I am trying to run rockstar algorithm using yt astro analysis. What I have with
me is gadget 1 data which was converted from big file data format. I have
generated 32, 34, 39 chunks of the same data in gadget 1 format. Majority of
the time, I get the following error at the start itself. File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py",
line 346, in create
self._run(save_halos, save_output, njobs=njobs, dynamic=dynamic)
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 322, in barrierize
retval = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py",
line 239, in _run
self.finder_method(self)
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py",
line 36, in __call__
return self.function(hc, *self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py",
line 88, in _rockstar_method
rh = RockstarHaloFinder(ds, **finder_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py",
line 290, in __init__
p = self._setup_parameters(ts)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py",
line 299, in _setup_parameters
tds.index # noqa: B018
^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/data_objects/static_output.py",
line 605, in index
self._instantiated_index = self._index_class(
^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/gadget/data_structures.py",
line 195, in __init__
super().__init__(ds, dataset_type)
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 73, in __init__
self._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/gadget/data_structures.py",
line 204, in _initialize_index
super()._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/sph/data_structures.py",
line 89, in _initialize_index
super()._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 237, in _initialize_index
max_hsml = self._initialize_coarse_index()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 280, in _initialize_coarse_index
self.regions.masks = self.comm.mpi_allreduce(self.regions.masks, op="sum")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 297, in passage
return func(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 913, in mpi_allreduce
self.comm.Allreduce(
File "src/mpi4py/MPI.src/Comm.pyx", line 1115, in mpi4py.MPI.Comm.Allreduce
P004 yt : [ERROR ] 2025-12-19 23:49:08,036 Exception: MPI_ERR_ARG: invalid
argument of some other kind
P004 yt : [ERROR ] 2025-12-19 23:49:08,036 Error occurred on rank 3.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 4 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
File "/home/user/p1cj_phy/fastpm/my.example/rockstar.py", line 14, in <module>
hc.create()
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py",
line 346, in create
self._run(save_halos, save_output, njobs=njobs, dynamic=dynamic)
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 322, in barrierize
retval = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py",
line 239, in _run
self.finder_method(self)
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py",
line 36, in __call__
return self.function(hc, *self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py",
line 88, in _rockstar_method
rh = RockstarHaloFinder(ds, **finder_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py",
line 290, in __init__
p = self._setup_parameters(ts)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py",
line 299, in _setup_parameters
tds.index # noqa: B018
^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/data_objects/static_output.py",
line 605, in index
self._instantiated_index = self._index_class(
^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/gadget/data_structures.py",
line 195, in __init__
super().__init__(ds, dataset_type)
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 73, in __init__
self._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/gadget/data_structures.py",
line 204, in _initialize_index
super()._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/sph/data_structures.py",
line 89, in _initialize_index
super()._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 237, in _initialize_index
max_hsml = self._initialize_coarse_index()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 280, in _initialize_coarse_index
self.regions.masks = self.comm.mpi_allreduce(self.regions.masks, op="sum")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 297, in passage
return func(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 913, in mpi_allreduce
self.comm.Allreduce(
File "src/mpi4py/MPI.src/Comm.pyx", line 1115, in mpi4py.MPI.Comm.Allreduce
P001 yt : [ERROR ] 2025-12-19 23:49:08,554 Exception: MPI_ERR_ARG: invalid
argument of some other kind
P001 yt : [ERROR ] 2025-12-19 23:49:08,554 Error occurred on rank 0.
File "/home/user/p1cj_phy/fastpm/my.example/rockstar.py", line 14, in <module>
hc.create()
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py",
line 346, in create
self._run(save_halos, save_output, njobs=njobs, dynamic=dynamic)
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 322, in barrierize
retval = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py",
line 239, in _run
self.finder_method(self)
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py",
line 36, in __call__
return self.function(hc, *self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py",
line 88, in _rockstar_method
rh = RockstarHaloFinder(ds, **finder_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py",
line 290, in __init__
p = self._setup_parameters(ts)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py",
line 299, in _setup_parameters
tds.index # noqa: B018
^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/data_objects/static_output.py",
line 605, in index
self._instantiated_index = self._index_class(
^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/gadget/data_structures.py",
line 195, in __init__
super().__init__(ds, dataset_type)
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 73, in __init__
self._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/gadget/data_structures.py",
line 204, in _initialize_index
super()._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/sph/data_structures.py",
line 89, in _initialize_index
super()._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 237, in _initialize_index
max_hsml = self._initialize_coarse_index()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 280, in _initialize_coarse_index
self.regions.masks = self.comm.mpi_allreduce(self.regions.masks, op="sum")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 297, in passage
return func(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 913, in mpi_allreduce
self.comm.Allreduce(
File "src/mpi4py/MPI.src/Comm.pyx", line 1115, in mpi4py.MPI.Comm.Allreduce
P002 yt : [ERROR ] 2025-12-19 23:49:08,936 Exception: MPI_ERR_ARG: invalid
argument of some other kind
P002 yt : [ERROR ] 2025-12-19 23:49:08,936 Error occurred on rank 1.
File "/home/user/p1cj_phy/fastpm/my.example/rockstar.py", line 14, in <module>
hc.create()
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py",
line 346, in create
self._run(save_halos, save_output, njobs=njobs, dynamic=dynamic)
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 322, in barrierize
retval = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_catalog.py",
line 239, in _run
self.finder_method(self)
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py",
line 36, in __call__
return self.function(hc, *self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_catalog/halo_finding_methods.py",
line 88, in _rockstar_method
rh = RockstarHaloFinder(ds, **finder_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py",
line 290, in __init__
p = self._setup_parameters(ts)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_analysis/yt_astro_analysis/halo_analysis/halo_finding/rockstar/rockstar.py",
line 299, in _setup_parameters
tds.index # noqa: B018
^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/data_objects/static_output.py",
line 605, in index
self._instantiated_index = self._index_class(
^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/gadget/data_structures.py",
line 195, in __init__
super().__init__(ds, dataset_type)
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 73, in __init__
self._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/gadget/data_structures.py",
line 204, in _initialize_index
super()._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/frontends/sph/data_structures.py",
line 89, in _initialize_index
super()._initialize_index()
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 237, in _initialize_index
max_hsml = self._initialize_coarse_index()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/geometry/particle_geometry_handler.py",
line 280, in _initialize_coarse_index
self.regions.masks = self.comm.mpi_allreduce(self.regions.masks, op="sum")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 297, in passage
return func(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/home/user/p1cj_phy/fastpm/yt_astro_v/lib/python3.12/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 913, in mpi_allreduce
self.comm.Allreduce(
File "src/mpi4py/MPI.src/Comm.pyx", line 1115, in mpi4py.MPI.Comm.Allreduce
P003 yt : [ERROR ] 2025-12-19 23:49:08,961 Exception: MPI_ERR_ARG: invalid
argument of some other kind
P003 yt : [ERROR ] 2025-12-19 23:49:08,961 Error occurred on rank 2.
[Node001:85381] 3 more processes have sent help message help-mpi-api.txt /
mpi-abort
[Node001:85381] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages
-- I have tried different reader and writer combinations (4&9, 4&11, 4&13, 8&11
etc.). I am not able to understand this error and solve it. Also I didn't
succeed in creating a code that converts data from big file to gadget 2 data
format. Plese help.
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