Arkansas High Performace Computing Center [hpcwiki]

Nebula http://nebula.uark.edu is a University of Arkansas privately hosted Open Stack https://www.openstack.org/ software platform for cloud computing. Some of the advantages of using a cloud computing environment are:

• the ability to bring up virtual machines using a wide range of operating systems.
• unrestricted root level control of the virtual machine

Currently Nebula allows it's hpc users to spin up the following operating systems/environment:

• Bioconda-CentOS7
• CentOS7
• CentOS7-atomic
• CentOS7-UA
• Cirros
• Debian8
• Debian9
• Fedora-Atomic-26
• Fedora26
• Jupyter-CentOS7
• Lamp-CentOS7
• RHEL7
• Ubuntu16.04-LTS
• Ubuntu16.04-LTS-Mate
• Ubuntu18.04-LTS

A dedicated queue on Razor, named nebula, has been set up for launching Nebula hosted virtual machines. Jobs to the nebula queue have to be submitted in the interactive mode (qsub -I -q nebula). The virtual machine is created at the beginning of the job, presists while the job is running and is deleted when the job finishes. The name of the job specifies the operating system of the nebula virtual machine (qsub -I -q nebula -N RHEL7). The queue has a maximum walltime of 72 hours, and a default walltime of 24 hours. So the command

qsub -I -q nebula -N RHEL7 -l walltime=72:00:00

would start a virtual machine on Nebula using Red Hat Enterprise Linux version 7 as the operating system, and the machine would run for 3 days, unless the interactive job is terminated earlier. Following is an example of launching an Ubuntu18.04-LTS Virtual machine:

razor-l1:pwolinsk:$ qsub -I -q nebula -N Ubuntu18.04-LTS
qsub: waiting for job 3986347.sched to start
qsub: job 3986347.sched ready

Nebula Ubuntu18.04-LTS job.
Starting Ubuntu18.04-LTS nebula instance...

PLAY [Launch a compute instance] ***********************************************
TASK [Gathering Facts] *********************************************************
ok: [localhost]
TASK [launch an instance] ******************************************************
changed: [localhost]
TASK [Ubuntu18.04-LTS-pwolinsk-3986347 facts] **********************************
ok: [localhost]
TASK [debug] *******************************************************************
...

PLAY RECAP *********************************************************************
localhost                  : ok=4    changed=1    unreachable=0    failed=0   
Waiting for the vm to boot up...............VM is up
Success! Ubuntu18.04-LTS-pwolinsk-3986347 Nebula instance created. 

******************************  VM ACCESS  ************************************
***                                                                         ***
*** Log in:                                                                 ***
***    ssh -i ~/.nebula/hpc-nebula.pem     ubuntu@10.9.1.166                ***
***                                                                         ***
*** Move data from Razor to the vm please run (on Razor):                   ***
***    scp -i ~/.nebula/hpc-nebula.pem <inputdata>  ubuntu@10.9.1.166:      ***
***                                                                         ***
*******************************************************************************

Currently Loaded Modulefiles:
  1) os/el6
compute1172:pwolinsk:$ 

This process should take about 1 minute once the job starts. At this point the virtual machine is created and ready to be used. To log into the VM copy and paste the ssh line from the printout above:

compute1172:pwolinsk:$  ssh -i ~/.nebula/hpc-nebula.pem     ubuntu@10.9.1.166
Warning: Permanently added '10.9.1.166' (RSA) to the list of known hosts.
Welcome to Ubuntu 18.04 LTS (GNU/Linux 4.15.0-20-generic x86_64)

 * Documentation:  https://help.ubuntu.com
 * Management:     https://landscape.canonical.com
 * Support:        https://ubuntu.com/advantage

  System information as of Mon May 14 20:50:39 UTC 2018

  System load:  0.16             Processes:           83
  Usage of /:   9.8% of 9.53GB   Users logged in:     0
  Memory usage: 11%              IP address for ens3: 192.168.0.13
  Swap usage:   0%

 * Meltdown, Spectre and Ubuntu: What are the attack vectors,
   how the fixes work, and everything else you need to know
   - https://ubu.one/u2Know

  Get cloud support with Ubuntu Advantage Cloud Guest:
    http://www.ubuntu.com/business/services/cloud

0 packages can be updated.
0 updates are security updates.



The programs included with the Ubuntu system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Ubuntu comes with ABSOLUTELY NO WARRANTY, to the extent permitted by
applicable law.

To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

ubuntu@ubuntu18:~$ 

The default user account for the vm is used to log in. To become root please run:

ubuntu@ubuntu18:~$ whoami
ubuntu
ubuntu@ubuntu18:~$ sudo /bin/bash
root@ubuntu18:~# whoami
root
root@ubuntu18:~# 

Now any software available in the software repository can be installed:

root@ubuntu18:~# gcc

Command 'gcc' not found, but can be installed with:

apt install gcc

root@ubuntu18:~# apt-get install gcc
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following package was automatically installed and is no longer required:
  grub-pc-bin
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-7 gcc-7 gcc-7-base libasan4 libatomic1 libbinutils libc-dev-bin libc6-dev
  libcc1-0 libcilkrts5 libgcc-7-dev libgomp1 libisl19 libitm1 liblsan0 libmpc3 libmpx2 libquadmath0 libtsan0 libubsan0 linux-libc-dev
  manpages-dev
...
root@ubuntu18:~# gcc -v
...
gcc version 7.3.0 (Ubuntu 7.3.0-16ubuntu3) 
root@ubuntu18:~#