Hi,
We have a little issue here getting CCPN3 to run on a Mac Book Pr, running under 10.15.3 (Catalina). (But the problem was there already before upgrading to Catalina.)
Having installed Xquartz (so I think that`s fine) and installed CCPN3, there is the following error message in a popup window, when starting CCPN3 Analysis from the console:
`libmkl_rt.dylib is damaged and cannot be opened`
Does anybody know a solution?
cheers,
Paul
Hi Paul,
Luca seems to think that it should work if you remove Anaconda from your Xquartz `include Path`.
See https://github.com/davisking/dlib/issues/437 for more info.
Vicky
Thank you Vicky.
The github discussion is pretty complex, I have not understood what exactly to do.
What is the fastest way? Just remove the X11 directory in anaconda? Is anaconda needed at all for CCPN?
Hi Paul, just to understand better, have you installed V3 from sources, including dependencies and compiled the C-code yourself or you used the pre-compiled distribution?
And Are you running from X-quartz or from the terminal?
Thanks, Luca.
The precompiled distribution was used, and it is run from the terminal.
Ok, can you run in debug mode, if we can extract more information?
./assign --debug
thanks
Dear Luca,
below is the output when starting ccpn in debug mode. As said, when launching analysis, a window pops up with the message
`libmkl_rt.dylib is damaged and cannot be opened`
When clicking `Cancel` in that window, the console shows the text below.
Help is greatly appreciated.
Thank you.
paul
[MacBook-Pro-de-Bla:/Applications/ccpnmr3.0.0/bin] bla% ./assign --debug
Program licence (non-profit) valid until Wed Sep 2 12:41:11 2020
Traceback (most recent call last):
File `/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/runpy.py`, line 193, in _run_module_as_main
`__main__`, mod_spec)
File `/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/runpy.py`, line 85, in _run_code
exec(code, run_globals)
File `/Applications/ccpnmr3.0.0/src/python/ccpn/AnalysisAssign/__main__.py`, line 25, in <module>
from ccpn.framework import Framework
File `/Applications/ccpnmr3.0.0/src/python/ccpn/framework/Framework.py`, line 36, in <module>
from ccpn.core.IntegralList import IntegralList
File `/Applications/ccpnmr3.0.0/src/python/ccpn/core/__init__.py`, line 307, in <module>
cls = getattr(importlib.import_module(`ccpn.core.%s` % className), className)
File `/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/importlib/__init__.py`, line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File `/Applications/ccpnmr3.0.0/src/python/ccpn/core/Project.py`, line 31, in <module>
import numpy as np
File `/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/site-packages/numpy/__init__.py`, line 142, in <module>
from . import add_newdocs
File `/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/site-packages/numpy/add_newdocs.py`, line 13, in <module>
from numpy.lib import add_newdoc
File `/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/site-packages/numpy/lib/__init__.py`, line 8, in <module>
from .type_check import *
File `/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/site-packages/numpy/lib/type_check.py`, line 11, in <module>
import numpy.core.numeric as _nx
File `/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/site-packages/numpy/core/__init__.py`, line 14, in <module>
from . import multiarray
ImportError: dlopen(/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/site-packages/numpy/core/multiarray.cpython-35m-darwin.so, 2): Library not loaded: @rpath/libmkl_rt.dylib
Referenced from: /Applications/ccpnmr3.0.0/miniconda/lib/python3.5/site-packages/numpy/core/multiarray.cpython-35m-darwin.so
Reason: no suitable image found. Did find:
/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/site-packages/numpy/core/../../../../libmkl_rt.dylib: code signing blocked mmap() of `/Applications/ccpnmr3.0.0/miniconda/lib/python3.5/site-packages/numpy/core/../../../../libmkl_rt.dylib`
/Applications/ccpnmr3.0.0/miniconda/bin/../lib/libmkl_rt.dylib: code signing blocked mmap() of `/Applications/ccpnmr3.0.0/miniconda/bin/../lib/libmkl_rt.dylib`
/Applications/ccpnmr3.0.0/miniconda/lib/libmkl_rt.dylib: code signing blocked mmap() of `/Applications/ccpnmr3.0.0/miniconda/lib/libmkl_rt.dylib`
[MacBook-Pro-de-Bla:/Applications/ccpnmr3.0.0/bin] bla%
This is kind of solved, or let`s say there is a workaround.
Launching the program from the console does not work, but the launcher works, so one can start it with the mouse.
We have not found out what`s the problem when launching from the console.
Thanks for the help!
It is very strange. Because the Launcher sends an OS command to the native Terminal app. I wonder if you have some incompatible setting in the terminal. Out of curiosity, are you able to install V3 in a guest account in your machine? and try again from terminal. Thanks.
We will prepare compiled version for Catalina too.
I experience the same issue running CCPN on a Macbook with Catalina (v10.15.3). I receive the `libmkl_rt.dylib is damaged and can`t be opened. You should move it to the Bin.` message as well as the same output in the terminal as Paul got. However, different from Paul, I am not able to open Assign from the Launcher. When clicking on the `Assign` button in the Launcher, a terminal window pops up with the output:
Sjensen@S-MacBook-Pro ~ % /Applications/CcpNmrLauncher.app/Contents/Resources/ccpnmr3.0.0/bin/assign ; exit;
ERROR: Analysis-V3 version number `3.0.0` has expired on Tue Mar 3 11:43:10 2020
Aborting program
[Process completed]
I have downloaded the newest license available (valid until 2nd September 2020) and checked for any updates using the terminal (./update), but nothing really helps.
My application folder is shared between all users, so I am not sure if it would be any different to install V3 from a guest account? I assume it should preferentially be installed in the Application folder?
(03-19-2020, 12:09 pm)LucaM Wrote: It is very strange. Because the Launcher sends an OS command to the native Terminal app. I wonder if you have some incompatible setting in the terminal. Out of curiosity, are you able to install V3 in a guest account in your machine? and try again from terminal. Thanks.
We will prepare compiled version for Catalina too.
Could be a code signing issue similar to....?
https://blog.supereasyapps.com/how-to-fi...r-profile/
The Launcher has all the signatures as recommended by Apple, the source code in the .tgz or .zip files don`t have any. We just made a new build for the launcher and the certificates are as suggested by the blog. Soon available for downloading with the new release. However, we are still waiting for an official developer ID, until then I would expect some issues with permissions.
Hi,
Version 3.0.1 is now out. You can download this at
https://www.ccpn.ac.uk/v3-software/downl...-downloads
Perhaps try having another go with this. If the the command line version doesn`t work, then try the Launcher and vice versa.
Overall, we are not recommending the use of Catalina at the moment, though some people do seem to have to got it to work.
Vicky
(04-23-2020, 03:50 pm)VickyH Wrote: Hi,
Version 3.0.1 is now out. You can download this at
https://www.ccpn.ac.uk/v3-software/downl...-downloads
Perhaps try having another go with this. If the the command line version doesn`t work, then try the Launcher and vice versa.
Overall, we are not recommending the use of Catalina at the moment, though some people do seem to have to got it to work.
Vicky
I just tried with the command line version, and after having entered the `sudo spctl --master-disable` command, I was able to open AssignAnalysis. Thank you so much!