No log messages when running Batch simulations on Windows 10

[Sumayya K.]

Hello,

I've recently started working on Batch simulations on Windows using Anaconda, simulations are smoothly run but I need some log messages as an output. Commands I use are:

(mpiexec -n 8 nrniv -python -mpi batch.py) - using this command, messages such as (Finished Submitting jobs... or messages of a syntax error in batch.py) aren't shown, instead there are only arrows at the start of the line. With (n=1 & n=2) 1 simulation is outputted, (n=3) 2 simulations outputted, (n=8) 7 simulations. In case of 10 batch combinations, I have to run it with n=8 (will get 7 sims), close the terminal and run it again to get the 3 last simulations.

(mpiexec -n 8 python -m mpi4py batch.py OR mpiexec -n 8 python batch.py) - messages like above are shown. However, whatever n value is, there's only 1 simulation
as the output and 8 copies of that same sim, so I always have to close the terminal and run it again to get the second simulation and so on.

You see, 1st doesn't show me log messages, and with the 2nd only 1 simulation is outputted at a time.

*Utilizing 8 cores.

thanks.

[Salvador Dura]

Hi Sumayya, sorry that you are having problems with the batch. Are you running the tutorial 8 example or some custom code?

We haven't really tested the batch simulations on Windows machines, so this sounds like might be a specific Windows issue. We will try to test this soon. 

In the meantime, any chance you have access to a Linux or Mac computer to check if you get the same issues? Otherwise, perhaps you can try a virtual machine? 

thanks

Salva

[Sumayya K.]

Hi Salvador - thank you for your time. Let's stick to tut8_batch.py from the tutorial because I sometimes get different results running my own batch files. I tested it on both Windows and Linux using the same command with n=4 (9 simulations were expected):

- On Linux, there were all the messages showing and all the 9 simulations were run at once.

- On Windows, since it was n=4, only 3 simulations were executed. To get outputs of the remaining simulations, I had to restart the terminal and run the command again.

Also, there were no log messages; I tried to insert a syntax error on purpose, but it showed me that through arrows not any messages as obvious in the attached screen shot.

I think these 2 problems originate from the same issue.

--Sumayya

[Joe Graham]

Hi Sumayya,

Sorry for the delay in responding to your issue!  Are you still having the same problem?  Have you tried updating to the latest versions of NEURON and NetPyNE?  If you're still having the same problem with the latest versions, I'll make looking into this a high priority.

Best wishes,

Joe

[Sumayya K.]

Hi Joe,

Sorry for the late response! I updated NEURON from v=7.7.2 to v=7.8.1 and Netpyne to v=0.9.7 - surprisingly, this version of Netpyne didn't work for some reason, so I had to downgrade it back to v=0.9.6 to properly run the simulations.

I retested with (mpiexec -n 8 nrniv -python -mpi batch.py), simulations were running fine but again there was no messages showing as before. 

--Sumayya

[Joe Graham]

Hi Sumayya,

Sorry for the problems, I will start looking into the issue.  

What was the error with v=0.9.7?  We could push a patch for the problem.

In the meantime, if you could try running batch sims in a virtual environment and letting us know the outcome, that would be very helpful.  Here's more information about virtual environments: https://groups.google.com/g/netpyne-forum/c/S3Agb93hws4/m/5NO9cEknBgAJ

They're not too complicated, but feel free to ask questions if you have any problems.

Cheers,
Joe

[Sumayya K.]

Hi Joe,

Sorry for the delay. Creating a virtualenv didn't help me back then. However, I'm currently working under Netpyne (development branch) which has my "no log messages" issue resolved.

thanks for your time.

Sumayya

[Joe Graham]

Thank you for letting us know, Sumayya!

I actually installed Windows on my Mac this morning to start really digging into this problem, but I'm glad it's resolved.  If you have future problems, I should be able to replicate them now.

Cheers,

Joe

[Sumayya K.]

Awesome - sure thing!

Best,

[Ruben Schoeters]

Dear all

I am working on windows and  am experiencing exactly the same issue as Sumayya K. stated above in the second post (29 jun. 2020).  After installing the development branch, I am still not getting any log messages. I also get only three results (n=4).  When executing tutorial 1 with 'mpiexec -n 4 nrniv -python -mpi tut1.py' the log messages appear after the simulation is finished and enter is pressed.  

Is there already a solution to this problem?

Thanks in advance

All the best

Ruben

Op vrijdag 2 oktober 2020 om 23:31:10 UTC+2 schreef Sumayya K.:

[Joe Graham]

Hi Ruben,

Thank you for posting your problem and sorry for the delayed response.  I hope to find time to explore this issue on Windows sometime this week and I will let you know what I figure out.  

Cheers,

Joe