Fix bootstrap

[babsey]

The bootstrap contains some unclear lines:

• Use newer cmake version (3.27)
• Install Python package correctly (otherwise some binaries will be lost)
• Remove unnecessary configs for NEST installation
• Insite should be installed after nest installation
• Insite installation config should find nest-config.
• Use Path to find binaries of python packages (/home/vagrant/multiscale-cosim/site-packages/bin)
• Add code to start nest-desktop and Insite in run_on_local.sh

[babsey]

I still have some issue to get activity from insite:

[Insite] Post Run Hook
2023-08-02 12:05:37,507 INFO NEST_Adapter [MainProcess:1734] simulation run counter: 25.0
[Insite] Pre Run Hook
[2023-08-02 12:05:37.507] [info] Run duration: 1.2
(2023-08-02 12:05:37) [INFO    ] Request: 10.0.2.2:43704 0x56130b01d480 HTTP/1.1 GET /nest/simulationTimeInfo/
(2023-08-02 12:05:37) [INFO    ] Response: 0x56130b01d480 /nest/simulationTimeInfo/ 200 0
2023-08-02 12:05:37,650 ERROR Application_Manager [MainProcess:1628] ['mpirun', '-n', '1', 'python3', '/home/vagrant/multiscale-cosim/Cosim_NestDesktop_Insite/action_adapters/nest_simulator/nest_adapter.py', b'gASVjAMAAAAAAACMVkVCUkFJTlNfQ29uZmlnTWFuYWdlci5nbG9iYWxfY29uZmlndXJhdGlvbnNfbWFuYWdlci54bWxfcGFyc2Vycy5jb25maWd1cmF0aW9uc19tYW5hZ2VylIwVQ29uZmlndXJhdGlvbnNNYW5hZ2VylJOUKYGUfZQojCtfQ29uZmlndXJhdGlvbnNNYW5hZ2VyX19kaXJlY3Rvcmllc19tYW5hZ2VylIxTRUJSQUlOU19Db25maWdNYW5hZ2VyLmdsb2JhbF9jb25maWd1cmF0aW9uc19tYW5hZ2VyLnhtbF9wYXJzZXJzLmRpcmVjdG9yaWVzX21hbmFnZXKUjBJEaXJlY3Rvcmllc01hbmFnZXKUk5QpgZR9lIwgX0RpcmVjdG9yaWVzTWFuYWdlcl9fZGlyZWN0b3JpZXOUfZQojFhFQlJBSU5TX0NvbmZpZ01hbmFnZXIuZ2xvYmFsX2NvbmZpZ3VyYXRpb25zX21hbmFnZXIueG1sX3BhcnNlcnMuZGVmYXVsdF9kaXJlY3Rvcmllc19lbnVtlIwSRGVmYXVsdERpcmVjdG9yaWVzlJOUjAZvdXRwdXSUhZRSlIw2Q29zaW11bGF0aW9uX291dHB1dHMvdmFncmFudF9vdXRwdXRzXzIwMjMtMDgtMDJfMTIwNTE2lGgPjARsb2dzlIWUUpSMO0Nvc2ltdWxhdGlvbl9vdXRwdXRzL3ZhZ3JhbnRfb3V0cHV0c18yMDIzLTA4LTAyXzEyMDUxNi9sb2dzlGgPjA9tb25pdG9yaW5nX2RhdGGUhZRSlIxGQ29zaW11bGF0aW9uX291dHB1dHMvdmFncmFudF9vdXRwdXRzXzIwMjMtMDgtMDJfMTIwNTE2L21vbml0b3JpbmdfZGF0YZRoD4wSc2ltdWxhdGlvbl9yZXN1bHRzlIWUUpSMSUNvc2ltdWxhdGlvbl9vdXRwdXRzL3ZhZ3JhbnRfb3V0cHV0c18yMDIzLTA4LTAyXzEyMDUxNi9zaW11bGF0aW9uX3Jlc3VsdHOUdXNijB5fQ29uZmlndXJhdGlvbnNNYW5hZ2VyX19wYXJzZXKUjEpFQlJBSU5TX0NvbmZpZ01hbmFnZXIuZ2xvYmFsX2NvbmZpZ3VyYXRpb25zX21hbmFnZXIueG1sX3BhcnNlcnMueG1sX3BhcnNlcpSMBlBhcnNlcpSTlCmBlHViLg==', b'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', '/home/vagrant/multiscale-cosim/Cosim_NestDesktop_Insite/userland/parameters/scientific/nest.xml', b'gASJLg==', b'gASVOwEAAAAAAABdlCh9lCiMF0RBVEFfRVhDSEFOR0VfRElSRUNUSU9OlIwLTkVTVF9UT19UVkKUjBNNUElfQ09OTkVDVElPTl9JTkZPlIw7dGFnIzAkZGVzY3JpcHRpb24jdWJ1bnR1LWZvY2FsJHBvcnQjNDA4NzUkaWZuYW1lIzEyNy4wLjEuMSSUjA5JTlRFUkNPTU1fVFlQRZSMCFJFQ0VJVkVSlHV9lCiMF0RBVEFfRVhDSEFOR0VfRElSRUNUSU9OlIwLVFZCX1RPX05FU1SUjBNNUElfQ09OTkVDVElPTl9JTkZPlIw7dGFnIzAkZGVzY3JpcHRpb24jdWJ1bnR1LWZvY2FsJHBvcnQjNTY0NjEkaWZuYW1lIzEyNy4wLjEuMSSUjA5JTlRFUkNPTU1fVFlQRZSMBlNFTkRFUpR1ZS4=']: (2023-08-02 12:05:37) [INFO    ] Request: 127.0.0.1:37854 0x7f7524002280 HTTP/1.1 GET /simulationTimeInfo
(2023-08-02 12:05:37) [INFO    ] Response: 0x7f7524002280 /simulationTimeInfo 200 0
(2023-08-02 12:05:37) [INFO    ] Request: 10.0.2.2:43704 0x56130b01d480 HTTP/1.1 GET /nest/simulationTimeInfo/
(2023-08-02 12:05:37) [INFO    ] Response: 0x56130b01d480 /nest/simulationTimeInfo/ 200 0
2023-08-02 12:05:37,868 INFO Application_Manager [MainProcess:1629] action <INTERSCALE_HUB_NEST_TO_TVB>: 2023-08-02 12:05:37,827 INFO InterscaleHub -- NEST_TO_TVB Manager [MainProcess:1702] Stop InterscaleHub and disconnect...
2023-08-02 12:05:37,827 ERROR EBRAINS_InterscaleHUB.Interscale_hub.communicator_nest_to_tvb [MainProcess:1702] stop() is not implemented yet
Traceback (most recent call last):
  File "/home/vagrant/multiscale-cosim/Cosim_NestDesktop_Insite/EBRAINS_InterscaleHUB/Interscale_hub/communicator_nest_to_tvb.py", line 90, in stop
    raise NotImplementedError
NotImplementedError
2023-08-02 12:05:37,847 INFO IntercommManager [MainProcess:1702] Successfully disconnected and closed port
2023-08-02 12:05:37,868 INFO Application_Manager [MainProcess:1630] action <TVB_SIMULATOR>: 2023-08-02 12:05:37,860 INFO TVB_MPI_Wrapper [MainProcess:1735] end receive [28.8 30. ]
2023-08-02 12:05:37,861 INFO TVB_MPI_Wrapper [MainProcess:1735] TVB start simulation 28.799999999999997
WARNING  random_state supplied for non-stochastic integration
2023-08-02 12:05:37,865 INFO TVB_MPI_Wrapper [MainProcess:1735]  TVB end simulation
2023-08-02 12:05:37,869 INFO Application_Manager [MainProcess:1628] action <NEST_SIMULATOR>: Aug 02 12:05:37 SimulationManager::run [Warning]: 
    The requested simulation time is not an integer multiple of the minimal 
    delay in the network. This may result in inconsistent results under the 
    following conditions: (i) A network contains more than one source of 
    randomness, e.g., two different poisson_generators, and (ii) Simulate is 
    called repeatedly with simulation times that are not multiples of the 
    minimal delay.

Aug 02 12:05:37 SimulationManager::start_updating_ [Info]: 
    Number of local nodes: 130
    Simulation time (ms): 1.2
    Number of OpenMP threads: 1
    Number of MPI processes: 1

Aug 02 12:05:37 SimulationManager::run [Info]: 
    Simulation finished.
[Insite] Post Run Hook
2023-08-02 12:05:37,827 INFO NEST_Adapter [MainProcess:1734] nest simulation is finished
2023-08-02 12:05:37,827 INFO NEST_Adapter [MainProcess:1734] cleaning up NEST
[Insite] Cleanup
2023-08-02 12:05:37,869 ERROR Application_Manager [MainProcess:1628] ['mpirun', '-n', '1', 'python3', '/home/vagrant/multiscale-cosim/Cosim_NestDesktop_Insite/action_adapters/nest_simulator/nest_adapter.py', b'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', b'gASVRwMAAAAAAAB9lCiMB3ZlcnNpb26USwGMGGRpc2FibGVfZXhpc3RpbmdfbG9nZ2Vyc5SJjApmb3JtYXR0ZXJzlH2UKIwHZGVmYXVsdJR9lIwGZm9ybWF0lIxMJShhc2N0aW1lKXMgJShsZXZlbG5hbWUpcyAlKG5hbWUpcyBbJShwcm9jZXNzTmFtZSlzOiUocHJvY2VzcylkXSAlKG1lc3NhZ2Upc5RzjAd2ZXJib3NllH2UaAeMjyUoYXNjdGltZSlzICUobGV2ZWxuYW1lKXMgJShuYW1lKXMgWyUocHJvY2Vzc05hbWUpczolKHByb2Nlc3MpZF0gWyUodGhyZWFkTmFtZSlzOiUodGhyZWFkKWRdIFslKGZpbGVuYW1lKXM6JShmdW5jTmFtZSlzOiUobGluZW5vKWRdICUobWVzc2FnZSlzlHN1jAhoYW5kbGVyc5R9lCiMB2NvbnNvbGWUfZQojAVjbGFzc5SMFWxvZ2dpbmcuU3RyZWFtSGFuZGxlcpSMBWxldmVslIwESU5GT5SMCWZvcm1hdHRlcpSMB2RlZmF1bHSUjAZzdHJlYW2UjBBleHQ6Ly9zeXMuc3Rkb3V0lHWMCWluZm9fZmlsZZR9lChoEIwTbG9nZ2luZy5GaWxlSGFuZGxlcpRoEowESU5GT5RoFIwHZGVmYXVsdJSMCGZpbGVuYW1llIxEQ29zaW11bGF0aW9uX291dHB1dHMvdmFncmFudF9vdXRwdXRzXzIwMjMtMDgtMDJfMTIwNTE2L2xvZ3MvaW5mby5sb2eUdYwKZXJyb3JfZmlsZZR9lChoEIwkbG9nZ2luZy5oYW5kbGVycy5Sb3RhdGluZ0ZpbGVIYW5kbGVylGgSjAVFUlJPUpRoFIwHdmVyYm9zZZRoHYxGQ29zaW11bGF0aW9uX291dHB1dHMvdmFncmFudF9vdXRwdXRzXzIwMjMtMDgtMDJfMTIwNTE2L2xvZ3MvZXJyb3JzLmxvZ5R1dYwHbG9nZ2Vyc5R9lIwEcm9vdJR9lChoEowFREVCVUeUaAxdlCiMB2NvbnNvbGWUjAlpbmZvX2ZpbGWUjAplcnJvcl9maWxllGWMCXByb3BhZ2F0ZZSMAm5vlHV1Lg==', '/home/vagrant/multiscale-cosim/Cosim_NestDesktop_Insite/userland/parameters/scientific/nest.xml', b'gASJLg==', b'gASVOwEAAAAAAABdlCh9lCiMF0RBVEFfRVhDSEFOR0VfRElSRUNUSU9OlIwLTkVTVF9UT19UVkKUjBNNUElfQ09OTkVDVElPTl9JTkZPlIw7dGFnIzAkZGVzY3JpcHRpb24jdWJ1bnR1LWZvY2FsJHBvcnQjNDA4NzUkaWZuYW1lIzEyNy4wLjEuMSSUjA5JTlRFUkNPTU1fVFlQRZSMCFJFQ0VJVkVSlHV9lCiMF0RBVEFfRVhDSEFOR0VfRElSRUNUSU9OlIwLVFZCX1RPX05FU1SUjBNNUElfQ09OTkVDVElPTl9JTkZPlIw7dGFnIzAkZGVzY3JpcHRpb24jdWJ1bnR1LWZvY2FsJHBvcnQjNTY0NjEkaWZuYW1lIzEyNy4wLjEuMSSUjA5JTlRFUkNPTU1fVFlQRZSMBlNFTkRFUpR1ZS4=']: (2023-08-02 12:05:37) [INFO    ] Request: 127.0.0.1:37858 0x7f7524003800 HTTP/1.1 GET /simulationTimeInfo

[babsey]

By the way, NEST Desktop works with NEST Server and Insite access node
as well as with CoSim Instance only (without Insite).

But with CoSim Instance and Insite it shows error (see above).

[sontheimer]

The bootstrap contains some unclear lines:

• Use newer cmake version (3.27)

• okay

• Install Python package correctly (otherwise some binaries will be lost)

• consider adding the --upgrade flag (for numpy==1.23)
• e.g. elephant will install the newest numpy but the TVB version used here needs the specific numpy 1.23

• Remove unnecessary configs for NEST installation

• maybe double check if it still runs, otherwise okay!
• Remember: on hpc, the flags are used in a specific way, so this only works for the local bootstrap.sh

• Insite should be installed after nest installation
• Insite installation config should find nest-config.

• okay

• Use Path to find binaries of python packages (/home/vagrant/multiscale-cosim/site-packages/bin)

• okay

• Add code to start nest-desktop and Insite in run_on_local.sh

• okay!
• In line 246 in your suggested bootstrap.sh: Is this the intended way of starting the INSITE access node? It seems to be incomplete.
• NOTE: This hides any error messages or crashes from the user (without vagrans ssh)
• NOTE: only one run possible.
• Every subsequent run would need:
  • vagrant halt and vagrant up again
  • future cosim releases with implemented 'rerun' instead of 'new run'

All points can be further discussed, if unclear.

[sontheimer]

By the way, NEST Desktop works with NEST Server and Insite access node as well as with CoSim Instance only (without Insite).

But with CoSim Instance and Insite it shows error (see above).

The above error messages are related to Cosim output, i.e. the responses/outputs from INSITE and NEST-Desktop are read via error stream. In other words, these logs do not reflect the errors from Cosim or reporting of any crash or so.

If you do not see any response from the of the NEST simulation via INSITE in NEST Desktop, it should be looked at from INSITE perspective.

Maybe Marcel can have a look into that.

[mfahdaz]

• NOTE: This hides any error messages or crashes from the user (without vagrans ssh)

• NOTE: only one run possible.

• Every subsequent run would need:

  • vagrant halt and vagrant up again
  • future cosim releases with implemented 'rerun' instead of 'new run'

This is particularly true if the idea is to run the usecase directly from bootstrap and without logging in to VM (vagrant ssh). However, we might also want to reboot the VM with a new provision (to be added for launching purposes and) to avoid the installation process when re-running the usecase.

Otherwise, one does not need to reloading the VM every time when (re)running the usecase with ./run_on_local.sh after logging in to VM.

[babsey]

@sontheimer Thank you for the review.

One point, can you please make code suggestion?

[jens-br]

Thank you very much! 👍
I discussed it with Muhammad. Please find the open points in the details.

[jens-br]

@marcelkrueger Could you check this and - if necessary - add the missing lines for the Insite start?

(see also #22 (comment))