LZU-Bio1

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Introduction

LZU authored a VM which provides two bioscience applications. This VM is reated on a Rocks 6.0 system with a KVM roll. The two applications are:

  • The first application is a spatially explicit species competition simulation to investigate, in a homogeneous habitat, the effects of dispersal and recruitment limitation on delaying competitive exclusion. This application examines the species diversity (measured by Simpson’s diversity index), SAD and SAR under the conditions of slight to moderate competitive asymmetries among species, and with dispersal and recruitment limitations.
  • The second VM application simulates the movement and function of ubiquitin, a small regulatory protein, using the molecular dynamics package NAMD. Ubiquitin is a protein that plays a key role on eukaryotic intracellular protein degradation, whose importance has been widely recognized in the scientific community.
  • Contact: Zhang Yang

VM migration

  • This gzip'ed VM image is little over 5GB in size. It's deposited in gfarm as /vm-images/LZU/lzu-bio1.img.gz.

For Rocks/Xen site

  • If you want to setup the image file locally, make sure that you update your local vmdb.txt file. you can download both vmdb.txt and lzu-bio1.img.gz from http://goc.pragma-grid.net/softdepot.
  • Use vm-deploy script. See bioapp as an example.
  • It requires 80GB free disk space and one available public IP address to deploy with the script

For other sites

  • Use your own deployment scripts/mechanisms if any, or
  • To manually deploy a VM, see Bloss+GeoGrid as an example.
  • It requires 40GB free disk space and one available public IP address to deploy manually.


After the deployment, please email Zhang Yang the new hostname/IP, so Zhang Yang can verify the results.

AIST KVM/OpenNebula Manual deployment example

I have done the following procedure by hands.

1. Mount the lzu-bio1 image file.
% sudo losetup /dev/loop0 lzu-bio1.img
% sudo kpartx -av /dev/loop0
add map loop0p1 (253:0): 0 32768000 linear /dev/loop0 2048 add map loop0p2 (253:1): 0 8192000 linear /dev/loop0 32770048 add map loop0p3 (253:2): 0 2048000 linear /dev/loop0 40962048 add map loop0p4 (253:3): 0 2 linear /dev/loop0 43010048 add map loop0p5 (253:4): 0 27299840 linear /dev/loop0 43012096

% sudo mount /dev/mapper/loop0p1 /mnt/file


2. Install a contextualization script customized for our environment.
% sudo cp -pi one_ipaddress_lzubio1 /mnt/file/etc/rc.d/init.d

% sudo chroot /mnt/file /bin/bash
# chkconfig one_ipaddress_lzubio1 on
# chkconfig --list one_ipaddress_lzubio1
one_ipaddress_lzubio1	      0:off  1:off	2:on	3:on	4:on	5:on	6:off

(I have deposited one_ipaddress_lzubio1 script on Gfarm:/vm-images/AIST/lzu-bio1)


3. Configure SSH.
(add our SSH public keys for debugging.) # vi /root/.ssh/authorized_keys

(change the sshd_config to follow our network policy.) # cp -p /etc/ssh/sshd_config /etc/ssh/sshd_config.original # vi /etc/ssh/sshd_config # diff /etc/ssh/sshd_config.original /etc/ssh/sshd_config
66c66
< PasswordAuthentication yes
---
> PasswordAuthentication no
97c97
< UsePAM yes
---
> UsePAM no


4. Unmount.
# exit
% sudo umount /mnt/file
% sudo kpartx -dv /dev/loop0
% sudo losetup -d /dev/loop0


5. Registrate the lzu-bio1 image file to OpenNebula, and VM create.
[oneadmin@ascsvc lzu-bio1]$ cat image_lzu-bio1.one 
NAME          = "lzu-bio1"
PATH          = /work/tmp/lzu-bio1.img
TYPE          = OS
PERSISTENT    = NO
DESCRIPTION   = "LZU-Bio1 VM image"

[oneadmin@ascsvc lzu-bio1]$ oneimage create image_lzu-bio1.one
ID: 42

[oneadmin@ascsvc lzu-bio1]$ cat vm_lzu-bio1.one 
NAME   = "lzu-bio1"
CPU    = 8
VCPU   = 8
MEMORY = 20480
OS     = [ boot = "hd", arch = "x86_64" ]
DISK   = [ image = "lzu-bio1", image_uname = "oneadmin", bus = virtio, target = vda ]
NIC    = [ network = "defaultpub", network_uname = "oneadmin", model = "virtio" ]
NIC    = [ network = "defaultpriv", network_uname = "oneadmin", model = "virtio" ]

[oneadmin@ascsvc lzu-bio1]$ onevm create vm_lzu-bio1.one
ID: 336

[oneadmin@ascsvc lzu-bio1]$ onevm list
    ID USER     GROUP    NAME         STAT CPU     MEM        HOSTNAME        TIME
(snip)
   336 oneadmin oneadmin lzu-bio1     runn   2     20G       asccmp126 00 01:31:05