Voyager Notes

1. Logging in:
                       ssh -X <name>@voyager.umsl.edu

2. .bashrc

           # Source global definitions
   if [ -f /etc/bashrc ]; then
           . /etc/bashrc
   fi
   export PATH=.:/usr/local/mpich/bin/:/usr/local/toolworks/totalview.8.0.0-1/bin:$PATH:
   export LD_LIBRARY_PATH=/usr/lib:/usr/local/mpich/lib:/usr/local/lib:$LD_LIBRARY_PATH
   export MPICHHOME=/usr/local/mpich/
           

3. Makefile

   NAME=
   PCOUNT= 4
   TVMACHINES=tvmachines
   APPLIBS = -lm  $(EXTRAS)
   EXTRAS=
   
   all:
           gcc -g -o $(NAME) $(NAME).c  -lsprng -lgmp  -lm $(EXTRAS)
   
   mpi:
           mpicc -g -o $(NAME) $(NAME).c  -lsprng -lgmp     $(APPLIBS)
   
   tv:
           mpirun -dbg=totalview -np $(PCOUNT) -machinefile $(TVMACHINES) $(NAME)
   
   kill:
           cluster-fork killall -9 $(NAME)
           killall -9 $(NAME)
   
           

4. gedit

   

5. nedit

   

Your .ssh directory should look like this

[siegelj@voyager ~]$ ls -al .ssh
total 32
drwx------   2 siegelj siegelj    4096 Jan 12 09:14 .
drwx------  42 siegelj instructor 4096 Jan 24 15:31 ..
-rw-------   1 siegelj siegelj     234 Jul 13  2006 authorized_keys
-rw-r--r--   1 siegelj root         47 Jan 12 08:23 config
-rw-------   1 siegelj siegelj     887 Jul 13  2006 id_rsa
-rw-r--r--   1 siegelj siegelj     234 Jul 13  2006 id_rsa.pub
-rw-r--r--   1 siegelj siegelj    4395 Oct 23 19:16 known_hosts
[siegelj@voyager ~]$


[siegelj@voyager .ssh]$ cat config
Host *
     ForwardX11 no
     ForwardAgent no

[siegelj@voyager .ssh]$

Using TotalView:

I placed a copy of preferences6.tvd in /usr/local/public on voyager. To use it you need to start TotalView once, or just create a subdirectory .totalview in your home directory. Again, there are TotalView screenshots for pirules at Using TotalView®.

If while trying to go to other processors(by cluster-fork for example) you are either asked for a password or given the following warning..
Bad owner or permissions on /home/mwh308/.ssh/config
compute-0-1:

here is how you fix it

a) First move your old .ssh file to a temporary location and then logout
[mwh308@voyager ~]$ mv .ssh .sshold
[mwh308@voyager ~]$ logout

b) Log back in to voyager

Connection to voyager.umsl.edu closed.
[mwh308@medal2 ~]$ ssh -X mwh308@voyager.umsl.edu
Connection to voyager.umsl.edu closed.
[mwh308@medal2 ~]$ ssh -X mwh308@voyager.umsl.edu
mwh308@voyager.umsl.edu's password:

c) Now it will prompt you for some information, just take the defaults by hitting Return each time until done.

Last login: Mon Jan 29 14:47:12 2007 from noname-00173185403b.dhcp.umsl.edu
Rocks Frontend Node - Voyager Cluster
Rocks 4.0.0 (Whitney)
Profile built 11:20 12-Jul-2006

Kickstarted 11:20 12-Jul-2006

It doesn't appear that you have set up your ssh key.
This process will make the files:
     /home/mwh308/.ssh/id_rsa.pub
     /home/mwh308/.ssh/id_rsa
     /home/mwh308/.ssh/authorized_keys

Generating public/private rsa key pair.
Enter file in which to save the key (/home/mwh308/.ssh/id_rsa):
Created directory '/home/mwh308/.ssh'.
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/mwh308/.ssh/id_rsa.
Your public key has been saved in /home/mwh308/.ssh/id_rsa.pub.
The key fingerprint is:
a5:da:6e:dd:94:e0:de:0e:6a:af:8d:08:9d:1e:65:0f mwh308@voyager.umsl.edu
[mwh308@voyager ~]$

d) Copy your old config file to the new .ssh directory that was just created

[mwh308@voyager ~]$ cp .sshold/config .ssh/config

e) Log out and back in and you should be good to go!


  

Notes for March 10 - Killing semapores

  My updated cleannodes on valhalla2 consists of...

cluster-fork '/opt/mpich/gnu/sbin/cleanipcs; skill -v $USER'

My updated checkall on valhalla2 is

#!/bin/bash
echo Checking all nodes
cluster-fork ps -u mwh308
cluster-fork ipcs -a


The only difference is checking for the semaphores when I do checkall.

  

  You want to make two changes in your .bashrc file to point it in the right direction to compile and run programs using cluster-openmp

Add the two lines

export PATH=/opt/intel/cc/9.1.047/bin:$PATH
export LD_LIBRARY_PATH=/opt/intel/cc/9.1.047/lib:$LD_LIBRARY_PATH

to the end of your .bashrc file

You can then compile a program using the intel C++ compiler using openmp with

icc -openmp hello.c -o hello

  

Notes for April 14 - Using OpenMP

My Makefile:

NAME=
PCOUNT= 4
TVMACHINES=tvmachines
APPLIBS = -lm  $(EXTRAS)
EXTRAS= 

all:
	gcc -g -o $(NAME) $(NAME).c  /usr/local/lib/libsprng.a /usr/local/lib/libgmp.a  -lm $(EXTRAS) 

omp:
	icc  -openmp  -I/opt/intel/cc/9.1.047/include $(NAME).c -o $(NAME) -lsprng -lgmp $(APPLIBS)

mpi:
	mpicc -g -o $(NAME) $(NAME).c  -lsprng -lgmp     $(APPLIBS)

tv:
	mpirun -dbg=totalview -np $(PCOUNT) -machinefile $(TVMACHINES) $(NAME)

kill:
	cluster-fork killall -9 $(NAME)
	killall -9 $(NAME)

My .bashrc:

# .bashrc

# User specific aliases and functions

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi
export PATH=.:/opt/intel/cc/9.1.047/bin:/usr/local/mpich/bin/:$PATH:/usr/local/toolworks/totalview.8.0.0-1/bin
export LD_LIBRARY_PATH=/usr/local/lib/omp:/usr/lib:/usr/local/mpich/lib:/usr/local/lib:$LD_LIBRARY_PATH
export MPICHHOME=/usr/local/mpich/
export OMP_NUM_THREADS=6