[yt-users] Installing yt on Xsede Smic and Comet

[Nathan Goldbaum]

On Wed, Jun 15, 2016 at 1:42 PM, Yuan Li <yuan at astro.columbia.edu> wrote:

> Hi all,
>
> I am having trouble installing/running the latest yt on Xsede Smic and
> Comet clusters. I used to have yt3 on both machines and they were working
> fine. Recently, after failing to update yt, I decided to delete the old one
> and install the latest version. I am using the unmodified file from
> http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh
>
>
> Here are the problems I have:
> *On Smic*
> When I do "yt update" on the login node, or when I try to submit a yt job,
> I get this error message
> ...
> ValueError: numpy.dtype has the wrong size, try recompiling
>
> I have seen this error message before and fixed it somehow, but I do not
> remember how...
>

Navigate to the checkout of the yt mercurial repository and do:

$ ./clean.sh
$ python setup.py develop


>
>
> *On Comet*
> When I do "yt update", I get this error message:
> ...
> YT site-packages not in path, so you must
> update this installation manually by committing and
> merging your modifications to the code before
> updating to the newest changeset.
>
> I manually set YT_DEST in my bash_profile, but that does not seem to help.
> I can however submit a yt job and it will run fine, but not in parallel.
> Before I reinstalled yt, I was able to run yt3 in parallel on Comet after
> loading mpi4py.
>
> Also, when I do
> "source ~/source/yt-conda/bin/activate" I get this error message:
> Error: no environment provided.
> and it seems that I do not even need to activate yt anymore (is it because
> I have "export PATH=/home/yuanli/source/yt-conda/bin:$PATH" in my
> bash_profile?). Maybe I missed something in the doc. I am very confused.
>

It looks like you ran the install script with INST_YT_SOURCE=0 (the
default). Try again with INST_YT_SOURCE=1. You will also likely need to do
"pip install mpi4py" to get an mpi4py installation linked against comet's
MPI libraries.


>
> Thanks in advance!
> Yuan
>
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