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mbezaire / ca1

ca1 repository from 2017, linked to Open Source Brain
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Investigate why Travis tests failing #15

Open pgleeson opened 7 years ago

pgleeson commented 7 years ago

@andrisecker can you look here: https://travis-ci.org/pgleeson/ca1/jobs/272150687

The NEURON omv tests are failing, with similar errors to what I get locally. Some differences are small, but others, e.g. olm are larger:

[omv] Running tests defined in .test.olm.nrn.omt
[omv] ==========================================
[omv]   Checking whether OMVEngine: NEURON is already installed...
[omv]     Running the commands: ['nrniv', '--version'] in (.; cwd=/home/padraig/git/ca1/NeuroML2; shell=False)
[omv]     Commands: ['nrniv', '--version'] completed successfully
[omv]     NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09 was already installed locally
[omv]   Checking whether NEURON is already installed...
[omv]     Running the commands: ['nrniv', '--version'] in (.; cwd=/home/padraig/git/ca1/NeuroML2; shell=False)
[omv]     Commands: ['nrniv', '--version'] completed successfully
[omv]     NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09 was already installed locally
[omv]   NEURON environment vars: {'PYTHONPATH': '/home/padraig/local/lib/python/site-packages', 'NEURON_HOME': '/usr/local/nrn/x86_64/'}, PATH: /usr/local/nrn/x86_64/bin
[omv]     Set env var PYTHONPATH: /home/padraig/opt/nest/lib64/python2.7/site-packages:/home/padraig/opt/nest/lib/python2.7/site-packages::/home/padraig/local/lib/python/site-packages
[omv]     Set env var NEURON_HOME: /usr/local/nrn/x86_64/
[omv]     Setting PATH: /home/padraig/opt/nest/bin:/home/padraig/bin:/usr/local/nrn/x86_64//bin:/usr/local/genesis:/home/padraig/moose:/sbin/:/home/padraig/neuroConstruct/NeuroML2:/home/padraig/jLEMS/:/home/padraig/neuroConstruct/jNeuroMLJar:/home/padraig/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin:/usr/local/cuda/bin:/usr/local/nrn/x86_64/bin
[omv]     Attention! Preexistent datafile: olm.soma.dat
[omv]   Found 1 experiment(s) to run on engine: NEURON 
[omv]   Running NEURON on /home/padraig/git/ca1/NeuroML2/olm.hoc...
[omv]     OUT:  1 
##### olm started #####
Starting simulation of duration 300 ms, dt: 0.001 ms
Finished simulation in 2.3199999 seconds

No plots shown. Change variable show_plot to view membrane potential traces

    1 

[omv]     ERR: NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits

Additional mechanisms from files
 ../ExpGABAab.mod ../MyExp2Sid.mod ../MyExp2Sidnw.mod ../SIN.mod ../ch_CavL.mod ../ch_CavN.mod ../ch_HCN.mod ../ch_HCNolm.mod ../ch_HCNp.mod ../ch_KCaS.mod ../ch_Kdrfast.mod ../ch_Kdrfastngf.mod ../ch_Kdrp.mod ../ch_Kdrslow.mod ../ch_KvA.mod ../ch_KvAdistp.mod ../ch_KvAngf.mod ../ch_KvAolm.mod ../ch_KvAproxp.mod ../ch_KvCaB.mod ../ch_KvGroup.mod ../ch_KvM.mod ../ch_Nav.mod ../ch_Navaxonp.mod ../ch_Navbis.mod ../ch_Navcck.mod ../ch_Navngf.mod ../ch_Navp.mod ../ch_leak.mod ../fastconn.mod ../iconc_Ca.mod ../mynetstim.mod ../positionfcns.mod ../repeatconn.mod ../sgate.mod ../xtra.mod
nrniv: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"

[omv]     returncode: 
[omv]   Running checks for experiment: current clamp olm
[omv] 
[omv]   Reading timeseries from: {'initial rows to disregard': '0', 'file name': 'olm.soma.dat', 'columns(time, voltage)': '[0, 1]'}
[omv]     Detecting spikes with method: threshold
[omv] Comparison of 
                    (observed data): [64.044, 81.16, 96.782, 111.747, 126.376, 140.823, 155.17, 169.464, 183.734, 197.997, 212.263, 226.538, 240.827]
                    and
                    (expected data): [62.433, 78.643, 93.897, 108.661, 123.153, 137.488, 151.73, 165.918, 180.075, 194.215, 208.349, 222.48, 236.614, 250.856]
                    failed against tolerance 0
[omv]       Observable                        Test Passed     
[omv]       --------------------------------------------------
[omv]       spike times                            ✘          
[omv]       +++++++++++++++++++++ Error info ++++++++++++++++++
[omv]        Return code: 0
[omv]        Output:    1 
       ##### olm started #####
       Starting simulation of duration 300 ms, dt: 0.001 ms
       Finished simulation in 2.3199999 seconds

       No plots shown. Change variable show_plot to view membrane potential traces

        1 

[omv]       +++++++++++++++++++++++++++++++++++++++++++++++++++
[omv] 
[omv]                     Test failed: .test.olm.nrn.omt
andrisecker commented 7 years ago

@pgleeson I have no clue what's happening... The NeuroML2 ones are still passing with the same .mep file and we didn't touch the .mod files... (or anything in those models)

Might be the same as issue #13 They're also failing for me locally with version 7.4 1370 (same as on travis). Just asked the NEURON developers about it: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=6&t=3747

-> Update on this: NEURON version 7.5 didn't solve the issue (but crashed the .mod file generated from Capool.nml) so we stick to 7.4

andrisecker commented 7 years ago

To be honest we skipped checking through the changes since our first clone from bitbucket and that's why some travis tests were failing...

@pgleeson Everything is passing for me!

pgleeson commented 7 years ago

Only one h5 based Netpyne network simulation is failing on Travis (and my machine) now... https://travis-ci.org/pgleeson/ca1/jobs/299699916