>& is the command to write standard output in the following file. & at last enables one to carry the next operations without waiting for the execution of the command.

If one wants to see the content of ***.log.

#tail –f ***.log

The file is closed by Ctrl+C.

To start apache automatically, the file of /etc/rc.d/init.d/httpd is edited as follows.

#! /bin/sh

#description: Apache

#chkconfig: 345 80 30

. /etc/rc.d/init.d/functions

APACHE=’/usr/local/apache/bin/apachectl’

if[ -x $APACHE ]; then

$APACHE $1

This file is registered as follows.

#chmod +x /etc/rc.d/init.d/httpd

#/sbin/chkconfig --add httpd

#/sbin/chkconfig httpd on

6. Installing PostgreSQL

The source file of PostgreSQL with the version of 7.1.2 is downloaded from

ftp://ftp.jp.postgresql.org/

The installation is carried out at the root account. The downloaded file is copied in the directory of /usr/local/src. Create the group named as "postgres". Register the account of "postgres" that belongs to the group, whose name is the same as the group, as a management user.

6.1 Creating group and management user

Delete the user named as postgres, which has been created by installing Redhat, and create a new group and accounts.

(Uninstalling Postgresql may delete the account.)

#userdel postgres

#groupadd postgres

#useradd –g postgres –d /home/postgres –m –s /bin/bash postgres

#passwd postgres

6.2 Creating the directory for postgreSQL and installation

Installing postgreSQL is carried out not at the root but at postgres. At the root, make the directory for postgreSQL, and expand the source file there. Transfer it to the group of postgres, and install it at postgres.

#mkdir /usr/local/pgsql

#chown postgres.postgres /usr/local/pgsql

#cd /usr/local/src

#tar –xvzf postgresql-7.1.2.tar.gz

The file is expanded and the directory of postgresql-7.1.2 is created.

#chown –R postgres.postgres postgresql-7.1.2

The following process is carried out at postgres.

#su – postgres

$cd /usr/local/src/postgresql-7.1.2

$./configure --enable-multibyte=EUC_JP --enable-syslog >& config.log &

$make >& make.log &

$make install >& install.log &

$exit

Installing postgreSQL is completed.

6.3 Environment setting for postgreSQL

The following process is carried out at the root.

#su –

The environment variables for postgreSQL are registered in the file of /etc/profile and /etc/ld.so.conf.

Add the following lines to the end of /etc/profile

export POSTGRES_HOME=/usr/local/pgsql

export PATH=$PATH:$POSTGRES_HOME/bin

export PGLIB=$POSTGRES_HOME/lib

export PGDATA=$POSTGRES_HOME/data

export MANPATH=$MANPATH:$POSTGRES_HOME/man

Add the following line to the end of /etc/ld.so.conf

/usr/local/pgsql/lib

Add the following line to reflect the changes

#/sbin/ldconfig –v

6.4 Initialization and setting database

The following processes are carried out at postgres.

#su – postgres

Initialization is done by:

$/usr/local/pgsql/bin/initdb

In order to set postgreSQL, the file of usr/local/pqsql/data/postgresql.conf is edited as follows.

The number in the left indicates the line number whose content is changed.

29: tcpip_socket = true (from false to true)

144: ifdef ENABLE_SYSLOG (delete comment out)

145: syslog = 0 # range 0-2 (delete comment out)

146: syslog_facility = 'LOCAL0' (delete comment out)

147: syslog_ident = 'postgres' (delete comment out)

148: endif (delete comment out)

When the database is made in another server, access it through internet. In this case, the file of /usr/local/pgsql/data/pg_hba.conf is edited as follows,

181: host all ***.***.***.*** 255.255.255.0 trust

where *** indicates the IP address that you like to refer as the database server. In addition, the referred server has to be edited as follows.

181: host all ***.***.***.0 255.255.255.0 trust

This enables the server to access the database within the network.

6.5 Setting automatic start

It is possible to start database by

pg_ctl –w start

at postgres.

In order to start the database automatically at the same time of machine startup, edit at root as follow.

#cd /etc/rc.d/init.d

#cp /usr/local/src/postgresql-7.1.2/controlib/start-scripts/linux postgres

Add the following lines to the copied file of postgres

2: #description: postgreSQL

3: #chkconfig: 345 98 02

4: . /etc/rc.d/init.d/functions

#chmod +x postgres

#/sbin/chkconfig --add postgres

#/sbin/chkconfig postgres on

6.6 Registration for users

Skip this section if you do not set any local database.

After confirming that postgreSQL is started up, the following procedures are carried out at postgres, where the user of nobody will be registered.

$/usr/local/pgsql/bin/pg_ctl –w start

$createuser nobody

When you are asked regarding the permission of database creation and the addition of users, input (n).

7. Installing php

The source file of php (version 4.0.6) is downloaded from

http://www.php.net/downloads.php

7.1 Installing php

The downloaded file is placed and expanded at the directory of /usr/local/src, resulting in creating the directory of php_4.0.6.The following process is carried out at the root.

#cd /usr/local/src

#tar -xvzf php-4.0.6.tar.gz

#cd php-4.0.6

#./configure --enable-mbstring --enable-mbstr-enc-trans

--with-apxs=/usr/local/apache/bin/apxs

--with-pgsql=/usr/local/pgsql

--with-gd=/usr

--with-jpeg-dir=/usr >& config.log & (No return key is required)

#make >& make.log &

#make install >& install.log &

The installation is completed, and set environments.

#cp php.ini-dist /usr/local/lib/php.ini

Add the following lines to the end of the copied file of php.ini.

[mbstring]

mbstring.internal_encoding = EUC-JP

mbstring.http_input = auto

mbstring.http_output = pass

mbstring.detect_order = auto

mbstring.substitute_character = none

7.2 Setting change of apache

In order to use php, the setting file for apach, /usr/local/apache/conf/httpd.conf, should be edited as follows.

The number on the left indicates the line that should be edited.

363or364: DirectoryIndex index.html index.php

765or768: AddType application/x-httpd-php .php

766or769: AddType application/x-httpd-php-source .phps

7.3 Function confirmation

Create info.php where <? phpinfo() ?> is just written at the directory of /usr/local/apache/htdocs. Restart apache by:

#/usr/local/apache/bin/apachectl restart

, or reboot the machine.

From browser, input

http://machine_name or IP machine_address/info.php,

If various data regarding php is displayed, php functions well.

7.4 Installing phplib

The source file of phplib (version 7.2d) from

http://prdownloads.sourceforge.net/phplib/phplib-7.2d.tar.gz?download

Expand the file at the directory of /usr/local/src.

The following process is carried out at the root.

#cd /usr/local/src

#tar –xvzf phplib-7.2d.tar.gz

Next, create the symbolic link to the directory for apache as follows:

#cd /usr/local/apache

#ln –s ../src/phplib7.2d phplib

Next, convert the extension of the files of the directories (/usr/local/apache/phplib/php, /usr/local/apache/phplib/pages, /usr/local/apache/phplib/pages/abmin)

) from "php3" to "php".

# mv ***.php3 ***.php

#cd /usr/local/apache/phplib/php

Here, edit prepend.php as follows.

13: $_PHPLIB["libdir"] = "";

15: require($_PHPLIB["libdir"] . "db_pgsql.inc");

The installation is completed.

8. Installing Java2 SDK

The source file of Java2 SDK (version1.4.1) is downloaded from

http://java.sun.com/products/archive/index.html

The file is placed at /root/, where the installation will be carried out.

The following process is carried out at the root.

#cd

#chmod +x j2sdk-1_4_1_03-linux-i586-rpm.bin

#./j2sdk-1_4_1_03-linux-i586-rpm.bin

When the license agreement is asked, click “yes” to make .rpm file.

#rpm –iv j2sdk-1_4_1_03-fcs-linux-i586.rpm

The file is installed at /usr/java/j2sdk1.4.1_03. Create the symbolic link of jdk to /usr/java.

#cd /usr/java

#ln –s j2sdk1.4.1_03 jdk

Installing Java is completed.

9. Installing Xerces2 Java Parser

The source file of Xerces2 Java Parser (2.2.1) is downloaded from

http://xml.apache.org/dist/xerces-j/.

The file is placed at /root/, where the installation is carried out.

Expand the file, which creates the directory of xerces-2_2_1.

The following process is carried out at the root.

#cd

#tar –xvzf Xerces-J-bin.2.2.1.tar.gz

The expanded files are transferred to /usr/local/, and create the symbolic link.

#mv xerces-2_2_1 /usr/local/.

#cd /usr/local/

#ln –s xerces-2_2_1 xerces

The installation is completed.

10. Installing mpich

The source file of mpich with the version1.2.2.2 is downloaded from

http://www-unix.mcs.anl.gov/mpi/mpich/

Expand mpich.tar.gz at root.

#cd

#tar -xvzf mpich.tar.gz

The directory of mpich-1.2.2.2 is automatically created.

#cd mpich-1.2.2.2

#./configure –prefix=/usr/local/mpich –fc=g77 –cc=gcc >& configure.log &

#make >& make.log &

#make install >& install.log &

The file is installed at the directory of /usr/local/mpich.

11. Installing CADLIVE Simulator

11.1 Installing CADLIVE Simulator

Using the root account, make the directory of /home/CADLIVE, and expand CADLIVE_DATA.tgz at the directory of /home/CADLIVE

#mkdir /home/CADLIVE

#cd /home/CADLIVE

#tar –xvzf CADLIVE_DATA.tgz

The directories necessary for the simulator are created automatically. In the directory of ./Session, one operates jobs via browser. Actually, since one operates jobs at the account of nobody, set the simulator so that "nobody" can read and write.

#chmod 777 Session

11.2 Setting apache

PC clients are required to access /home/CADLIVE/Life via a browser. Thus, the file of /usr/local/apache/conf/httpd.conf is reedited as follows,

284: DocumentRoot "/home/CADLIVE"

309: <Directory "/home/CADLIVE">

319: Options MultiViews

326: AllowOverride FileInfo Options

331: Order allow, deny

332: Allow from all

333: </Directory>

In the above case, a PC browser is able to access the simulator by http://machine\name/Life.

(Use ID:kris Passwd:test)

11.3 Installing batch job

CADLIVE/Tools is the directory for batch jobs. Create the load modules and libraries necessary for system operations by the following commands:

#cd /home/CADLIVE/Tools

#make depend

#make install

11.4 Setting php

Since php controls batch jobs, one changes the environment setting according to the installation directory or machine environments. The file of CADLIVE/Chemi/define.inc is changed as follows:

CADLIVE/Chemi/define.inc

2: // definition of path

3: $CADLIVE_home = "/home/CADLIVE";

4: $dirBin = $CADLIVE_home."/Tools/bin/";

5: $dirPhpSource = $CADLIVE_home."/Chemi/";

13: // parallel computing

14: $num_cpu = 8;

15: $mpirun = "/usr/local/mpich/bin/mpirun -np ";

$CADLIVE_home is the absolute path for the installation directory. $num_cpu indicates the number of PCs controlled by MPI.

Since the setting of apache is altered, restat.

#/usr/local/apache/bin/apachectl restart

Installing CADLIVE is completed.

11.5 Setting database

One has to set database.

Brief instruction of postgreSQL (at postgres)

START: pg_ctl –w start

SHUTDOWN pg_ctl stop

(If one fails, pg_ctl –m immediate stop)

LIST DB psg –l

CREATE DB createdb name_database

DELETE DB dropdb name_database

FORMAT DB psql –e name_database < definition_file

BACKUP DB pg_dump name_database > BackUp_file

RESTORE DB psql < BackUp_file

Create the database for CADLIVE,

$create life_db

Next, define the format type for DB. The following two files are employed as the definition files.

$psql –e life_db /home/CADLIVE/Life/create_database.pgsql

$psql –e life_db /home/CADLIVE/Life/create_mydb.pgsql

11.6 Others

One has to set the file of local.inc.

At user account, edit /home/CADLIVE/Life/local.inc as follows.

12: var $Host = "***.***.***.***" ;

13: var $Database = "name_database";

"name_database" is the same that has been created previously. In the line 12, when one makes DB at local, Host is localhost. When DB is referred from outside, Host is the its own host name. When one refers to another host, Host is the host name that one wants to refer.

For example,

var $Host = "kurata01.bse.kyutech.ac.jp";