From 687f04e14f5e1f4ab9fbf02a7a9ed4d95bed4e81 Mon Sep 17 00:00:00 2001 From: Michael Buehlmann Date: Mon, 12 Feb 2024 16:32:56 +0000 Subject: [PATCH] add polaris env; remove rebalance GIO option; update lock file --- env/bashrc.polaris | 6 + .../mergertrees/assemble/catalogs2trees.py | 11 - .../scripts/treenodes2forest.example.cfg | 4 - ...enodes2forest.galaxymergertree.example.cfg | 3 - haccytrees/scripts/treenodes2forest.py | 5 - poetry.lock | 1841 ++++++++--------- 6 files changed, 902 insertions(+), 968 deletions(-) create mode 100644 env/bashrc.polaris diff --git a/env/bashrc.polaris b/env/bashrc.polaris new file mode 100644 index 0000000..43ef630 --- /dev/null +++ b/env/bashrc.polaris @@ -0,0 +1,6 @@ +module load PrgEnv-gnu +module load gcc/10.3.0 +module load cudatoolkit-standalone +module load cray-python +export CC=cc +export CXX=CC \ No newline at end of file diff --git a/haccytrees/mergertrees/assemble/catalogs2trees.py b/haccytrees/mergertrees/assemble/catalogs2trees.py index da8e683..a9800fd 100644 --- a/haccytrees/mergertrees/assemble/catalogs2trees.py +++ b/haccytrees/mergertrees/assemble/catalogs2trees.py @@ -126,7 +126,6 @@ def _read_data( filename: str, logger: Callable, fields_config: FieldsConfig, - rebalance: bool, verbose: Union[bool, int], ): fields_xyz = [ @@ -140,7 +139,6 @@ def _read_data( filename, fields_config.read_fields, method=pygio.PyGenericIO.FileIO.FileIOMPI, - rebalance_sourceranks=rebalance, ) # mask invalid data @@ -201,7 +199,6 @@ def _catalog2tree_step( fields_config: FieldsConfig, do_all2all_exchange: bool, fail_on_desc_not_found: bool, - rebalance_gio_read: bool, verbose: Union[bool, int], logger: Callable[[str], None], ): @@ -219,7 +216,6 @@ def _catalog2tree_step( filename=treenode_filename, logger=logger, fields_config=fields_config, - rebalance=rebalance_gio_read, verbose=verbose, ) @@ -285,7 +281,6 @@ def catalog2tree( do_all2all_exchange: bool = False, split_output: bool = False, fail_on_desc_not_found: bool = True, - rebalance_gio_read: bool = False, mpi_waittime: float = 0, logger: Callable[[str], None] = None, verbose: Union[bool, int] = False, @@ -327,10 +322,6 @@ def catalog2tree( ranks. If ``False``, the orphaned halo will become the root of the subtree. - rebalance_gio_read - if ``True``, will reassign the reading ranks for the treenode files. Can - be slower or faster. - mpi_waittime time in seconds for which the code will wait for the MPI to be initialized. Can help with some MPI errors (on cooley) @@ -397,7 +388,6 @@ def logger(x, **kwargs): treenode_filename, logger, fields_config, - rebalance=rebalance_gio_read, verbose=verbose, ) @@ -436,7 +426,6 @@ def logger(x, **kwargs): fields_config, do_all2all_exchange, fail_on_desc_not_found, - rebalance_gio_read, verbose, logger, ) diff --git a/haccytrees/scripts/treenodes2forest.example.cfg b/haccytrees/scripts/treenodes2forest.example.cfg index 5e4bd43..788ab79 100644 --- a/haccytrees/scripts/treenodes2forest.example.cfg +++ b/haccytrees/scripts/treenodes2forest.example.cfg @@ -18,10 +18,6 @@ treenode_base = ./treenodes/m000p- # alternatively, you can specify it like this: (useful for galaxymergertrees!) # treenode_base = ./treenodes/m000p-#.treenodes -# this flag will try to rebalance the GenericIO reading of each rank. Can be -# faster or much slower – test! -rebalance_gio_read = no - [columns] # how the fields in the treenode catalogs are named – can change from simulation diff --git a/haccytrees/scripts/treenodes2forest.galaxymergertree.example.cfg b/haccytrees/scripts/treenodes2forest.galaxymergertree.example.cfg index 6df9abf..369d613 100644 --- a/haccytrees/scripts/treenodes2forest.galaxymergertree.example.cfg +++ b/haccytrees/scripts/treenodes2forest.galaxymergertree.example.cfg @@ -15,9 +15,6 @@ simulation = simulation_example.cfg # the base-path of the treenode catalogs. The files are assumed to be named e.g. # ./treenodes/m000p-499.treenodes treenode_base = ../trees/m000p-#.galaxytreenodes -# this flag will try to rebalance the GenericIO reading of each rank. Can be -# faster or much slower – test! -rebalance_gio_read = no [columns] diff --git a/haccytrees/scripts/treenodes2forest.py b/haccytrees/scripts/treenodes2forest.py index 9d294fc..e8c5ea6 100644 --- a/haccytrees/scripts/treenodes2forest.py +++ b/haccytrees/scripts/treenodes2forest.py @@ -47,9 +47,6 @@ def parse_config(config_path: Path) -> Dict[str, Any]: if not treenode_base.is_absolute(): treenode_base = base_path / treenode_base - rebalance_gio_read = config["simulation"].getboolean( - "rebalance_gio_read", fallback=False - ) # Output output_base = Path(config["output"]["output_base"]) @@ -103,7 +100,6 @@ def parse_config(config_path: Path) -> Dict[str, Any]: return { "simulation": simulation, "treenode_base": str(treenode_base), - "rebalance_gio_read": rebalance_gio_read, "output_base": output_base, "split_output": split_output, "temporary_path": temporary_path, @@ -139,7 +135,6 @@ def cli(config_path: Path): do_all2all_exchange=config["do_all2all_exchange"], split_output=config["split_output"], fail_on_desc_not_found=config["fail_on_desc_not_found"], - 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