centos 7 installation issues

[Luke Bloy]

Hi.

I just used the centos7-installer from github and have run into some problems...

1) post install running hnn -> gave me a python import error. ImportError: No module named 'PyQt5.QtWidgets'

      the issue strangely was that the directories in /usr/lib64/python3.4/site-package and /usr/lib/python3.4/site-package were only readable by root. I'm not sure if that is due to the installation script or something else. Once I changed the permissions I was able to run the software.

2) Working through the erp tutorial. hnn crashed when i clicked on 'Run Simulation' with 'FileNotFoundError: [Errno 2] No such file or directory: 'mpiexec''

     so I installed openmpi and got the same error. Seems the openmpi rpm doens't set the path so. after an 'export PATH=$PATH:/usr/lib64/openmpi/bin/' I can click on the 'Run Stimulation' button

3) When I click on the 'Run Stimulation' button I get a simulation log window... which says somethings but disapears very quickly. Nothing shows on the screen and in the terminal I get the following

WARN: could not read simulation outputs: dict_values(['/home/bloyl/hnn/data/ERPYes100Trials/spk.txt', '/home/bloyl/hnn/data/ERPYes100Trials/dpl.txt', '/home/bloyl/hnn/data/ERPYes100Trials/rawspec.npz', '/home/bloyl/hnn/data/ERPYes100Trials/param.txt'])

So I don't think it worked. But the simulation log window closes too fast for me to see so I'm not sure how to debug. Is there a system log somewhere?

Sorry for the long email and thanks for any help/suggestions.

-Luke

    

[McDougal, Robert]

My guess is that it can’t find NEURON, which does the calculation for HNN behind-the-scenes.

 

You can verify this by typing “nrniv” at the command line… if it gives an error, that’s confirmation.

 

If so, you can fix this by adding /usr/local/nrn/$CPU/bin to your $PATH like you did for openmpi.

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[Luke Bloy]

Thanks.

I got a little bit farther this time. I erased everything and re ran the install script step by step. and changing the permissions( sudo chmod -R 755 /usr/local/iv) after each install step.

doing that at least let me run "nrniv" which seemed to start ok.

[bloyl@reslnmeglabws03 tmp_hnn_install]$ nrniv
NEURON -- VERSION 7.6.3-12-g50728e6 master (50728e6) 2018-12-14
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2018
See http://neuron.yale.edu/neuron/credits
oc>

Unfortunately, there is still something wrong with my neuron install, as i now get this error when i run stims.

>>> >>> Traceback (most recent call last):
  File "run.py", line 31, in <module>
    from morphology import shapeplot, getshapecoords
  File "/usr/local/hnn/morphology.py", line 558, in <module>
    from neuron.rxd.morphology import parent, parent_loc
  File "/usr/lib64/python3.4/site-packages/neuron/rxd/__init__.py", line 13, in <module>
    from . import rxd
  File "/usr/lib64/python3.4/site-packages/neuron/rxd/rxd.py", line 79, in <module>
    nrn_tree_solve = neuron.nrn_dll_sym('nrn_tree_solve')
  File "/usr/lib64/python3.4/site-packages/neuron/__init__.py", line 416, in nrn_dll_sym
    return dll.__getattr__(name)
  File "/usr/lib64/python3.4/ctypes/__init__.py", line 359, in __getattr__
    func = self.__getitem__(name)
  File "/usr/lib64/python3.4/ctypes/__init__.py", line 364, in __getitem__
    func = self._FuncPtr((name_or_ordinal, self))
AttributeError: /usr/local/nrn/x86_64/lib/libnrnpython.so.0: undefined symbol: nrn_tree_solve

I tried explicitly setting my LD_LIBRARY_PATH but that didn't change the error at all.

[bloyl@reslnmeglabws03 ~]$ echo $LD_LIBRARY_PATH
/mnt/isilon/meg_lab/Linux_software/mne/MNE-2.7.3-3268-Linux-x86_64//lib:/mnt/isilon/meg_lab/Linux_software/mne/MNE-2.7.3-3268-Linux-x86_64//lib:/usr/local/iv/x86_64/lib:/usr/local/nrn/x86_64/lib
[SNIP]

AttributeError: /usr/local/nrn/x86_64/lib/libnrnpython.so.0: undefined symbol: nrn_tree_solve

I also tried to run hnn as root, to see if there is a permissions issue somewhere but that failed because running mpiexec as root is dsiabled.

Any thoughts?

Thanks

Luke

[McDougal, Robert]

Sorry to hear you’re still having trouble.

 

Please try the following:

 

Replace line 558 of /usr/local/hnn/morphology.py with the following two function definitions:

 

def parent(sec):

    seg = sec.trueparentseg()

    if seg is None:

        return None

    else:

        return seg.sec

 

def parent_loc(sec, trueparent):

    seg = sec.trueparentseg()

    if seg is None:

        return None

    else:

        return seg.x

[sam n]

Should those changes get pushed to the default code on github?

Thanks

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[Luke Bloy]

If it works for me I can do a pr including the changes to the install script. I'll try it tomorrow.

[sam n]

Thanks, Robert - what do you think? Is that a NEURON-version issue?

[Luke Bloy]

Hi Robert,

that did the trick. Thank you.

Additionally, where is the best place to discuss issues etc. there seems to be a google group, a bulletin board and github issues. Is one of those preferred?

Thanks again,

Luke

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[McDougal, Robert]

Glad to hear it worked.

 

I’ll defer to Sam as far as where to ask questions.

 

Sam: I’ve made a pull request with this change, because there’s no reason to load all of rxd in just to get that information. (In older versions of NEURON, this was a little harder to get.) We’re going to keep trying to see if we can reproduce the issue (I suspect it’s some form of path issue), because that means rxd won’t work on Luke’s setup… but there should be no HNN implications.

 

- Robert

[Stephanie Jones]

Hi - 

I’m also glad to hear it worked. 

Luke, thanks for your patience  and clarity in helping to troubleshoot. Based on your comment about confusion in where to go to troubleshoot we have updated our webpage to include a troubleshooting section. This links to github for discussion of installation issues, and to the HNN users forum for all other software issues. 

Robert, as always thanks  for fixing the problem. 

Best, 

Stephanie

*******************************************

Stephanie R. Jones, PhD

Associate Professor 

Brown University 
Department of Neuroscience 
Stephan...@Brown.edu

https://blogs.brown.edu/joneslab/

Human Neocortical Neurosolver

https://hnn.brown.edu

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