Tag: 'gromacs'

Projects

Project Title	Project Institution	Tags	Project Status
Understanding Mechanical Properties of Bio-interfaces with HPC Molecular Simulations	University of Vermont	HPC BioInformatics Molecular-Dynamics gromacs Simulations mpi python Computational-Chemistry	In progress

Students

Name	Institution	Interests
Joshua Gyllinsky	Joshua Gyllinsky	Admin accounts Cloud/VM Cloud aws azure comet osg gce moc cyverse containers Storage s3 ceph swift HPC network dtn firewall ib tcp sdn vpn scheduler condor pbs sge slurm storage acls permissions cifs privacy gpfs quota lustre nfs SoftwareInstallation Compiling debugging conda cuda parallelization vectorization dependencies OS jupyterhub profilling mpi Platform kubernetes openshift openstack pip rstudio-server tuning spark tensorflow DomainSpecific AI Astrophysics BioInformatics gatk trinity ddocent DeepLearning geographicinformationsystem arcgis ImageProcessing opencv Machine-Learning scikit-learn Molecular-Dynamics lammps namd gromacs amber charmm desmond NaturalLanguageProcessing Parametersweeps ParticlePhysics root Quantum-Mechanics gaussian Simulations VideoProcessing EndUser ClusterSupport file-transfer globus nomachine ondemand parallelization putty rdp samba ScienceDMZ sftp site-specific smb ssh vpn x11 DataManagement archive CUI data-lifecycle doi ELN metadata security storage SoftwareSupport bash comsol environment-modules mathematica matlab mpi python r sas scripting spss stata unclassified atlas backup batch jobs big data bu cgroups Computational-Chemistry containers cpus cyberInfrastructure CyberSecurity data handling data storage data wrangling desktops distributed computing fastx filesystem gpus graphics hadoop hardware hardware architecture harvard harvardssh HPC Cluster build hpc operations HPCs HTNs hw/sw integration identity internet job sizing julia linear programming machine learning natural language processing nese networking nx odyssey oodatlas parallelism performance performance tuning Personnel Resource Capacity Building professional development programming programming best practices provisioning resources scc scheduling scientific gateway screen security Security in CyberInfrastructure software software identity Testest tier 3 tmux unix environment visualization web xsede
Benjamin Himberg	University of Vermont	slurm cuda parallelization vectorization mpi spark tensorflow AI DeepLearning Machine-Learning scikit-learn Molecular-Dynamics gromacs Quantum-Mechanics parallelization ssh x11 bash environment-modules mathematica matlab mpi scripting gpus hadoop julia machine learning parallelism performance performance tuning professional development programming programming best practices unix environment visualization

Mentors

Name	Institution	Areas of HPC Expertise/Interests	E-mail
Juan Vanegas	University of Vermont	HPC slurm storage nfs Compiling conda jupyterhub pip BioInformatics Molecular-Dynamics gromacs Simulations ssh x11 bash environment-modules mpi python batch jobs HPC Cluster build hpc operations	jvanegas@uvm.edu

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