J. Allard, V. Gouranton, L. Lecointre, S. Limet, E. Melin et al., FlowVR: A Middleware for Large Scale Virtual Reality Applications, Proceedings of Euro-par, 2004.
DOI : 10.1007/978-3-540-27866-5_65

URL : https://hal.archives-ouvertes.fr/hal-00085302

C. Docan, M. Parashar, and S. Klasky, DataSpaces, Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, HPDC '10, 2012.
DOI : 10.1145/1851476.1851481

M. Dorier, G. Antoniu, F. Cappello, M. Snir, and L. Orf, Damaris: How to Efficiently Leverage Multicore Parallelism to Achieve Scalable, Jitter-free I/O, 2012 IEEE International Conference on Cluster Computing, 2012.
DOI : 10.1109/CLUSTER.2012.26

URL : https://hal.archives-ouvertes.fr/hal-00715252

M. Dorier, R. Sisneros, R. Peterka, T. Antoniu, G. Semeraro et al., Damaris/Viz: A nonintrusive, adaptable and user-friendly in situ visualization framework, 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), 2013.
DOI : 10.1109/LDAV.2013.6675160

URL : https://hal.archives-ouvertes.fr/hal-00859603

M. Dreher and B. Raffin, A Flexible Framework for Asynchronous in Situ and in Transit Analytics for Scientific Simulations, 2014 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, 2014.
DOI : 10.1109/CCGrid.2014.92

URL : https://hal.archives-ouvertes.fr/hal-00941413

M. Dreher, M. Piuzzi, T. Ahmed, C. Matthieu, M. Baaden et al., Interactive Molecular Dynamics: Scaling up to Large Systems, International Conference on Computational Science, ICCS 2013, 2013.
DOI : 10.1016/j.procs.2013.05.165

URL : https://hal.archives-ouvertes.fr/hal-00809024

N. Fabian, K. Moreland, D. Thompson, A. Bauer, P. Marion et al., The ParaView Coprocessing Library: A scalable, general purpose in situ visualization library, 2011 IEEE Symposium on Large Data Analysis and Visualization, 2011.
DOI : 10.1109/LDAV.2011.6092322

R. Hagan and Y. Cao, Multi-gpu load balancing for in-situ visualization, The 2011 International Conference on Parallel and Distributed Processing Techniques and Applications, 2011.

B. Hess, C. Kutzner, D. Van-der-spoel, and E. Lindahl, GROMACS 4:?? Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation, Journal of Chemical Theory and Computation, vol.4, issue.3, 2008.
DOI : 10.1021/ct700301q

W. Humphrey, A. Dalke, and K. Schulten, VMD: Visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1, pp.33-38, 1996.
DOI : 10.1016/0263-7855(96)00018-5

S. Klasky, S. Ethier, Z. Lin, K. Martins, D. Mccune et al., Grid -Based Parallel Data Streaming implemented for the Gyrokinetic Toroidal Code, Proceedings of the 2003 ACM/IEEE conference on Supercomputing, SC '03, 2003.
DOI : 10.1145/1048935.1050175

M. Krone, J. E. Stone, T. Ertl, and K. Schulten, Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories, EuroVis 2012 Short Papers, 2012.

B. G. Levine, J. E. Stone, and A. Kohlmeyer, Fast analysis of molecular dynamics trajectories with graphics processing units???Radial distribution function histogramming, Journal of Computational Physics, vol.230, issue.9, 2011.
DOI : 10.1016/j.jcp.2011.01.048

M. Li, S. S. Vazhkudai, A. R. Butt, F. Meng, X. Ma et al., Functional Partitioning to Optimize End-to-End Performance on Manycore Architectures, Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis. SC '10, 2010.
DOI : 10.1109/sc.2010.28

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

B. Lorendeau, Y. Fournier, and A. Ribes, In-Situ visualization in fluid mechanics using Catalyst: A case study for Code Saturne, 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), 2013.
DOI : 10.1109/LDAV.2013.6675158

K. Moreland, Oh, $#*@! Exascale! The Effect of Emerging Architectures on Scientific Discovery, 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, 2012.
DOI : 10.1109/SC.Companion.2012.38

J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, vol.84, issue.16, pp.1781-1802, 2005.
DOI : 10.1002/jcc.20289

S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar et al., GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics, vol.29, issue.7, 2013.
DOI : 10.1093/bioinformatics/btt055

A. Singh, P. Balaji, and W. C. Feng, GePSeA: A General-Purpose Software Acceleration Framework for Lightweight Task Offloading, 2009 International Conference on Parallel Processing, 2009.
DOI : 10.1109/ICPP.2009.39

J. Soumagne and J. Biddiscombe, Computational Steering and Parallel Online Monitoring Using RMA through the HDF5 DSM Virtual File Driver, Proceedings of the International Conference on Computational Science, ICCS 2011, 2011.
DOI : 10.1016/j.procs.2011.04.050

URL : https://hal.archives-ouvertes.fr/hal-00652816

J. E. Stone, D. J. Hardy, I. S. Ufimtsev, and K. Schulten, GPU-accelerated molecular modeling coming of age, Journal of Molecular Graphics and Modelling, vol.29, issue.2, 2010.
DOI : 10.1016/j.jmgm.2010.06.010

J. E. Stone, A. Kohlmeyer, K. L. Vandivort, and K. Schulten, Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware, 2010.
DOI : 10.1007/978-3-642-17274-8_38

J. E. Stone, R. Mcgreevy, B. Isralewitz, and K. Schulten, GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting, Faraday Discuss., vol.97, 2014.
DOI : 10.1039/C4FD00005F

J. E. Stone, K. L. Vandivort, and K. Schulten, GPU-accelerated molecular visualization on petascale supercomputing platforms, Proceedings of the 8th International Workshop on Ultrascale Visualization, UltraVis '13, 2013.
DOI : 10.1145/2535571.2535595

T. Tu, H. Yu, L. Ramirez-guzman, J. Bielak, O. Ghattas et al., From Mesh Generation to Scientific Visualization: An End-to-End Approach to Parallel Supercomputing, ACM/IEEE SC 2006 Conference (SC'06), 2006.
DOI : 10.1109/SC.2006.32

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

V. Vishwanath, M. Hereld, and M. Papka, Toward simulation-time data analysis and I/O acceleration on leadership-class systems, 2011 IEEE Symposium on Large Data Analysis and Visualization, 2011.
DOI : 10.1109/LDAV.2011.6092178

B. Whitlock, J. M. Favre, and J. S. Meredith, Parallel In Situ Coupling of Simulation with a Fully Featured Visualization System, Proceedings of the 11th Eurographics Conference on Parallel Graphics and Visualization. EGPGV '11, 2011.

H. Yu, C. Wang, R. Grout, J. Chen, and K. L. Ma, In situ visualization for large-scale combustion simulations, Computer Graphics and Applications IEEE, 2010.

F. Zheng, H. Abbasi, J. Cao, J. Dayal, K. Schwan et al., In-situ I/O processing, Proceedings of the sixth workshop on Parallel Data Storage, PDSW '11, 2011.
DOI : 10.1145/2159352.2159362

F. Zheng, H. Yu, C. Hantas, M. Wolf, G. Eisenhauer et al., GoldRush, Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis on, SC '13, 2013.
DOI : 10.1145/2503210.2503279

F. Zheng, H. Zou, G. Eisenhauer, K. Schwan, M. Wolf et al., FlexIO: I/O Middleware for Location-Flexible Scientific Data Analytics, 2013 IEEE 27th International Symposium on Parallel and Distributed Processing, 2013.
DOI : 10.1109/IPDPS.2013.46