Closed rythorpe closed 2 years ago
Thanks @rythorpe! Might be worth doing some googling to see what changed after the workshop. Seems like something on the conda end?
I think it was an operating system or NEURON thing actually.
For future reference, here's part of the error traceback that this PR fixed. I couldn't capture the whole traceback due to the fact that it only prints in HNN's tiny dialog box (i.e., not the terminal) that's only open while a simulation is actively running.
0x000A): tried: '/Users/rv_01/opt/miniconda3/envs/hnn/lib/python3.7/site-packages/neuron/.data/lib/../lib/libmpi.dylib' (no such file), '/Users/rv_01/opt/miniconda3/envs/hnn/lib/python3.7/site-packages/neuron/.data/bin/../lib/libmpi.dylib' (no such file), 'libmpi.dylib' (no such file), '/usr/local/lib/libmpi.dylib' (no such file), '/usr/lib/libmpi.dylib' (no such file), '/Users/rv_01/Desktop/hnn_source_code/libmpi.dylib' (no such file)
Is openmpi or mpich installed? If not in default location, need a LD_LIBRARY_PATH on Linux or DYLD_LIBRARY_PATH on Mac OS. On Mac OS, full path to a MPI library can be provided via environmental variable MPI_LIB_NRN_PATH
could not dynamically load libmpi.so or libmpich.so
Try loading libmpi
load_mpi: dlopen(libmpi.dylib, 0x000A): tried: '/Users/rv_01/opt/miniconda3/envs/hnn/lib/python3.7/site-packages/neuron/.data/lib/../lib/libmpi.dylib' (no such file), '/Users/rv_01/opt/miniconda3/envs/hnn/lib/python3.7/site-packages/neuron/.data/bin/../lib/libmpi.dylib' (no such file), 'libmpi.dylib' (no such file), '/usr/local/lib/libmpi.dylib' (no such file), '/usr/lib/libmpi.dylib' (no such file), '/Users/rv_01/Desktop/hnn_source_code/libmpi.dylib' (no such file)
Is openmpi or mpich installed? If not in default location, need a LD_LIBRARY_PATH on Linux or DYLD_LIBRARY_PATH on Mac OS. On Mac OS, full path to a MPI library can be provided via environmental variable MPI_LIB_NRN_PATH
could not dynamically load libmpi.so or libmpich.so
INFO: Failed starting mpiexec, retrying with 2 cores
Try loading libmpi
load_mpi: dlopen(libmpi.dylib, 0x000A): tried: '/Users/rv_01/opt/miniconda3/envs/hnn/lib/python3.7/site-packages/neuron/.data/lib/../lib/libmpi.dylib' (no such file), '/Users/rv_01/opt/miniconda3/envs/hnn/lib/python3.7/site-packages/neuron/.data/bin/../lib/libmpi.dylib' (no such file), 'libmpi.dylib' (no such file), '/usr/local/lib/libmpi.dylib' (no such file), '/usr/lib/libmpi.dylib' (no such file), '/Users/rv_01/Desktop/hnn_source_code/libmpi.dylib' (no such file)
Is openmpi or mpich installed? If not in default location, need a LD_LIBRARY_PATH on Linux or DYLD_LIBRARY_PATH on Mac OS. On Mac OS, full path to a MPI library can be provided via environmental variable MPI_LIB_NRN_PATH
could not dynamically load libmpi.so or libmpich.so
Simulation exited with return code 1. Stderr from console:
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[62940,1],0]
Exit code: 1
--------------------------------------------------------------------------
Try loading libmpi
load_mpi: dlopen(libmpi.dylib, 0x000A): tried: '/Users/rv_01/opt/miniconda3/envs/hnn/lib/python3.7/site-packages/neuron/.data/lib/../lib/libmpi.dylib' (no such file), '/Users/rv_01/opt/miniconda3/envs/hnn/lib/python3.7/site-packages/neuron/.data/bin/../lib/libmpi.dylib' (no such file), 'libmpi.dylib' (no such file), '/usr/local/lib/libmpi.dylib' (no such file), '/usr/lib/libmpi.dylib' (no such file), '/Users/rv_01/Desktop/hnn_source_code/libmpi.dylib' (no such file)
Is openmpi or mpich installed? If not in default location, need a LD_LIBRARY_PATH on Linux or DYLD_LIBRARY_PATH on Mac OS. On Mac OS, full path to a MPI library can be provided via environmental variable MPI_LIB_NRN_PATH
could not dynamically load libmpi.so or libmpich.so
Thanks @rythorpe for taking care of it!
This is an urgent fix for the workshop today. @ntolley @jasmainak please rebase and merge when ready!