aligned_alloc in gcc@7 but not in Mojave

[rmspencer]

I have been running my code for years on macOS and gcc@7 from homebrew. When I updated gcc@7 for Mojave, by run-time asks for a function that it depends on the OS having, but it doesn't where it is looking for it. Why is the gcc@7 build asking for it now when it didn't previously? Can I get another formula that doesn't? I tried building at lower C++ standards but that doesn't help. I have seen that this is a common lament for many years, so why wasn't it avoided or remedied? My main code is not calling it, but maybe something in anaconda is. Thanks for any suggestions.

ImportError: dlopen(/Users/rspencer/Applications/CompuCell3D_3.7.4/CC3D_INSTALL/lib/python/_CC3DXML.so, 2): Symbol not found: _aligned_alloc
Referenced from: /usr/local/opt/gcc@7/lib/gcc/7/libstdc++.6.dylib (which was built for Mac OS X 10.14)
Expected in: /usr/lib/libSystem.B.dylib
in /usr/local/opt/gcc@7/lib/gcc/7/libstdc++.6.dylib

[carlocab]

Does this path exist on your system?

/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk

[rmspencer]

Yes (base) iMac-Pro:~ rspencer$ ls /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk Entitlements.plist SDKSettings.json System Library SDKSettings.plist usr In my cmake file though, it auto-inserted: CMAKE_OSX_DEPLOYMENT_TARGET 10.14 CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk I think installing gfortran from hpc.sourceforge may have hammered something in gcc. Or there are just some changes in builds with Mojave. I removed that as best as I could, but they warn to try this also: “And on Catalina, you may have to specify an additional include and library path -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib for the compiler to find the system headers and libraries.” Is that what you may be recommending? I am staying on Mojave because I am not sure of OpenCL support on Catalina yet. Thanks so much Richard

…

-- Richard Spencer Computational Biologist T 919.541.0022 | M 919.306.9098 ***@***.******@***.***> 109 T.W. Alexander Dr. Research Triangle Park, NC 27711 www.gdit.com<http://www.gdit.com/> ***@***.***D4EE0A.A8F66270] From: Carlo Cabrera ***@***.***> Date: Sunday, April 11, 2021 at 3:26 PM To: Homebrew/discussions ***@***.***> Cc: Spencer, Richard ***@***.***>, Author ***@***.***> Subject: Re: [Homebrew/discussions] aligned_alloc in ***@***.*** but not in Mojave (#1256) Does this path exist on your system? /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgh.neting.cc%2FHomebrew%2Fdiscussions%2Fdiscussions%2F1256%23discussioncomment-597051&data=04%7C01%7CSpencer.Richard%40epa.gov%7C64542688f9b7466612f808d8fd1fa812%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637537660016768188%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=RfbBZlT0srxC4o%2FOUMqrUBgLEF5YrfXBm%2Fvd2OEysn0%3D&reserved=0>, or unsubscribe<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgh.neting.cc%2Fnotifications%2Funsubscribe-auth%2FADKXDKR7G7WDQHUCWLKTLY3TIHZUXANCNFSM42X3DCEA&data=04%7C01%7CSpencer.Richard%40epa.gov%7C64542688f9b7466612f808d8fd1fa812%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637537660016778147%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=E2t8Hvio6Wu9aGZowHP1ey24vuVUubQfDHxwh7HiF%2Bs%3D&reserved=0>.

[carlocab]

This will hopefully be fixed by a rebuild of gcc@7, which was done in this PR (for incidental reasons). Please try brew update && brew upgrade gcc@7 then try again.

In my cmake file though, it auto-inserted:
CMAKE_OSX_DEPLOYMENT_TARGET 10.14
CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk

That doesn't look right. You want CMAKE_OSX_SYSROOT to be /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk.

I think installing gfortran from hpc.sourceforge may have hammered something in gcc.

The gcc@7 formula also provides gfortran, though it might be called something like gfortran-7 instead. I think you'll want to use that to ensure version compatibility.

but they warn to try this also:
“And on Catalina, you may have to specify an additional include and library path -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib for the compiler to find the system headers and libraries.”

Something similar might help, but, as above, you actually want to use

/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk

rather than an unversioned path. The unversioned path likely points to the headers and libraries (library stubs, actually) for macOS 10.15, which will define an aligned_alloc function but isn't supported on Mojave.

[rmspencer]

(cc3d_macos_10.13) iMac-Pro:CC3D_BUILD rspencer$ brew update && brew upgrade ***@***.*** Updated 2 taps (homebrew/core and homebrew/cask). ==> New Formulae dua-cli ==> Updated Formulae ***@***.*** ✔ ***@***.*** ✔ ***@***.*** ✔ bind cimg dbdeployer file-roller ***@***.*** libserdes mlt monero navi serverless sphinx-doc stunnel v2ray wxmaxima ==> Updated Casks koodo-reader latexit monero-wallet tunnelblick webcatalog You have 3 outdated formulae installed. You can upgrade them with brew upgrade or list them with brew outdated. ==> Upgrading 1 outdated package: ***@***.*** 7.5.0_3 -> 7.5.0_4 ==> Upgrading ***@***.*** 7.5.0_3 -> 7.5.0_4 ==> Downloading https://homebrew.bintray.com/bottles/gcc%407-7.5.0_4.mojave.bottle.tar.gz ==> Downloading from https://d29vzk4ow07wi7.cloudfront.net/95659aa77c264356df8c2eb9d24800aba62f0d308b86d601e0d259885700aebf?response-content-disposition=attachment%3Bfilename%3D%22gcc%407-7.5.0_4.mojave.bottle.tar.gz%22&Policy=eyJTdGF0ZW1lbnQiOiBbeyJSZXNvdXJjZSI6Imh0dHAqOi8vZDI5dnprNG93MDd3a ######################################################################## 100.0% ==> Pouring ***@***.***_4.mojave.bottle.tar.gz 🍺 ***@***.***/7.5.0_4: 1,404 files, 254.4MB Removing: ***@***.***/7.5.0_3... (1,402 files, 249.5MB) But interestingly, surprisingly, CommandTools looks ahead and routes it like this too. I can’t choose MacOSX.sdk\ 1 because CMake changes backslashes to forward slashes and doesn’t recognize the space if not escaped. (base) iMac-Pro:~ rspencer$ ls -al /Library/Developer/CommandLineTools/SDKs total 0 drwxr-xr-x 6 root wheel 192 Apr 11 08:12 . drwxr-xr-x 5 root admin 160 Apr 9 19:25 .. lrwxr-xr-x 1 root wheel 15 Apr 11 08:12 MacOSX.sdk -> MacOSX10.15.sdk drwxr-xr-x 7 root wheel 224 Apr 9 19:25 MacOSX.sdk 1 lrwxr-xr-x 1 root wheel 10 Nov 10 16:07 MacOSX10.14.sdk -> MacOSX.sdk drwxr-xr-x 8 root wheel 256 Apr 11 08:12 MacOSX10.15.sdk (base) iMac-Pro:~ rspencer$ ls -alt /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/ total 0 drwxr-xr-x 5 rspencer staff 160 Nov 10 17:09 . lrwxr-xr-x 1 rspencer staff 10 Nov 10 17:08 MacOSX10.15.sdk -> MacOSX.sdk drwxr-xr-x 6 rspencer staff 192 Dec 19 2019 .. drwxr-xr-x 4 rspencer staff 128 Nov 7 2019 DriverKit19.0.sdk drwxr-xr-x 8 rspencer staff 256 Nov 7 2019 MacOSX.sdk Then I get an OpenCL error I wasn’t getting with the Xcode.app Frameworks. /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/dispatch/queue.h:926:3: error: 'dispatch_qos_class_t' has not been declared dispatch_qos_class_t qos_class, int relative_priority); ^~~~~~~~~~~~~~~~~~~~ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/dispatch/queue.h:1109:1: error: 'dispatch_qos_class_t' does not name a type; did you mean 'dispatch_queue_attr_t'? dispatch_qos_class_t ^~~~~~~~~~~~~~~~~~~~ dispatch_queue_attr_t Now I am confused that I get it here too, but that is probably a different thread unrelated to homebrew. /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/dispatch/queue.h:926:3: error: 'dispatch_qos_class_t' has not been declared dispatch_qos_class_t qos_class, int relative_priority); ^~~~~~~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/dispatch/queue.h:1109:1: error: 'dispatch_qos_class_t' does not name a type; did you mean 'dispatch_queue_attr_t'? dispatch_qos_class_t ^~~~~~~~~~~~~~~~~~~~ dispatch_queue_attr_t I will try to get back to the original error which I thought was coming from the ***@***.*** library, but granted CommandTools should provide it. With kind regards -- Richard Spencer Computational Biologist From: Carlo Cabrera ***@***.***> Date: Sunday, April 11, 2021 at 6:08 PM To: Homebrew/discussions ***@***.***> Cc: Spencer, Richard ***@***.***>, Author ***@***.***> Subject: Re: [Homebrew/discussions] aligned_alloc in ***@***.*** but not in Mojave (#1256) This will hopefully be fixed by a rebuild of ***@***.***, which was done in this PR<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgh.neting.cc%2FHomebrew%2Fhomebrew-core%2Fpull%2F74930&data=04%7C01%7CSpencer.Richard%40epa.gov%7Cd40dd7c52d31456d3a4508d8fd365258%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637537757040560683%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=FIcOfzGaCQ%2BN5rnXgz%2Bh2bVsLlj2X1KqiUr0HXCARkE%3D&reserved=0> (for incidental reasons). Please try brew update && brew upgrade ***@***.*** then try again. In my cmake file though, it auto-inserted: CMAKE_OSX_DEPLOYMENT_TARGET 10.14 CMAKE_OSX_SYSROOT >/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk That doesn't look right. You want CMAKE_OSX_SYSROOT to be /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk. I think installing gfortran from hpc.sourceforge may have hammered something in gcc. The ***@***.*** formula also provides gfortran, though it might be called something like gfortran-7 instead. I think you'll want to use that instead to ensure version compatibility. but they warn to try this also: “And on Catalina, you may have to specify an additional include and library path -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib for the compiler to find the system headers and libraries.” Something similar might help, but, as above, you actually want to use /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk rather than an unversioned path. The unversioned path likely points to the headers and libraries (library stubs, actually) for macOS 10.15, which will define an aligned_alloc function but isn't supported on Mojave. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgh.neting.cc%2FHomebrew%2Fdiscussions%2Fdiscussions%2F1256%23discussioncomment-597351&data=04%7C01%7CSpencer.Richard%40epa.gov%7Cd40dd7c52d31456d3a4508d8fd365258%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637537757040570634%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=5IaMCKnIM0IrJkdezclwM5VIkd4eo69NO11hyYHfA80%3D&reserved=0>, or unsubscribe<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgh.neting.cc%2Fnotifications%2Funsubscribe-auth%2FADKXDKUUDCOH7POMPIPOBV3TIIMVFANCNFSM42X3DCEA&data=04%7C01%7CSpencer.Richard%40epa.gov%7Cd40dd7c52d31456d3a4508d8fd365258%7C88b378b367484867acf976aacbeca6a7%7C0%7C0%7C637537757040570634%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=%2FXI2ZVSR5NP4pD0d9s3CLtR3eko%2BD%2BrWtV5ntKxVnD0%3D&reserved=0>.

[rmspencer]

Actually, the OpenCL error is emitted by gcc. There is a 2015 solution to create a second object.h that gcc can read. But has it been fixed in gcc since then but forgotten? Thanks again.

andrewgho/movewin-ruby#1

[Bo98]

A working CLT install looks like this:

$ ls -al /Library/Developer/CommandLineTools/SDKs
total 0
drwxr-xr-x 5 root wheel 160 Feb  7 03:22 .
drwxr-xr-x 5 root admin 160 Apr 20  2020 ..
lrwxr-xr-x 1 root wheel  15 Feb  2 16:38 MacOSX.sdk -> MacOSX10.15.sdk
drwxr-xr-x 7 root wheel 224 Feb  2 16:38 MacOSX10.14.sdk
drwxr-xr-x 8 root wheel 256 Feb  2 16:39 MacOSX10.15.sdk

Note that simply running the installer again will not fix it. You need to actually delete /Library/Developer/CommandLineTools entirely and run the installer again.

[carlocab]

Ah, yes. I should've suspected that from the aligned_alloc failure, but it's been a while. Good catch, Bo.

@rmspencer you need to do

sudo rm -rf /Library/Developer/CommandLineTools

and reinstall the Command Line Tools.

[rmspencer]

Bo98. You are right! I deleted CommandTools and reinstalled it again. I did not have the MacOSX10.14.sdk before. I don't know why the install, and reinstall, did not do that before. Something in the package script. Now I do:

(base) iMac-Pro:CC3D_INSTALL rspencer$ ls -alt /Library/Developer/CommandLineTools/SDKs/
total 0
drwxr-xr-x 5 root wheel 160 Apr 13 14:00 .
lrwxr-xr-x 1 root wheel 15 Apr 13 14:00 MacOSX.sdk -> MacOSX10.15.sdk
drwxr-xr-x 5 root wheel 160 Apr 13 13:59 ..
drwxr-xr-x 8 root wheel 256 Nov 7 2019 MacOSX10.15.sdk
drwxr-xr-x 7 root wheel 224 Aug 27 2019 MacOSX10.14.sdk

I will try my rebuild soon.

[rmspencer]

OK. Great. Erasing CommandLineTools completely and reinstalling fixed the build problem and your latest gcc@7 build probably was part of the original error fix after I rebuilt the first time. My overwriting something important with the hpc.sourceforge version of gfortran probably broke my original run-time. I used brew doctor to clean that out I hope.

I am back in business for 10.14. I don't know if I want to rush going to 10.15 until forced to, especially for OpenCL.

Thanks very much. I was stuck before asking for help on this forum.

[carlocab]

Glad it's working for you.

Note that you don't need gfortran from hpc.sourceforge -- gcc@7 (and all the other gcc formulae) all come with gfortran.