass: top
objectClass: organizationalUnit

# Computers, cluster.spms.ntu.edu.sg
dn: ou=Computers,dc=cluster,dc=spms,dc=ntu,dc=edu,dc=sg
ou: Computers
objectClass: top
objectClass: organizationalUnit
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Installing and Compiling Mankai Common Lisp on CentOS 5

ManKai Common Lisp (MKCL) aims to be a full implementation of the Common Lisp language in compliance with the ANSI X3J13 Common Lisp standard.

MKCL supports the operating systems Linux and Microsoft Windows, running on top of Intel x86 or AMD64 compatible processors.

For more information on installation of MKCL, do look at http://common-lisp.net/project/mkcl/

Do note that Starting with MKCL 1.1.0, MKCL requires the platform supplied GMP
library, and GMP development version when compiling MKCL from its
sources.

Installing GMP can be taken from a section Compiling GNU 4.7.2 on CentOS 5

GMP

  Download the following prerequistics applications libraries from ftp://gcc.gnu.org/pub/gcc/infrastructure/

1. Install gmp-4.3.2

# bunzip2 gmp-4.3.2.tar.bz2
# tar -zxvf gmp-4.3.2.tar
# cd gmp-4.3.2
# ./configure --prefix=/usr/local/gmp-4.3.2
# make
# make install

Update your .bashrc

.....
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/gmp-4.3.2/lib........
......

Compiling mkl

# tar xvf mkcl-1.1.8.tar.gz
# cd mkcl-1.1.8
#./configure
# make -j 8 install
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Xeon Phi Updates (22 Mar 2014)

The test was done with 2 socket of Xeon E5-2670 with Xeon Phi Coprocessor. For more information, see Intel® Xeon Phi™ Coprocessor

Segment Application/Code Performance1 vs. 2S Xeon*
DCC NEC / Video Transcoding Up to 3.0x2
Energy Seismic Imaging ISO3DFD Proxy 16th order Isotropic kernel  RTMSeismic Imaging 3DFD TTI  3- Proxy  8th order  RTM  (complex structures)
Petrobras  Seismic ISO-3D RTM 2s XEON and 2 cards		 Up to 1.45X1Up to 1.24 (24 threads)1

Up to 1.97 (16 threads)1

Up to 3.4x3
Financial Services BlackScholes SPMonte Carlo  EMEA Option SP

Monte Carlo  RNG SP

 Up to 2.21x1Up to 7.05x1

Up to 1.58x1
Life Science BWA/Bio-InformaticsWayne State University/MPI-Hmmer

GROMACS /Molecular Dynamics

TUM (Technische Universität München) / SG++ Astronomy

 Up to 1.86x2Up to 5.4x2

Up to 1.36x1

Up to 1.7x1
Manufacturing ANSYS  / Mechanical SMPSandia Mantevo / miniFE (Finite Element Solver) Up to 1.76x2Up to 2.3x2
Physics ZIB (Zuse-Institut Berlin) / Ising 3D (Solid State Physics)AWE (Atomic Weapons Estab’t/Cloverleaf (2D Structured Hydrodynamics)

Princeton / GTC-P ( Gyrokinetic Torodial) Turbulence Simulation

 Up to 3.46x4Up to 1.77x1

Up to 1.18x (four 2S Xeon)
Weather WRF /Code WRF V3.5 1.56x2
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Summary of Job Management Commands for MAUI

This is a good summary taken from Adaptive Computing 4.3 Job Managament Commands to manage jobs for MAUI.

Command Flags Description
canceljob cancel existing job
checkjob display job state, resource requirements, environment, constraints,
credentials, history, allocated resources, and resource utilization
diagnose -j display summarized job information and any unexpected state
releasehold [-a] remove job holds or defers
runjob start job immediately if possible
sethold set hold on job
setqos set/modify QoS of existing job
setspri adjust job/system priority of job