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NCATSTranslator / Babel Public

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Getting Babel to work on Hatteras#594

Open

hyi wants to merge 141 commits intobabel-1.15NCATSTranslator/Babel:babel-1.15from

35-run-distribute-hatterasNCATSTranslator/Babel:35-run-distribute-hatterasCopy head branch name to clipboard

Conversation Commits141 (141)Checks Files changed

Open

Getting Babel to work on Hatteras#594
hyi wants to merge 141 commits intobabel-1.15from
35-run-distribute-hatteras

Commits

Commits on Dec 14, 2025

added slurm folder to support running babel in a distributed fashion on hatteras

hyi
authored and
gaurav
committed
Attempt to make a script to run Babel on Slurm.
gaurav
committed
Added hashbang to sbatch script.
gaurav
committed
Increased memory on the leader node.
gaurav
committed
Tweaked some settings.
gaurav
committed
Tweaked some commands.
gaurav
committed
Added snakemake-executor-plugin-slurm.
gaurav
committed
Cleaned up Slurm Snakemake profile.
gaurav
committed
Cleaned up and documented the Slurm profile.
gaurav
committed
Added retries to OBO downloads.
gaurav
committed
Added additional run-specific config file, which is initially empty.
gaurav
committed
That didn't work.
gaurav
committed
Made configfile a list.
gaurav
committed
Added more Slurm configuration options.
gaurav
committed
Added sleep between Ubergraph queries.
gaurav
committed
Removed old cluster config file that's no longer used.
gaurav
committed
Increased time for the Snakemake runner.
gaurav
committed
Upgraded packages.
gaurav
committed
Don't build anatomy, build whatever is on the command line.
gaurav
committed
Removed anatomy, now build everything.
gaurav
committed
Removed unnecessary import.
gaurav
committed
Reduced requirements for each node.
gaurav
committed
Added Hatteras partition information.
gaurav
committed
Added a runtime of 4h for get_ensembl.
gaurav
committed
Modified EFO to explicate OWL file dependency.
gaurav
committed
Added retries to get_protein_uniprotkb_ensembl_relationships.
gaurav
committed
Added memory in GB to give a sense of what's available.
gaurav
committed
Don't delete log files.
gaurav
committed
Reduced BIOMART_MAX_ATTRIBUTE_COUNT to 7.
gaurav
committed
Increased runtime for generate_pubmed_concords.
gaurav
committed
Increased memory required by chembl_labels_and_smiles.
gaurav
committed
Reduced BIOMART_MAX_ATTRIBUTE_COUNT to 6.
gaurav
committed
Fixed bug in EFO OWL file reading.
gaurav
committed
Note sure why we're opening this file in binary mode.
gaurav
committed
Increased runtime for generate_pubmed_concords.
gaurav
committed
Increased timeout for generate_pubmed_concords to 12h.
gaurav
committed
Increased memory for chemical_unichem_concordia.
gaurav
committed
Added /usr/bin/time to Python code to monitor memory usage.
gaurav
committed
Increased memory for untyped_chemical_compendia.
gaurav
committed
Increased get_ensembl runtime to 6h.
gaurav
committed
Increased untyped_chemical_compendia to 256G.
gaurav
committed
Increased timeout on the initial node to 24h.
gaurav
committed
Increased memory for some chemical and protein tasks.
gaurav
committed
Increased timeout for generate_pubmed_concords to 24h.
gaurav
committed
Increased memory for generate_pubmed_concords.
gaurav
committed
Added runtime and mem to gene_compendia and protein_compendia.
gaurav
committed
Increased gene_compendia memory and protein_compendia timeout.
gaurav
committed
Turn on --keep-going when building on Slurm.
gaurav
committed
Increased memory for generate_pubmed_compendia (128G).
gaurav
committed
Added runtime=6h to chemical_compendia.
gaurav
committed
Increased memory and runtime for export_compendia_to_duckdb.
gaurav
committed
Increased CPUs per task and timeout for rule protein.
gaurav
committed
Increased runtime for drugchemical_conflated_synonyms.
gaurav
committed
It's "runtime", not "timeout".
gaurav
committed
Increased memory for export_compendia_to_duckdb.
gaurav
committed
Increased memory and runtime for geneprotein_conflated_synonyms.
gaurav
committed
Increased memory for export_compendia_to_duckdb to 750G.
gaurav
committed
Increased runtime for generate_sapbert_training_data.
gaurav
committed
Added some settings to DuckDB initialization.
gaurav
committed
Attempt to improve compendium load in DuckDB.
gaurav
committed
Tried to reduce requirements.
gaurav
committed
Fixed cpus_per_task.
gaurav
committed
Tried to reduce the memory limit.
gaurav
committed
Let's try increasing the memory limit again.
gaurav
committed
Reduce cpus_per_task.
gaurav
committed
Increased memory further.
gaurav
committed
What if we reduce the memory limit?
gaurav
committed
Tried some new things, laid out a possible solution.
gaurav
committed
Removed duckdb_config, fixed (?) Node generation.
gaurav
committed
Fully removed duckdb_config.
gaurav
committed
Attempt to fix Node.parquet generation.
gaurav
committed
Added an extraneous print to hopefully trigger a rebuild.
gaurav
committed
Attempted new syntax for Node generation.
gaurav
committed
Next attempt at fixing nodes.
gaurav
committed
Next attempt at getting the JSON export working correctly.
gaurav
committed
Next attempt.
gaurav
committed
Moved Node generation to the top so it will fail first.
gaurav
committed
Added Node.parquet as an explicit output.
gaurav
committed
Tweaked rule to force a rebuild.
gaurav
committed
Okay, maybe this will work.
gaurav
committed
Maybe this work.
gaurav
committed
First stab at a compendium splitter.
gaurav
committed
Small improvements.
gaurav
committed
Fail if the row counts don't match.
gaurav
committed
Improved outputs.
gaurav
committed
Wait, we actually wouldn't expect these to line up.
gaurav
committed
Reorganized/cleaned up code a bit.
gaurav
committed
Add a TODO that will come in handy later.
gaurav
committed
Increased resources for DuckDB reports.
gaurav
committed
Oops, missed one.
gaurav
committed
Further increased memory to generate_prefix_report.
gaurav
committed
Increased memory for a bunch of DuckDB reports.
gaurav
committed
Maybe we're going to 1024G everywhere.
gaurav
committed
Increased memory even further.
gaurav
committed
Cleaned up code for CURIE prefix summary.
gaurav
committed
Improved check_for_identically_labeled_cliques and reduced memory.
gaurav
committed
Tried to improve check_for_duplicate_curies.
gaurav
committed
Tried to improve check_for_duplicate_clique_leaders.
gaurav
committed
Gave generate_prefix_report 512G of memory.
gaurav
committed
Fixed SQL error.
gaurav
committed
Simplified check_for_duplicate_clique_leaders.
gaurav
committed
Increased all memory to its max.
gaurav
committed
Turn off preserve_insertion_order=false for all reports.
gaurav
committed
Separated db.sql() from writing out the result.
gaurav
committed
Added some memory tracking.
gaurav
committed
Tried to improve logging.
gaurav
committed
More debugging.
gaurav
committed
Incorporated additional settings.
gaurav
committed
Moved progress bar to overall DuckDB settings.
gaurav
committed
Improved DuckDB configuration documentation.
gaurav
committed
Improved DuckDB settings output.
gaurav
committed
Moved progress bar as a local setting.
gaurav
committed
Gah.
gaurav
committed
Increased memory for check_for_duplicate_curies.
gaurav
committed
Partially improved generate_prefix_report.
gaurav
committed
Removed orders from generate_prefix_report.
gaurav
committed
Increased memory availability.
gaurav
committed
Split prefix report into by-clique and by-prefix reports.
gaurav
committed
Fixed Snakemake rules.
gaurav
committed
Cleaned up some `all` rules.
gaurav
committed
We don't want a list of all cliques labeled ''.
gaurav
committed
Look out for double-quotes too.
gaurav
committed
Let's compress identically_labeled_cliques.tsv.
gaurav
committed
Fixed filename in dependencies.
gaurav
committed
Improved script.
gaurav
committed
Simplified by-clique report.
gaurav
committed
Added retries to some Ubergraph queries.
gaurav
committed
Improved by-clique report.
gaurav
committed
Fixed script.
gaurav
committed
More fixes maybe.
gaurav
committed
Fixed SQL error.
gaurav
committed
For by_clique report, only look at non-conflated edges.
gaurav
committed
For CURIE report, use only non-conflated edges.
gaurav
committed
Improved command line.
gaurav
committed
Updated pull_via_urllib() to be able to verify a gzipped file.
gaurav
committed
Add verify_gzip to UniChem downloads because they are being wobbly.
gaurav
committed
Wow.
gaurav
committed
Fail verification if the downloaded file is too small.
gaurav
committed
Replaced UniChem download with wget download.
gaurav
committed
Reverted to urllib, added retries.
gaurav
committed
Fixed references to datetime.
gaurav
committed

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