Difference between revisions of "Template:FedCloudUseCases"
m (→Tasks) |
m (→Tasks) |
||
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 image size is of 16.4 GB in compressed qcow2 kvm format (from a 50 GB raw image).<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: | ||
:* modifying the file /etc/network/interfaces as follows: | :* modifying the file /etc/network/interfaces as follows: |
Revision as of 17:47, 26 November 2012
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 image size is of 16.4 GB in compressed qcow2 kvm format (from a 50 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. Operations to be done on the NMR server nmr.cmbi.ru.nl hosted at CMBI:
- setting the environment
iLnmr/~/ source cingStableSettings.csh
- adding the 534 tokens for the demo to the Topos server https://topos.grid.sara.nl/4.1/pools/<string to keep private>
iLnmr/~/ $C/python/cing/Scripts/vCing/vCing.py addTokenListToTopos $D/NRG-CING/token_list_todo.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 1i2u 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 0
Additional Files
- File 1
- File 2