Help for getting ScientificPython on OSX

[jbryson3]

On OSX El Capitan, I'm trying to run build/examples/online_prediction/build_netcdf.sh. I'm running into problems with the ScientificPython.

The latest ScientificPython binary on osx require python 2.4. That python is so old that pyenv is having trouble building it.

So I tried build the latest development ScientificPython (2.9.4) with the python I have installed 2.7.11. Other than spitting out a ton of unused function warnings, the build seems to have succeeded. However, when I attempt to run build_netcdf, this is what I get:

./build_netcdf.sh

Traceback (most recent call last):
  File "./online_delta.py", line 3, in <module>
    import netcdf_helpers
  File "/Users/jbryson3/code/libs/rnnlib/utils/netcdf_helpers.py", line 18, in <module>
    from Scientific.IO.NetCDF import NetCDFFile
  File "/usr/local/lib/python2.7/site-packages/Scientific/IO/NetCDF.py", line 168, in <module>
    from Scientific._netcdf import *
ImportError: dlopen(/usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so, 2): Symbol not found: _H5P_CLS_DATASET_ACCESS_ID_g
  Referenced from: /usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so
  Expected in: flat namespace
 in /usr/local/lib/python2.7/site-packages/Scientific/_netcdf.so

I realize this may be a bit out of scope for this codebase, but was hoping someone could point me in the right direction. Thanks!

[aferriss]

I just went through this as well. Instead of downloading the mac binaries, just get the most recent development release tar file and do as their instructions say for the basic installation.

I also had an issue during the install phase (was getting an operation not permitted error, even with sudo) where I had to run my mac in recovery mode (cmd + R on bootup) and then enter the terminal and do csrutil disable followed by a reboot

[akshaypardeshi26]

@ jbryson3 I am facing the same issue. Were you able to resolve it?If yes, could you please tell how?
Thanks.

[jbryson3]

I was unable to resolve this issue on OSX. Instead I booted up a Ubuntu VM using Virtualbox and was successful after 3-4 days of slow going. I have since removed the vm, so I can't remember the exact steps that I used to get it up an running but before I deleted it, I exported a list of things that I had installed on the box to get it working. Hope it helps.
dpkglist.txt
piplist.txt

[ghost]

I'm facing the same issue, too. But when I use the VM, I can't solve this problem. Could you tell me how I can handle it ? @jbryson3