Comments (24)
smbaca
commented on August 30, 2024
1
Ha!
Yeah, there is an OS update today and others have complained about this weird error with various solutions that work for some and not for all. I am going to go ahead and update the OS and make sure that the Xcode is also up to date. At some point the ability to compile worked fine but now I am getting FAILED for everything when I try xolotl.testConductances.
…-smb
On Jul 21, 2022, at 10:48 AM, Srinivas Gorur-Shandilya ***@***.***> wrote:
Xcode.DebuggerFoundation.AppExtensionToBundleIdentifierMap.watchOS
thanks apple watch!
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sg-s
commented on August 30, 2024
do those files exist?
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sg-s
commented on August 30, 2024
I got a different error in testDocs, which I fixed, please let me know if this error persists.
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smbaca
commented on August 30, 2024
Now I get this:
/Users/smbaca/Desktop/github_xolotl/xolotl/docs/how-to/change-existing-models.md
Error using xolotl/testDocs
Error while running /Users/smbaca/Desktop/github_xolotl/xolotl/docs/how-to/change-existing-models.md
Error in xolotl.run_all_tests (line 52)
xolotl.testDocs()
… On Jul 19, 2022, at 12:33 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
I got a different error in testDocs, which I fixed, please let me know if this error persists.
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alec-hoyland
commented on August 30, 2024
I was not able to reproduce the issue on R2022a with gcc 11.2.0 (on Pop!_OS), but I don't have a mac environment to test on.
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sg-s
commented on August 30, 2024
@smbaca this is telling me that some code on this page is failing on your computer. can you verify this independently?
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smbaca
commented on August 30, 2024
So everything runs on that page except this:
> x = xolotl.examples.neurons.HodgkinHuxley;
x.HH.Kd.gbar = 300;
x.HH.Leak.gbar = 0.1;
x.HH.NaV.gbar = 1000;
2022-07-21 10:03:06.920 xcodebuild[54298:947603] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionSentinelHostApplications for extension Xcode.DebuggerFoundation.AppExtensionHosts.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
2022-07-21 10:03:06.921 xcodebuild[54298:947603] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionPointIdentifierToBundleIdentifier for extension Xcode.DebuggerFoundation.AppExtensionToBundleIdentifierMap.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
2022-07-21 10:03:07.519 xcodebuild[54303:947635] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionSentinelHostApplications for extension Xcode.DebuggerFoundation.AppExtensionHosts.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
2022-07-21 10:03:07.519 xcodebuild[54303:947635] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionPointIdentifierToBundleIdentifier for extension Xcode.DebuggerFoundation.AppExtensionToBundleIdentifierMap.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
2022-07-21 10:03:10.886 xcodebuild[54312:947704] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionSentinelHostApplications for extension Xcode.DebuggerFoundation.AppExtensionHosts.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
2022-07-21 10:03:10.886 xcodebuild[54312:947704] Requested but did not find extension point with identifier Xcode.IDEKit.ExtensionPointIdentifierToBundleIdentifier for extension Xcode.DebuggerFoundation.AppExtensionToBundleIdentifierMap.watchOS of plug-in com.apple.dt.IDEWatchSupportCore
… On Jul 19, 2022, at 5:15 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
@smbaca <https://github.com/smbaca> this is telling me that some code on this page <https://xolotl.readthedocs.io/en/master/how-to/change-existing-models/> is failing on your computer. can you verify this independently?
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sg-s
commented on August 30, 2024
Xcode.DebuggerFoundation.AppExtensionToBundleIdentifierMap.watchOS
thanks apple watch!
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sg-s
commented on August 30, 2024
is that the full error message or is there more?
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smbaca
commented on August 30, 2024
That was the full message.
… On Jul 21, 2022, at 10:49 AM, Srinivas Gorur-Shandilya ***@***.***> wrote:
is that the full error message or is there more?
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sg-s
commented on August 30, 2024
i'm on macOS 12.4 too, and everything works for me. let me know how it works -- it's also possible that there are multiple copies of xolotl on your computer and that's confusing the compiler
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smbaca
commented on August 30, 2024
Yeah, I have only the one xolotl on the computer. Reinstalled a non-beta version of Xcode and am running 12.5.
xolotl.run_all_tests does everything fine until it gets to the testConductances and then they all fail.
/usr/bin/xcrun -sdk macosx12.3 clang++ this does not give any errors in terminal but I still think I have a weird mex_C++_maci64.xml file as I don’t see anyplace to change the LinkerName. That said, the LinkerName is correct so not sure what the issue is now. So close!
…-smb
On Jul 21, 2022, at 8:32 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
i'm on macOS 12.4 too, and everything works for me. let me know how it works -- it's also possible that there are multiple copies of xolotl on your computer and that's confusing the compiler
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sg-s
commented on August 30, 2024
oof, might want to stay away from the bleeding edge there. I'm on Xcode 13.4.1 -- what version are you on?
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smbaca
commented on August 30, 2024
Yes, I rolled back and think I cleaned everything out but still have the testconductances failing. I am using Xcode Version 13.4.1 (13F100). If someone can send their mex_C++_maci64.xml for comparison that might be helpful.
I have been in the various Mac XCode usergroups and a lot of people often have to reset in the terminal the default paths for various things anytime there is an Xcode upgrade. Maybe the roll back is not complete for all files or something. Who knows.
…-smb
On Jul 22, 2022, at 11:47 AM, Srinivas Gorur-Shandilya ***@***.***> wrote:
oof, might want to stay away from the bleeding edge there. I'm on Xcode 13.4.1 -- what version are you on?
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sg-s
commented on August 30, 2024
have you seen this:
https://github.com/sg-s/matlab-catalina-compiler-fix
(you'll need to update the numbers for your version, but i wonder if this is the issue you're facing)
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smbaca
commented on August 30, 2024
Yes, I saw that and can give it a go. But I think the issue may be that xolotl is just not seeing the GitHub conductances folder…
I was going through the tutorials and noticed that if I search for prinz I get nothing even though I can go into my folder (which is also in the MATLAB path) and see that I have the prinz folder with 7 different .hpp files for the conductances.
xolotl.search('prinz')
------------------------------------------------------------------------------------
Name Parent Class Object Information
------------------------------------------------------------------------------------
------------------------------------------------------------------------------------
… On Jul 22, 2022, at 12:31 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
have you seen this:
https://github.com/sg-s/matlab-catalina-compiler-fix <https://github.com/sg-s/matlab-catalina-compiler-fix>
(you'll need to update the numbers for your version, but i wonder if this is the issue you're facing)
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sg-s
commented on August 30, 2024
there is something wrong with your path. before you mess around with xcode and compilers, let's fix that.
can you send me your path? type path and copy over everything that is outside the MATLAB folder
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smbaca
commented on August 30, 2024
/Users/smbaca/Desktop/github_xolotl
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/Users/smbaca/Desktop/github_xolotl/xolotl/experimental
/Users/smbaca/Desktop/github_xolotl/xolotl/experimental/proof-of-concept
/Users/smbaca/Desktop/github_xolotl/xolotl/git-hooks
/Users/smbaca/Desktop/github_xolotl/xolotl/optimization
… On Jul 22, 2022, at 2:19 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
there is something wrong with your path. before you mess around with xcode and compilers, let's fix that.
can you send me your path? type path and copy over everything that is outside the MATLAB folder
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sg-s
commented on August 30, 2024
there's your problem right there -- you have .git folders on your path. this means there are multiple versions of code on your path -- a very bad idea.
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smbaca
commented on August 30, 2024
Unfortunately, now I even have more bizarre errors after removing those folders. I have another Mac so will try to start fresh from there as I feel there are residual folders or preferences that are mucking up things.
…-smb
On Jul 22, 2022, at 5:39 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
there's your problem right there -- you have .git folders on your path. this means there are multiple versions of code on your path -- a very bad idea.
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sg-s
commented on August 30, 2024
i've seen this problem several times before -- you should never include a .git folder in your path. this is especially bad if you're using mex because caches aren't updated as frequently. i would do the following:
- remove everything from your path
- restart matlab
- add only what you need to to your path (make sure you don't choose "add subfolders")
there are install instructions here that should get you to a good place
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smbaca
commented on August 30, 2024
Yeah, this is really upside-down world at this point. I feel like there are some low level preferences that aren’t getting wiped. At this point I have reinstalled both MATLAB and Xcode and there are still weird errors relating to the path. Going to try on a different Mac because at this point it seems like I need to do a deep clean and or system re-install.
…-smb
On Jul 22, 2022, at 9:21 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
i've seen this problem several times before -- you should never include a .git folder in your path. this is especially bad if you're using mex because caches aren't updated as frequently. i would do the following:
remove everything from your path
restart matlab
add only what you need to to your path (make sure you don't choose "add subfolders")
there are install instructions here <https://xolotl.readthedocs.io/en/master/how-to/install-configure/#using-git> that should get you to a good place
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smbaca
commented on August 30, 2024
Ok, I see now that some all the regular folders need to be in the path. When I did that it looks like things are now up and running. There are a couple of conductances that failed but the rest are not showing OK.
Just in time for my vacation but at least I know I can work on the planned models when I return.
Thanks for all of the fast feedback. I am sure I will have more questions down the line.
-Serapio
BELOW are the only Warnings or errors I received when I ran xolotl.run_all_tests
Warning: Saving object of class 'parallel.FevalFuture' is not supported. Avoid storing objects of this
class in MAT files or sending them between MATLAB Sessions.
Starting worker #6
demo_manipulate
Warning: File 'test.m' not found.
In xolotl.testDocs (line 44)
In xolotl.run_all_tests (line 52)
… On Jul 22, 2022, at 9:21 PM, Srinivas Gorur-Shandilya ***@***.***> wrote:
i've seen this problem several times before -- you should never include a .git folder in your path. this is especially bad if you're using mex because caches aren't updated as frequently. i would do the following:
remove everything from your path
restart matlab
add only what you need to to your path (make sure you don't choose "add subfolders")
there are install instructions here <https://xolotl.readthedocs.io/en/master/how-to/install-configure/#using-git> that should get you to a good place
—
Reply to this email directly, view it on GitHub <#584 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAVXMEQZ2NZGGGIAT7MVPRLVVNCITANCNFSM54ASASQQ>.
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sg-s
commented on August 30, 2024
excellent, glad something is working!
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Related Issues (20)
- are there a whole bunch of useless includes? HOT 1
- synapse activation functions binaries being stored in the wrong place
- Is it possible to build a model without recompiling everything?
- xolotl.uninstall doesn't work when installed with a toolbox
- merge neuron-db into this HOT 1
- Can we re-architecture the entire thing to cut out cpplab? HOT 1
- Trouble building C++ code from matlab HOT 5
- New C++11 features may allow us to do away with much of the type heirarchy HOT 5
- Struggling with inhibitory synapses HOT 11
- Implementing dynamic clamp / real-time simulation HOT 2
- add rectifying electrical synapse
- there should exist infrastructure to pass vectors of data to compartments
- AlphaSynapse is broken (at least in some version) HOT 5
- demo page on docs shows colors in plot, which is not produced because defaults are changed HOT 1
- i can't test xolotl without the global optimization toolbox HOT 1
- testConductances not working on Windows 10 machine HOT 23
- xolotl needs a new release
- xolotl x.fit issue HOT 2
- add new course info
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