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Difference between revisions of "FedCloudWeNMR"
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== General Information == | == General Information == | ||
*Status: {{{FCUC_Status | | *Status: {{{FCUC_Status |closed }}} | ||
*Start Date: {{{FCUC_StartDate | 01/01/13 }}} | *Start Date: {{{FCUC_StartDate | 01/01/13 }}} | ||
*End Date: {{{FCUC_EndDate | 30/04/14}}} | *End Date: {{{FCUC_EndDate | 30/04/14}}} | ||
*EGI.eu contact: {{{FCUC_EGIName | Gergely Sipos / gergely.sipos@egi.eu}}} | *EGI.eu contact: {{{FCUC_EGIName | Gergely Sipos / gergely.sipos@egi.eu}}} | ||
*External contact: {{{FCUC_EXTName | Marco Verlato / Marco.Verlato@pd.infn.it}}} | *External contact: {{{FCUC_EXTName | Marco Verlato / Marco.Verlato@pd.infn.it}}} | ||
== Short Description == | == Short Description == | ||
{{{FCUC_ShortDesc | | {{{FCUC_ShortDesc | | ||
The objective of [http://www.wenmr.eu WeNMR] is to optimize and extend the use of the NMR and SAXS research infrastructures through the implementation of an e-infrastructure in order to provide the user community with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling. Access to the e-NMR infrastructure is provided through a portal integrating commonly used software and GRID technology. | The objective of [http://www.wenmr.eu WeNMR] is to optimize and extend the use of the NMR and SAXS research infrastructures through the implementation of an e-infrastructure in order to provide the user community with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling. Access to the e-NMR infrastructure is provided through a portal integrating commonly used software and GRID technology. | ||
}}} | }}} | ||
== Tasks == | == Tasks == | ||
{{{FCUC_Tasks | | {{{FCUC_Tasks | | ||
=====Use case 1===== | Proof of concept demonstrating the validation and improvement of biomolecular NMR structures using VirtualCing, a Virtual Machine equipped with a complex suite of ~25 programs. | ||
== Outcome == | |||
It was demonstrated at the EGI Technical Forum held in September 2012, at the Cloudscape V Workshop held in February 2013 and at the EGI CF 2013 held in April. | |||
== Additional Files == | |||
* [https://prezi.com/hrzwekguwfkx/virtualcing-cloud-demo-on-wnodes/ Demonstration of VCIng over WNoDeS cloud] | |||
* [https://documents.egi.eu/public/ShowDocument?docid=1593 Demostrations of VCing over the EGI Federated Cloud] | |||
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=====Use case 1 (in progress)===== | |||
Using VMs prepared with Gromacs and some other software to run MD simulations for educational purpose, possibly on multi-core VMs. | 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 [http://nmr.chem.uu.nl/~adrien/course/molmod/ here].<br/> | These VMs are currently run on the SARA cloud for a computer practical of University courses, see [http://nmr.chem.uu.nl/~adrien/course/molmod/ here].<br/> | ||
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Of course that would require a not negligible effort in order to adapt the WeNMR/Gromacs portal to submit jobs to the cloud, for example a possible option could be to go through a JSAGA-OCCI adaptor as described [https://indico.egi.eu/indico/contributionDisplay.py?sessionId=33&contribId=189&confId=1417 here]. | Of course that would require a not negligible effort in order to adapt the WeNMR/Gromacs portal to submit jobs to the cloud, for example a possible option could be to go through a JSAGA-OCCI adaptor as described [https://indico.egi.eu/indico/contributionDisplay.py?sessionId=33&contribId=189&confId=1417 here]. | ||
=====Use case 2===== | =====Use case 2 (not more supported)===== | ||
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/> 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. Further [https://documents.egi.eu/public/ShowDocument?docid=1593 demostrations of VCing over the EGI Federated Cloud] testbed were shown at the Cloudscape V Workshop held in February 2013 and at the EGI CF 2013 held in April.<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/> 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. Further [https://documents.egi.eu/public/ShowDocument?docid=1593 demostrations of VCing over the EGI Federated Cloud] testbed were shown at the Cloudscape V Workshop held in February 2013 and at the EGI CF 2013 held in April.<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). This demo version of the VCing image is in the [http://marketplace.egi.eu/metadata EGI marketplace] and is freely available for demonstration shows.<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). This demo version of the VCing image is in the [http://marketplace.egi.eu/metadata EGI marketplace] and is freely available for demonstration shows.<br/> | ||
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:* WeNMR can take advantage of the VM machinery in DIRAC and the web monitoring and management | :* WeNMR can take advantage of the VM machinery in DIRAC and the web monitoring and management | ||
:* VMDIRAC can be prooved as a toool for VM scheduling without the use of DIRAC broker | :* VMDIRAC can be prooved as a toool for VM scheduling without the use of DIRAC broker | ||
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}}} | }}} | ||
Latest revision as of 16:33, 7 May 2015
| Overview | For users | For resource providers | Infrastructure status | Site-specific configuration | Architecture |
| Federated Cloud Communities menu: | Home • | Production use cases • | Under development use cases • | Closed use cases • | High level tools use cases |
General Information
- Status: closed
- Start Date: 01/01/13
- End Date: 30/04/14
- EGI.eu contact: Gergely Sipos / gergely.sipos@egi.eu
- External contact: Marco Verlato / Marco.Verlato@pd.infn.it
Short Description
The objective of WeNMR is to optimize and extend the use of the NMR and SAXS research infrastructures through the implementation of an e-infrastructure in order to provide the user community with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling. Access to the e-NMR infrastructure is provided through a portal integrating commonly used software and GRID technology.
Tasks
Proof of concept demonstrating the validation and improvement of biomolecular NMR structures using VirtualCing, a Virtual Machine equipped with a complex suite of ~25 programs.
Outcome
It was demonstrated at the EGI Technical Forum held in September 2012, at the Cloudscape V Workshop held in February 2013 and at the EGI CF 2013 held in April.