Alert.png The wiki is deprecated and due to be decommissioned by the end of September 2022.
The content is being migrated to other supports, new updates will be ignored and lost.
If needed you can get in touch with EGI SDIS team using operations @ egi.eu.

Difference between revisions of "Template:FedCloudUseCases"

From EGIWiki
Jump to navigation Jump to search
Line 20: Line 20:
=====Use case 2=====
=====Use case 2=====
Validating and improving biomolecular NMR structures using VirtualCing (VCing), a Virtual Machine (VM) equipped with a complex suite of ~25 programs.<br/> A presentation of the current deployment at the Dutch National HPC Cloud is available [http://www.sara.nl/sites/default/files/Jurgen_Doreleijers_HPC_Cloud_Day_20111004_2.pdf here], and recently a paper has been published [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245154/?tool=pmcentrez here].<br/> The cloud usage framework is based on a pilot job mechanism making use of the [https://grid.sara.nl/wiki/index.php/Using_the_Grid/ToPoS ToPoS] tool. Therefore, such a framework would naturally allow for execution of VCing tasks across multiple cloud providers. Do notice that the framework is independent on the cloud access interface: it would work also with simple grid jobs, as far as the user-defined (or VO manager defined) VCing VM is available at the grid site e.g. in a SE (or in the VO software area mounted by the WNs) and the grid job is allowed to start the VM. Technical details about its current implementation are available [http://code.google.com/p/cing/w/list here]. <br/> Furthermore, a live [http://prezi.com/hrzwekguwfkx/virtualcing-cloud-demo-on-wnodes/ demonstration] about the deployment and use of VCing on the WNoDeS testbed of the INFN-CNAF computing centre has been shown at the EGI TF 2012 held in September.<br/>
Validating and improving biomolecular NMR structures using VirtualCing (VCing), a Virtual Machine (VM) equipped with a complex suite of ~25 programs.<br/> A presentation of the current deployment at the Dutch National HPC Cloud is available [http://www.sara.nl/sites/default/files/Jurgen_Doreleijers_HPC_Cloud_Day_20111004_2.pdf here], and recently a paper has been published [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245154/?tool=pmcentrez here].<br/> The cloud usage framework is based on a pilot job mechanism making use of the [https://grid.sara.nl/wiki/index.php/Using_the_Grid/ToPoS ToPoS] tool. Therefore, such a framework would naturally allow for execution of VCing tasks across multiple cloud providers. Do notice that the framework is independent on the cloud access interface: it would work also with simple grid jobs, as far as the user-defined (or VO manager defined) VCing VM is available at the grid site e.g. in a SE (or in the VO software area mounted by the WNs) and the grid job is allowed to start the VM. Technical details about its current implementation are available [http://code.google.com/p/cing/w/list here]. <br/> Furthermore, a live [http://prezi.com/hrzwekguwfkx/virtualcing-cloud-demo-on-wnodes/ demonstration] about the deployment and use of VCing on the WNoDeS testbed of the INFN-CNAF computing centre has been shown at the EGI TF 2012 held in September.<br/>
VCing OS is Ubuntu 11.04 i386, and its image size is of 8.1 GB in compressed qcow2 kvm format (from a 20 GB raw image).<br/>
VCing OS is Ubuntu 11.04 i386, and its image size has been recently shrinked to 8.1 GB in compressed qcow2 kvm format (from a 20 GB raw image).<br/>
<br/>
<br/>
1. Here below are the steps carried out to make the VCing image work with the WNoDeS framework for the network and debian/ubuntu:
1. Here below are the steps carried out to make the VCing image work with the WNoDeS framework for the network and debian/ubuntu:

Revision as of 12:38, 14 January 2013

General Information

  • Status: planned, active, completed
  • Start Date: DD/MM/YY
  • End Date: DD/MM/YY
  • EGI.eu contact: contact@egi.eu
  • External contact: contact@something


Short Description

Short description of the FedCloud Use Case.


Tasks

Use case 1

Using VMs prepared with Gromacs and some other software to run MD simulations for educational purpose, possibly on multi-core VMs. These VMs are currently run on the SARA cloud for a computer practical of University courses, see here.

Use case 2

Validating and improving biomolecular NMR structures using VirtualCing (VCing), a Virtual Machine (VM) equipped with a complex suite of ~25 programs.
A presentation of the current deployment at the Dutch National HPC Cloud is available here, and recently a paper has been published here.
The cloud usage framework is based on a pilot job mechanism making use of the ToPoS tool. Therefore, such a framework would naturally allow for execution of VCing tasks across multiple cloud providers. Do notice that the framework is independent on the cloud access interface: it would work also with simple grid jobs, as far as the user-defined (or VO manager defined) VCing VM is available at the grid site e.g. in a SE (or in the VO software area mounted by the WNs) and the grid job is allowed to start the VM. Technical details about its current implementation are available here.
Furthermore, a live demonstration about the deployment and use of VCing on the WNoDeS testbed of the INFN-CNAF computing centre has been shown at the EGI TF 2012 held in September.
VCing OS is Ubuntu 11.04 i386, and its image size has been recently shrinked to 8.1 GB in compressed qcow2 kvm format (from a 20 GB raw image).

1. Here below are the steps carried out to make the VCing image work with the WNoDeS framework for the network and debian/ubuntu:

  • modifying the file /etc/network/interfaces as follows:
auto lo
iface lo inet loopback
auto eth0
allow-hotplug eth0
iface eth0 inet dhcp
auto eht1
allow-hotplug eth1
iface eth1 inet dhcp
  • deleting /etc/udev/rules.d/70-persistent-net.rules file
  • removing the hostaname in the file /etc/hostname

2. From any machine having the Topos library add the tokens to the Topos server https://topos.grid.sara.nl/4.1/pools/<string to keep private>

$ ./topos createTokensFromLinesInFile <string to keep private> demo_token_list.txt

For testing purpose you can before try with one token by adding manually from the Topos web interface e.g. the following line:

refineEntryNrg 1iy6 9 http://nmr.cmbi.ru.nl/NRG-CING/data i@nmr.cmbi.ru.nl:/mnt/data/D/NMR_REDO . . BY_CH23_BY_ENTRY CING 0 auto 0 0 1

3. You can start now as many as possible VCing instances on the federated cloud. Job payloads will be retrieved automatically by the VCing from the Topos server pool until all the tokens are processed.
4. Output data are copied at the end of the processing from VCing to the NMR server nmr.cmbi.ru.nl hosted at CMBI.


Additional Files

  • File 1
  • File 2