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My media shares live on a Synology NAS, model 216j. I have no problem accessing those shares as NFS shares from a Pivos XIOS DS running TOFULinux.

Recently bought a MacBook Pro running OSX El Capitan 10.11.6 and installed Kodi for OSX 16.1 Git:2016-04-24-c327c53.

When setting up the shares for video sources (Videos/Files/Add Videos.../Browse/NFS) I can see the Synology NAS listed (its IP address) and clicking on that I can see the NFS shares but I cannot add them. No error message given. If I try to add the NFS share manually it says "Couldn't retrieve directory information"

The NFS permissions on the Synology NAS are set up as Hostname *, Read/Write, No mapping, Security (sys) and options "Enable Asynchronus", "Allow connections from non-privileged ports" and "Allow users to access mounted subfolders" all checked. The mac is running with uid 501.

Also (as I said above) I can access the NFS shares, scan etc with no problems from Kodi installed on my Pivos XIOS.
which uid is tofu using? might be you need a user mapping (filesystem permission seem incorrect for uifd 501) - post a debug log (wiki) from manually added shares...
Thanks, should have had a look at the logs in the first place.

Log file is here: http://paste.ubuntu.com/23372230/ It shows this error when trying to access the NFS shares from OSX "failed with NFS3ERR_ACCES(-13)"

This pointed me to this thread: http://forum.kodi.tv/showthread.php?tid=...pid1767790

NFS on Synology seems a bit of a mess. The above thread talks setting permissions at the local level in addition to share level. I did that by giving the group "Everyone" Read access at the file level (bit of security issue). I could then add the NFS shares on the mac. Access to the shares after rebooting the mac is persistent. However, after scraping and rebooting, the Movies and TV Shows menu options are once again greyed out and both the shares lose their scraper settings (no scraper set). I can still access the shares via Videos/Files, but ofcourse no fanart or other niceties.

The above thread also talks about things like squashing all users to admin on the Synology NFS share permissions (again a bit of a security issue). I did that but it didn't make any difference, still no fanart etc after reboot.

Here is a log file I produced after first scanning Movies (after which Movies can be accessed via the main Movies menu item) and then rebooting the mac (after which there is no longer a Movies menu):
http://paste.ubuntu.com/23372675/

Not sure where to look from here. Have tried to get it working using the brute force approach (give everything access) but even that still doesn't quite work fully. I'm not sure how to go about mapping the macs uid to whatever it's using on the Synology.
There is no error at all in that log. I also somehow doubt that the issue has something to do with nfs. Do you autostart kodi after login by any chance?
Well, this is my daughter's macbook and I know next to nothing about apple gear. So I haven't really looked into that, but it does sometimes go straight into Kodi after restarting the mac, not always, which I thought was rather odd. This is shutting down the mac after kodi has been shut down. I don't have the mac with me right now.

I agree, it does not look like an NFS issue now because I can now connect to the share on the Synology via NFS from the mac and that connection is persistent between boots, but only accessible via Videos/Files. Any scanning to the library is lost after a boot. I have no idea what could be causing that, it's as if there was no video source in place, or a scan had never been done, but neither of those is the case. Looks like a mac issue now, but I'm not sure what. Will end up being something simple I'm sure.
Not sure if i read your problem right but,
Something to try.
Add your nfs server as a permanent source.

File Manager > Add Source > Choose Network Location > Choose Nfs > Server Address 192.168.?.? or whatever your server address. > ok.
nfs share route should now be available.
I have already added the video sources, so the NFS shares are available, even after booting the mac. The library (fanart/video info etc etc etc) is all there after doing a full scan. The problem is after reboot the library is no longer there, the video sources are still accessible but there is no library and the Movies and TV menus are greyed out after reboot.

Still looking for a solution.........
The strange thing is that your log shows that it is running database myvideos99.

Can you provide me that database file from the userdata folder?
I scan just movies and check all the fanart etc is there. Restart Kodi and it's all still there. Boot the mac, back into Kodi and can no longer see it (remember it is just the library I can't see anymore, the share is still available and I can still play videos)

OK, reading the Kodi wiki I see that macs hide the library folder. I have the MyVideos99.db, it is 8.2mb created on October 15 which sounds about right. How do you want me to send it to you, compress and email?

I permanently unhid the library folder via terminal command as outlined in the wiki, fired up Kodi but still can't see the database. I was hoping that unhiding that hidden folder might fix it, not even after rebooting.

Has this problem possibly come about because Kodi is installed on the desktop in the mac and not in the the Applications folder?
That might be a problem - you should really have kodi in the applications folder like everything else. You said you start osx into kodi - do you have kodi autostart at login or so?
You could provide the db via dropbox. But i doubt the db is faulty - you said it screws up on restart of the mac but works after just restarting kodi. Seems like a really uncommon thing you are hitting there.