Comments (7)
bloyl
commented on May 23, 2024
Interestingly I just spent today doing exactly that.
Attached is the install script i ended up using. There are a few stray
/usr/local s in the hnn src i can put up a PR tomorrow if its desired.
…-Luke
On Wed, Dec 19, 2018, 4:37 PM Mainak Jas ***@***.*** wrote:
@samnemo <https://github.com/samnemo> I started trying to play around
with hnn but I hit a roadblock.
It seems that the installation process
<https://github.com/jonescompneurolab/hnn/blob/master/installer/ubuntu/installer.sh>
requires one to have sudo rights. This is a no go for many people working
in labs since they do not necessarily have sudo rights. Typically, in the
python world, we use the anaconda package which is added to the path. Then
everything else can be done without sudo.
Are there any libraries that *really* need sudo? Otherwise, I would
recommend, replacing this with non-sudo options. I'm going to attempt an
install without sudo, so I can make a pull request for this if you agree.
Also, it would be good to have some developer documentation -- such as a
CONTRIBUTING.md (that github recommends) so those wanting to edit the
code can understand how to get into it! Happy to help with it
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jasmainak
commented on May 23, 2024
Wow, that would be great! I don't see the attached script. Could you share it via a gist or something? Thanks!
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samnemo
commented on May 23, 2024
Hi Mainak & Luke, Thanks for your suggestions! Sounds good to go ahead with the adjustments as PRs or changes to a development branch. Sam
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bloyl
commented on May 23, 2024
Mainak,
I'm on my phone so hopefully this link will do for now.
Note this doesn't deal with the system dependencies. Only the Python and things that need building.
https://drive.google.com/file/d/0B4FnwYbkdwdlWnk2MVNoT0lzeWNGNWNSREhVMGFiOW5JNmtv/view?usp=drivesdk
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jasmainak
commented on May 23, 2024
Power of open science :) Thanks Luke! So far I am making good progress, and I managed to install nrn and iv but I had to make two modifications but I had to make the following modifications:
- Add
$ export PATH="$PATH:/usr/lib64/mpich/bin/"for installing mpi4py using pip $ conda install libtool=2.4.2for installing iv. I had 2.4.6 and it didn't like it
And then I stopped before $ rm -rf ${install_prefix}/hnn + edited the file hnn/hnn to have:
$ python3 ./hnn.py ./hnn.cfgJust writing it all down while it's still in my head.
@bloyl are you going to make the PR or should I make it? Either way, one of us can test it while the other makes the PR.
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samnemo
commented on May 23, 2024
@ramcdougal - may want to take note of what Mainak & Luke are working on
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blakecaldwell
commented on May 23, 2024
Closing this with our completion of new Docker-based installation instructions on the HNN website:
https://hnn.brown.edu/index.php/installation-instructions/
The original points raised about sudo rights during installation is addressed in two ways:
- If Docker is installed and usable by non-root users, any user can instantiate the HNN container without sudo.
- In the Dockerfile the installation is done as "hnn_user". If someone wishes to reproduce this on an Ubuntu system without Docker, the Docker file will be prescriptive.
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