Merge pull request #25 from opensciencegrid/master

Merging with upstream

mappings/project_institution.yaml

@@ -15,6 +15,7 @@ Cincinnati: "University of Cincinnati"
 Clarkson: "Clarkson University"
 Coe: "Coe College"
 Creighton: "Creighton University"
+CSUN: "California State University, Northridge"
 CUBoulder: "University of Colorado Boulder"
 CUAnschutz: "University of Colorado Anschutz Medical Campus"
 CSUSB: "California State University, San Bernadino"
@@ -35,6 +36,7 @@ LoyolaChicago: "Loyola University Chicago"
 LSMSA: "Louisiana School for Math, Science, and the Arts"
 LSU: "Louisiana State University"
 LSUHSC: "Louisiana State University Health Sciences Center"
+MiamiOH: "Miami University"
 Michigan: "University of Michigan"
 Mines: "Colorado School of Mines"
 MIT: "Massachusetts Institute of Technology"
@@ -50,6 +52,7 @@ NJIT: "New Jersey Institute of Technology"
 NMSU: "New Mexico State University"
 NOAA: "National Oceanic and Atmospheric Administration"
 Northeastern: "Northeastern University"
+NorthwesternMed: "Northwestern Medicine"
 NSHE: "Nevada System of Higher Education"
 OHSU: "Oregon Health & Science University"
 OSU: "The Ohio State University"

projects/Auburn_Hauck.yaml

@@ -0,0 +1,9 @@
+Department: Pathobiology
+Description: Experimental infections with avian reovirus and co-infections with other micro-organisms. We analyze bioinformatic data pertaining to microbiome, gene expression, metagenome and transcriptome obtained from these experiments.
+FieldOfScience: Agricultural Sciences specifically Poultry Science
+Organization: Auburn University
+PIName: Ruediger Hauck
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/CMU_Isayev.yaml

@@ -0,0 +1,8 @@
+Department: Chemistry
+Description: Quantum chemical and machine learning insights into supra-molecular organization
+  of molecular crystals.
+FieldOfScience: Chemistry
+Organization: Carnegie-Mellon University
+PIName: Olexandr Isayev
+
+

projects/CSUN_Katz.yaml

@@ -0,0 +1,6 @@
+Department: Department of Mathematics
+Description: Large scale searches for binary sequences with identical autocorrelation
+  spectra (https://arxiv.org/abs/2308.07467).
+FieldOfScience: Mathematics
+Organization: California State University, Northridge
+PIName: Daniel Katz

projects/IIT_Minh.yaml

@@ -0,0 +1,8 @@
+Description: >
+  Computational scientists who focus on chemical biology, the interactions between 
+  small molecules and biological macromolecules. We develop and apply new methods that
+  may be helpful for structure-based drug design.
+Department: Chemistry
+FieldOfScience: Biological and Biomedical Sciences
+Organization: Illinois Institute of Technology
+PIName: David Minh

projects/IIT_Rosa.yaml

@@ -0,0 +1,9 @@
+Description: "Generating trajectories in high-dimensional parameter spaces using numerical continuation methods.  The software repo is available here: https://github.com/nr-codes/BipedalGaitGeneration."
+Department: Mechanical, Materials, and Aerospace Engineering Deptartment
+FieldOfScience: Mechanical Engineering
+Organization: Illinois Institute of Technology
+PIName: Nelson Rosa
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/MIT_Takei.yaml

@@ -0,0 +1,6 @@
+Department: Global Programs
+Description: I am working on models for quantifying the effects on the change of financial
+  regulations
+FieldOfScience: Finance
+Organization: Massachusetts Institute of Technology
+PIName: Ikuo Takei

projects/MiamiOH_Staff.yaml

@@ -0,0 +1,9 @@
+Department: Research Office
+Description: Staff at Miami University in Ohio
+FieldOfScience: Research Computing
+Organization: Miami University
+PIName: Jens Mueller
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/ND_Chen.yaml

@@ -0,0 +1,5 @@
+Department: College of Engineering
+Description: Training AI models on public medical image data
+FieldOfScience: Engineering
+Organization: University of Notre Dame
+PIName: Danny Chen

projects/ND_Lalor.yaml

@@ -0,0 +1,8 @@
+Department: Department of IT, Analytics, and Operations
+Description: >
+  Conduct research on efficient training for large language models and other analytics methods. 
+  My research uses GPU compute to evaluate the efficiency improvements of LLM training modifications 
+  to develop smaller, more efficient, and easier-to-train models that reduce the computational and cost burden.
+FieldOfScience: Computer and Information Sciences
+Organization: University of Notre Dame
+PIName: John Lalor

projects/NorthwesternMed_Yadav.yaml

@@ -0,0 +1,6 @@
+Department: Department of Radiation Oncology
+Description: 'Monte Carlo simulations of the Boltzmann radiation transport equation to investigate radiation absorbed dose delivered from megavoltage linear accelerators. '
+FieldOfScience: Physics
+Organization: Northwestern Medicine
+PIName: Poonam Yadav
+

projects/OSG_SoftwareInventory.yaml

@@ -1,5 +1,5 @@
 Department: Computing Sector (OSG Security Team)
-Description: OSG Security Team collaboration group currently working on building a worker node scanning tool. They are using OSG Connect for testing this tool. This group of researchers will likely evolve over time, as will their projects and collaborations. As of June 2022, Josh Drake and Brian Chase are points of contact.
+Description: OSG Security Team collaboration group currently working on building a worker node scanning tool. They are using OSG Connect for testing this tool. This group of researchers will likely evolve over time, as will their projects and collaborations. As of October 2023, Josh Drake is a point of contact.
 FieldOfScience: Computer and Information Science and Engineering
 Organization: OSG
 PIName: Josh Drake

projects/Rice_Mulligan.yaml

@@ -0,0 +1,11 @@
+Description: This project attempts to find novel geometric symmetries
+  in the folding of polygons. It has already produced several interesting
+  solutions, and I have now refactored it to be generalizable and
+  linearly scalable in an HTC workflow. A small version of it
+  serves as an example for HTC parallelization in our workshops.
+  https://github.com/JohnMulligan/parallel_folding_example/
+Department: Center for Research Computing
+FieldOfScience: Mathematics and Statistics
+Organization: Rice University
+PIName: John Connor Mulligan
+

projects/Seattle_Herman.yaml

@@ -0,0 +1,8 @@
+Description: >
+  Teaching a distributed systems course. Assignments will be at-scale applications 
+  including a parallel video rendering pipeline, a genome analysis application,
+  and a text analysis workflow.
+Department: Computer Science
+FieldOfScience: Computer and Information Sciences
+Organization: Seattle University
+PIName: Nate Kremer-Herman

projects/TG-CHE200122.yaml

@@ -29,19 +29,14 @@ ResourceAllocations:
   - Type: XRAC
     SubmitResources:
       - CHTC-XD-SUBMIT
+      - CHTC-ap40
     ExecuteResourceGroups:
       - GroupName: SDSC-Expanse
         LocalAllocationID: "cwr109"
-      # Bridges2
-      - GroupName: PSC-Bridges2
-        LocalAllocationID: "che200052p"
-      # Stampede2 (OSG allocation)
-      - GroupName: TACC-Stampede2
-        LocalAllocationID: "TG-DDM160003"
   - Type: Other
     SubmitResources:
       - CHTC-XD-SUBMIT
-      - UChicago_OSGConnect_login04
+      - CHTC-ap40
     ExecuteResourceGroups:
       - GroupName: TACC-Frontera
         LocalAllocationID: "CHE20009"

projects/UCF_Khan.yaml

@@ -0,0 +1,10 @@
+Description: >
+  Investigating the ability of neural networks to represent functions in the context of approximation theory.
+  We seek to uncover areas of scientific computing in which neural networks provide a 'better-than-nothing' 
+  approximation of a solution in high-dimensional problems wherein classical scientific computing methods fail. 
+  The primary area of investigation is the ability of a neural network to capture inherent low-dimensional 
+  structure present in high-dimensional functions.
+Department: Research Cyberinfrastructure
+FieldOfScience: Mathematics and Statistics
+Organization: University of Central Florida
+PIName: Fahad Khan

projects/UCLA_Huang.yaml

@@ -0,0 +1,11 @@
+Description: Studying $\Omega$-hadron correlation to search for signatures of baryon junction mechanisms at RHIC BES energies.
+Department: Physics and Astronomy
+FieldOfScience: Astronomy
+Organization: Arizona State University
+PIName: Huan Zhong Huang
+
+ID: '731'
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

projects/UCSD_George.yaml

@@ -0,0 +1,7 @@
+Description: >
+  We develop rodent models of addiction, test addiction-like behaviors, neuroadaptations, and novel treatment approaches
+  Applying machine learning and causal inference methods to the analysis of biomedical data.
+Department: Psychiatry
+FieldOfScience: Health Sciences
+Organization: University of California, San Diego
+PIName: Olivier George

projects/UOregon_Melgar.yaml

@@ -0,0 +1,8 @@
+Department: Cascadia Region Earthquake Science Center
+Description: >-
+    Conducting earthquake simulations as part of a larger collaboration
+    (https://github.com/Marcus-Adair/Accelerating-Data-Intensive-Seismic-Research-Through-Parallel-Workflow-Optimization-and-Federated-CI).
+    Planning to eventually run some ML for graph neural network GNSS denoising."
+FieldOfScience: Geological and Earth Sciences
+Organization: University of Oregon
+PIName: Diego Melgar

projects/UTA_Jones.yaml

@@ -0,0 +1,7 @@
+Description: >
+  works on the NEXT neutrinoless double beta decay experiment: https://next.ific.uv.es/next/ which is an international collaboration. 
+  The experiment is trying to determine if the neutrino is its own anti-particle.
+Department: Physics
+FieldOfScience: Physics
+Organization: University of Texas at Arlington
+PIName: Ben Jones

projects/UWMadison_DeWerd.yaml

@@ -0,0 +1,6 @@
+Department: Medical Physics
+Description: Simulations for radiation therapy applications
+FieldOfScience: Physics
+Organization: University of Wisconsin-Madison
+PIName: Larry DeWerd
+

projects/Washington_Savage.yaml

@@ -0,0 +1,9 @@
+Description: Quantum simulations of many-body systems for nuclear and high-energy physics (https://iqus.uw.edu).
+Department: IQuS, Department of Physics
+FieldOfScience: Physics
+Organization: University of Washington
+PIName: Martin J. Savage
+
+Sponsor:
+  CampusGrid:
+    Name: OSG Connect

src/README.md

@@ -442,7 +442,7 @@ For every cache resource, add a `u <DN HASH> <PATH1> rl <PATH2> rl ...` ACL for
 The Authfile for a public cache is served at `/cache/Authfile-public?fqdn=<CACHE FQDN>`.
 
 The public Authfile is basically a giant `u *` list:
-- Explicitly deny read access to `/user/ligo` (with `-rl` permissions)
+- Explicitly deny read access to `/user/ligo` (with `-rl` permissions); this is needed, because granting access to the OSG VO `/user` path would otherwise also grant access to `/user/ligo`
 - Allow read access to the path of each namespace supported by the cache (`rl` permissions) 
 
 ### Cache authenticated Authfile generation
@@ -452,9 +452,9 @@ The Authfile for an authenticated cache is served at `/cache/Authfile?fqdn=<CACH
 - Add a `u <DN HASH> <PATH1> rl <PATH2> rl ...` for every DN listed in the Authorizations list of every namespace supported by the cache.
 - Add a `g <FQAN> <PATH1> rl <PATH2> rl ...` for every FQAN listed in the Authorizations list of every namespace supported by the cache.
 
-In addition, if the cache supports the `/user/ligo` namespace and the webapp can access LIGO's LDAP server:
+In addition, if the cache supports the LIGO VO and the webapp can access LIGO's LDAP server:
 
-- Add a `u <DN HASH> /user/ligo rl` for every DN obtained from the LIGO's LDAP server.
+- Add a `u <DN HASH> <LIGO PATH1> rl <LIGO PATH2> rl ...` for every DN obtained from the LIGO's LDAP server.
 
 
 ### Origin xrootd-scitokens config generation
@@ -538,6 +538,10 @@ The JSON also contains an attribute `namespaces` that is a list of namespaces wi
     Note that scopes are usually relative to the namespace path.
   - `vault_server`: the Vault server for the `Vault` strategy or null
   - `vault_issuer`: the Vault issuer for the `Vault` strategy (or null).
+- `scitokens` is information about any `SciTokens` sections in the `Authorizations` list for that namespace (or the empty list if there are none). Each list item has:
+  - `issuer`: the value of the `Issuer` field in the scitokens block
+  - `base_path`: a list which is the value of the `BasePath` (or `Base Path`) field split on commas
+  - `restricted_path`: a list which is the value of the `RestrictedPath` (or `Restricted Path`) field split on commas, or the empty list if unspecified
 
 The final result looks like
 ```json
@@ -567,6 +571,7 @@ The final result looks like
       "dirlisthost": null,
       "path": "/xenon/PROTECTED",
       "readhttps": true,
+      "scitokens": [],
       "usetokenonread": false,
       "writebackhost": null
     },
@@ -582,6 +587,11 @@ The final result looks like
       "dirlisthost": "https://origin-auth2001.chtc.wisc.edu:1095",
       "path": "/ospool/PROTECTED",
       "readhttps": true,
+      "scitokens": {
+        "issuer": "https://osg-htc.org/ospool",
+        "base_path": ["/ospool/PROTECTED", "/s3.amazonaws.com/us-east-1", "/s3.amazonaws.com/us-west-1"],
+        "restricted_path": []
+      },
       "usetokenonread": true,
       "writebackhost": "https://origin-auth2001.chtc.wisc.edu:1095"
     }

src/rundev

@@ -12,9 +12,10 @@ ask_yn () {
 }
 
 export FLASK_ENV=development
+export FLASK_DEBUG=True
 cd "$(dirname "$0")"
 while true; do
-    python app.py; ret=$?
+    python3 app.py; ret=$?
     if [[ $ret -eq 0 ]]; then
         exit
     elif [[ $ret -eq 130 ]]; then  # control-C