I am trying to add a profile object to a Plot Collection (via
pc.add_profile_object(data,fields) ) while running in parallel on Kraken. I
get the following error: "TypeError: message: expecting a list or tuple"
which ultimately comes from mpi4py.MPI.Comm.Allreduce which is called by
ParallelAnalysisInterface._mpi_allsum(). In ._mpi_allsum() there is the
following comment: "# We use old-school pickling here on the assumption the
arrays are relatively small ( < 1e7 elements )". The dataset I am working
with is larger than 1e7 elements, so is _mpi_allsum not able to pass such a
large array to Comm.Allreduce?
Here is the traceback:
line 146, in add_fields
self._lazy_add_fields(fields, weight, accumulation)
line 94, in _lazy_add_fields
for gi,grid in enumerate(self._get_grids(fields)):
line 134, in __iter__
if not self.just_list: self.pobj._finalize_parallel()
line 122, in _finalize_parallel
self.__data[key] = self._mpi_allsum(self.__data[key])
line 185, in passage
return func(self, data)
line 1124, in _mpi_allsum
MPI.COMM_WORLD.Allreduce(data, tr, op=MPI.SUM)
File "Comm.pyx", line 530, in mpi4py.MPI.Comm.Allreduce
File "message.pxi", line 426, in mpi4py.MPI._p_msg_cco.for_allreduce
File "message.pxi", line 33, in mpi4py.MPI.message_simple
TypeError: message: expecting a list or tuple
In the development repository I have just swapped out the old-style
projections, which were based on geometric overlap at the *grid*
level, to a quadtree projection method that operates at the *cell*
level. This operation should scale better, should provide much faster
runtimes, and is able to operate inline with simulation codes (I have
All your projections should now be much, much faster -- on the yt-dev
list, speedups of 2-10x were reported before this change was made.
If you choose to upgrade and run into any issues, please let me know
or file a bug report. "yt bugreport" can help with this, or see
Adam Jundt at SDSC just let me know that there's now a yt module on
Trestles. If you're running there you should be able to load yt with
"module load yt".
We now have modules at Trestles, Nautilus, Kraken and I'm also told on
Odyssey and SciNet. Having modules created for community usage is a
strategy we're going to try to keep pursuing, so let me know if there
are modules elsewhere; this will soon be on a central wiki or document
of "maintained installations."
I've been trying to do a clump finding on some 2D data, however I'm having
difficulties visualizing it. I had sifted through the yt mailing list and
came across Dave Collin's clump_tools, but when I use it and attempt to
overlay the clump results on a slice of density, it seems as though they
don't want to overlap.
Here is the script, and the image is attached.
Does yt support FLASH data with 2D cylindrical coordinates?
If yes, how to enable it? If not, is it easy to implement it?
I couldn't find info about it in the website.
Thank you very much.