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H5Tset_size(): size must be positive #1021
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Update on trying to use an environment: didn't go very well - in spack/spack#24520 |
Hi Diana, I tested your example and that looks good to me. I think that's a system issue mismatching compiler and package for your Ubuntu/WSL setup. I commented a spack suggestion now in the linked spack issue. Alternatively, you should be able to spin up a full development env from the Ubuntu/WSL packages alone: sudo apt update
sudo apt install build-essential ca-certificates cmake curl g++ gnupg libopenmpi-dev libhdf5-openmpi-dev libadios-dev python3 python3-numpy python3-mpi4py python3-pandas pkg-config wget |
Thanks @ax3l ! I just saw your reply. I'm testing it now. |
Hi @ax3l , Your suggestion seems to work. $ spack find -c
==> In environment jn
==> Root specs
git graphviz mercurial openpmd-api +python py-matplotlib py-notebook py-numpy py-scipy py-sphinx py-sphinx-rtd-theme py-sphinxcontrib-programoutput py-sympy python
==> Concretized roots
-- linux-ubuntu20.04-skylake / gcc@9.3.0 ------------------------
git@2.31.1 mercurial@5.8 py-matplotlib@3.4.2 py-numpy@1.20.3 py-sphinx@3.2.0 py-sphinxcontrib-programoutput@0.15 python@3.8.10
graphviz@2.47.2 openpmd-api@0.13.4 py-notebook@6.1.4 py-scipy@1.6.3 py-sphinx-rtd-theme@0.5.2 py-sympy@1.4 And it did had some conflict notice when updating the The other issue was with loading data - I was getting everything = 0 - but I think this is a problem on my side that I think I know how to fix. So you may close this issue if you want! |
Hi @LDAmorim, thanks for the update! Glad to hear you made good progress! 🎉
If you install everything in one go, do you still get conflicts? sudo apt update
sudo apt install build-essential curl gcc git g++ make cmake Then this: spack env create openpmd-dev
spack env activate openpmd-dev
spack add cmake
spack add mpich
spack add openpmd-api
spack add python
spack add py-pip
spack install Then optionally: python -m pip install matplotlib yt openpmd-viewer # etc etc ... Adding more software after a first
Curious, feel free to share more if need be. Glad to see you got further! |
Hi @ax3l , So I think I did the "one go" option, but I might have been confusing on my previous post, sorry for that. I did the update of the ubunto gcc as you had mentioned before.
Only the python one gave a conflict and it still worked, it just didn't update the final This is what I get from ==> Concretized roots
-- linux-ubuntu20.04-skylake / gcc@9.3.0 ------------------------
openpmd-api@0.13.4 py-notebook@6.1.4 py-scipy@1.6.3 python@3.8.10
py-matplotlib@3.4.2 py-numpy@1.20.3 py-sympy@1.4 Regarding the curious incident, I think I might have discussed this before with you (sorry!), when writing Instead I just need to merge the information of the variable (say mass) from the ranks with particles to all of the ranks, to use Thank you for all your help @ax3l ! |
Good one - you could post the exact packages that you created for this environment as a Spack issue, that's probably an upstream issue that can be figured out. In the meantime, you could build a simple environment like this for 2.) that gets most things from pypi:
That will still install in the spack environment and you re-activate with
That's interesting and could be similar to #961 . |
I just tried the latter and there is more to it. So even if you write zero particles from some MPI-ranks, make sure that all of them go through the code path that calls
Yes, exactly. Given that limitation for HDF5 attributes (which we use for constants as well), this means you need to |
Hi, Yes, that's a great idea to use Regarding the write issue, it is just as you put it in your last message. Also, I didn't use |
Glad this helped you.
That's right, broadcast only makes sense if you know for sure which rank has at least one particle (and thus knows the mass) upfront. |
Hi,
I have been using
openpmd-api
(much appreciated tool!), but, in a recent installation, my code got an error message connected to it (wellHDF5
) and I tested using your example file and found that same error.Since I am not able to understand how to solve it and I haven't found similar topics in other issues/PRs (here, or in
spack
or inHDF5
's repos), I decided to open this issue.Performed steps
Installed
spack
with the commands below (directly copied fromhistory
command with added comments):Then I used the following files (the
.cc
one I copied from https://openpmd-api.readthedocs.io/en/latest/usage/parallel.html#writing) - except with correct extensions (instead of.txt
):opmd_build.sh.txt
opmd_run.sh.txt
test_opmd.cc.txt
CMakeLists.txt
This led to the output file and errors below:
output.txt
These errors didn't occur if I commented out everything in
test_opmd.cc
between the "Ctreated an empty series ..."cout
andseries.flush
(i.e. lines 45 to 72).And occurred when I kept the
iterations
mesh construction (i.e. un-commenting lines 45 to 50).These errors also don't seem to appear with the serial example.
System environment
gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
)spack debug report
:Additional context
I will try to follow @ax3l 's suggestion of using environments with
spack
and will report back on it asap.The text was updated successfully, but these errors were encountered: