Comments (8)
from hnn.
Do you have MPI installed ? What do you get if you do:
$ which mpiexec
?
from hnn.
Yes it's installed, I get:
/usr/bin/mpiexec
And when I check the version I get:
mpiexec (OpenRTE) 4.0.3
from hnn.
I see that you also installed hnn-core
. Maybe try running this example first:
to see if that works or if you see the same error there?
from hnn.
I suspect this might be an mpi4py
or python environment issue.
- Is it possible that you have two versions of OpenMPI installed, one at /usr/bin and another within your Anaconda environment (assuming you're using Anaconda)?
- Do you have mpi4py installed in your Anaconda environment? If not, try
$ conda install mpi4py
from hnn.
I did a full wipe of the computer and reinstalled the hnn GUI, so the only thing installed in the computer at the moment is HNN (anaconda is not installed).
I also made sure that mpi4py is installed.
But I'm getting the same error:
Warning: could not read file: /home/joshuabruce/hnn_out/data/default/dpl.txt
Warning: could not read file: /home/joshuabruce/hnn_out/data/default/spk.txt
Warning: could not read file: /home/joshuabruce/hnn_out/data/default/dpl.txt
Warning: could not read file: /home/joshuabruce/hnn_out/data/default/spk.txt
Starting simulation (8 cores). . .
INFO: Failed starting mpiexec, retrying with 4 cores
Simulation exited with return code 134. Stderr from console:
Invalid MIT-MAGIC-COOKIE-1 key--------------------------------------------------------------------------
mpiexec was unable to find the specified executable file, and therefore
did not launch the job. This error was first reported for process
rank 0; it may have occurred for other processes as well.
NOTE: A common cause for this error is misspelling a mpiexec command
line parameter option (remember that mpiexec interprets the first
unrecognized command line token as the executable).
Node: pop-os
Executable: nrniv
Warning: could not read file: /home/joshuabruce/hnn_out/data/default/dpl.txt
Warning: could not read file: /home/joshuabruce/hnn_out/data/default/spk.txt
Warning: could not read file: /home/joshuabruce/hnn_out/data/default/dpl.txt
Warning: could not read file: /home/joshuabruce/hnn_out/data/default/spk.txt
Any ideas on what could be going on?
from hnn.
I would really suggest trying to run the hnn-core
example that uses MPI first. That way you can rule out problems due to something specific in the GUI code. I don't know if anyone is actively maintaining the GUI code, so it's easier for us to start with HNN-core to troubleshoot the problem.
See:
https://jonescompneurolab.github.io/hnn-core/stable/parallel.html
What OS are you using?
from hnn.
Hi @jasmainak and @rythorpe, I wanted to follow up on an error I just encountered and found a workaround for which generated nearly identical error messages to the one described here.
I've noticed that HNN displays buggy behavior when trying to load a simulation that has previously been canceled manually or by killing the terminal running HNN GUI during the run, which I always assumed is due to corruption of the associated simulation output files in the hnn_out/data folder, which it still tries to load the next time the associated parameter file is loaded. We solved this by renaming the associated folder in hnn_out/data, so it didn't attempt to load the output files anymore and were able to get it to load in the parameter file again (albeit with no ouput yet until the sim is run). I don't know if you think this constitutes an issue with the manual shutdown option of an ongoing simulation that you would like me to open an issue for or not (if it doesn't exist already).
from hnn.
Related Issues (20)
- can't update cell properties
- Issue running HNN-Netpyne (hnn2) examples HOT 3
- ODict instead of OrderedDict HOT 4
- Tonic input throws error HOT 3
- Problem downloading and running a script that will install HNN HOT 12
- Issue installing HNN HOT 8
- Problems downloading HNN HOT 2
- Version issue with windows native install powershell script HOT 4
- Failed running sim using default.param (Mac) HOT 2
- can't compile HNN source code HOT 5
- can't do bash hnn-ubuntu.sh - permissions error HOT 1
- CentOS installation script not found HOT 1
- errors with HNN GUI installation HOT 2
- Setting LD_LIBRARY_PATH for mac installation HOT 2
- Instructions for Displaying GUI on VNC Client HOT 3
- Installing HNN on Windows HOT 3
- "Failed Running Sim" HOT 4
- Can't update Synaptic gain HOT 1
- Error executing Set Parameters from File HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
π Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. πππ
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google β€οΈ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hnn.