ifort and mkl

Install location:
    /opt/intel/composer_xe_2013_sp1.3.174

Component(s) selected:
    Intel(R) Fortran Compiler XE 14.0 Update 3                             563MB
        Intel Fortran Compiler XE                                              

    Intel(R) Debugger 13.0                                                 477MB
        Intel Debugger                                                         

    Intel(R) Math Kernel Library 11.1 Update 3                             1.9GB
        Intel MKL core libraries                                               
        Intel(R) Xeon Phi(TM) coprocessor support                              
        Fortran 95 interfaces for BLAS and LAPACK                              
        GNU* Compiler Collection support                                       

    GNU* GDB 7.5                                                           119MB
        GNU* GDB 7.5 on Intel(R) 64 (Provided under GNU General Public License 
v3)
        GDB Eclipse* Integration on Intel(R) 64 (Provided under Eclipse Public 
License v.1.0)

Install WEBMO

yum install tcsh
yum install ncompress
yum install gcc
yum install gcc-c++
yum install gcc-gfortran
yum install atlas (Math Lib)
yum install autoconf
yum install libtool
yum install bison
yum install flex
yum install pcre
yum install pcre-devel
yum install perl-CGI
yum install apr
yum install apr-util
yum install httpd
yum install php
service iptables start (must be running before httpd is turned on)
 chkconfig iptables on (did not work; still need to "service iptables star" after reboot)
service httpd start
chkconfig httpd on
/etc/httpd/conf.d> diff userdir.conf userdir.conf.orig
33,41c33,35
<         Options Indexes Includes FollowSymLinks
< 
<         ## Apache 2.4 users use following ##
<           Require all granted
< 
<         ## Apache 2.2 users use following ##
<           AllowOverride All
<           Allow from all
<           Order deny,allow
---
>     AllowOverride FileInfo AuthConfig Limit Indexes
>     Options MultiViews Indexes SymLinksIfOwnerMatch IncludesNoExec
>     Require method GET POST OPTIONS


set the hostname straight -- the eburg-##.reg.cwu.edu hostname won't work. Use pc#####.d.cwu.edu

Installation as root:

Get WebMO.14.0.007.tar (License Number in Email)
tar xvf WebMO.14.0.007.tar
cd WebMO.install
perl setup.pl

Here are the configuration options that you have chosen
License number:       ...
Path to perl:         /usr/bin/perl
Webserver name:       eburg-10.reg.cwu.edu
HTML directory:       /var/www/html/webmo
HTML URL:             /webmo
CGI script directory: /var/www/cgi-bin/webmo
CGI script URL:       /cgi-bin/webmo
User files directory: /var/webmo

Once WEBMO is installed, the login URL is
http://hostname/cgi-bin/webmo/login.cgi

username: admin
password: blank

change password after login. Set up new users with passwords.

Now GAMESS:

Put GAMESS under the webmo prefered /usr/local/gamess
./config
(choose gfortran and atlas both are freely available for Fedora 20)
The actvte.code will be automatically modified, compiled, and executed.

When doing lked, ld may not be able to find -latlas and -lf77blas because in the /usr/lib64/atlas folder these two library's names contains version numbers that need to be removed:

cd /usr/lib64/atlas
sudo ln -s libatlas.so.3.0 libatlas.so
sudo ln -s libf77blas.so.3.0 libf77blas.so

cp -r /home/yingbin/gamess /usr/local/gamess (default directory of WEBMO)

cd /var/www/cgi-bin/webmo
vi run_gamess.cgi
add "$ENV{'ERICFMT'} = "/home/yingbin/gamess/ericfmt.dat";" and other environmental variables if needed.

Installation as regular
[webmo@pc##### webmo]$ diff run_gamess.cgi run_gamess.cgi.orig
70d69
< $ENV{'ERICFMT'}="/home/yingbin/gamess/ericfmt.dat";

Installation of Fedora 20 (64 bit)

1. Download Fedora-20-x86_64-DVD.iso (4.3 GB).

https://fedoraproject.org/en_GB/download-splash?file=http://download.fedoraproject.org/pub/fedora/linux/releases/20/Fedora/x86_64/iso/Fedora-20-x86_64-DVD.iso

2. Burn the iso file to a DVD (I used BurnAware).

3. Insert the DVD, connect the computer to Ethernet jack, restart the computer. Mine is Dell PowerEdge 1950 with one quad-core processor (2.5GHz).

4. Press F11 to enter the boot device menu. Choose "IDE CD-ROM device." IDE stands for "Integrated Drive Electronics."

5. Set  the  hostname to be pc#####.d.cwu.edu.

6. I decides to erase all previous data and system files. Click "Installation Destination."
The partition for the slave nodes:
/boot: 500 MB, standard partition,  ext4
swap: 16 GB, LVM, swap, fedora_pc89830 (8GB should be enough. 16GB just in case)
/:  412.73 GB LVM, ext4, fedora_pc89830

The partition for the master node:
/boot: 500 MB, standard partition,  ext4
swap: 16 GB, LVM, swap, fedora_pc89830
/home:  100 GB LVM, ext4, fedora_pc89830
/:  312.73 GB LVM, ext4, fedora_pc89830

The partition for the web server:
/boot: 500 MB, standard partition,  ext4
swap: 16 GB, LVM, swap, fedora_pc89830
/var:  300 GB LVM, ext4, fedora_pc89830 (webmo, etc)
/:  112.73 GB LVM, ext4, fedora_pc89830

7. The installation will start and take ~30 minutes. During which you may take time to set password for root and set up a local user account (for yourself).

8. p1p1 connected  to the internet. em1 and em2 (192.168.2.1?[1-2]) to the switch.  Open Firefox to register the computer (CWU policy). The hardware address is the MAC address of the network interface card (or NIC, network interface controller, network adapter, LAN adapter) connected to the Internet.

9. If you have several network cards like I do, only one will be connected on reboot by default. To enable all NICs, open a terminal, "cd /etc/sysconfig/network-scripts", "vi ifcfg-*", then replace every "ONBOOT=no" to "ONBOOT=yes". It is optional to enclose "yes" with double quotes. Note that p1p1 may not  connect to the internet until ifdown em1 and ifdown em2.

10. Then run "shutdown -P now" to power off the computer and wait for 5 minutes (CWU procedures) before turning on the computer. Again the computer should be connected to the Internet. Run "ifconfig" to see all NIC information including their 48-bit MAC (media access control) address.

11. Install tcsh and ncompress on all nodes. Then gcc, gfortran, and whatever is needed on  the master node.

12. "service iptables start/stop" to turn on/off the Firewall. "chkconfig iptables on/off" to turn on/off the firewall on reboot.

13. vi /etc/host* to edit hostnames, allowed and denied ones. Do NOT rush setting denied hostnames using regular expressions; this may block computers you want to connect to the server.

14. Install clamav. SELINUX must be disabled for the ifort installation. "cat /etc/selinux/config" to view the file.

15. yum install gcc-c++ (g++ is needed for ifort installation)  yum install libstdc++.so.5 before the installation of ifort and mkl.

How to clean up semaphores

A. Identify all semaphores

ipcs -a

------ Shared Memory Segments --------
key        shmid      owner      perms      bytes      nattch     status     
0x00000000 9043975    yingbin    600        160525768  1          dest        
0x00000000 9306129    yingbin    600        160525768  1          dest        
0x00000000 9076754    yingbin    600        160525768  1          dest        

------ Semaphore Arrays --------
key        semid      owner      perms      nsems    
0x00000000 17924096   yingbin    600        25       
0x00000000 17956865   yingbin    600        25       
0x00000000 17989634   yingbin    600        1        
0x00000000 17137682   yingbin    600        25       
0x00000000 17170451   yingbin    600        25       
0x00000000 17203220   yingbin    600        1        
0x00000000 17235992   yingbin    600        25       
0x00000000 17268761   yingbin    600        25       
0x00000000 17301530   yingbin    600        1        

------ Message Queues --------
key        msqid      owner      perms      used-bytes   messages   

B. Identify the process ID (pid) that are associated with the semaphores

 ipcs -s -i 17301530

Semaphore Array semid=17301530
uid=1005         gid=100         cuid=1005       cgid=100
mode=0600, access_perms=0600
nsems = 1
otime = Mon Apr  7 09:27:24 2014 
ctime = Mon Apr  7 09:27:24 2014 
semnum     value      ncount     zcount     pid      
0                1000              0          0          27036    

C. Find if the process 27036 is still active or has been killed.

ps -ef |grep 27036


D. If the process has been killed, the associated semaphores can be safely cleaned.

ipcrm -s 17301530