deal stopped working with latest macOS update (10.15)

[Ester Comellas]

Hi,

I'm pretty new to macOS and updated the system when prompted to do so, and several software stopped working! Among them, deal.ii. I tried reinstalling CMake, Xcode and deal.ii, but can't get it to work. Xcode and CMake seem to be working fine. Deal.ii appears to be installed correctly but, when I try to open it, a system window pops up saying deal.II.app couldn't be opened. Any ideas on what may be wrong and how I can fix this? I'm on macOS Catalina Version 10.15.

Thanks,

Ester

[luca.heltai]

Dear Ester,

please take a look at the release page:

https://github.com/dealii/dealii/releases/tag/v9.1.1

There is a package for Mac OS Catalina. In Catalina, permissions are much more restrictive, and you’ll have to explicitly enable the application to run (the first time), by right clicking on it, and selecting “open” (which pops up a dialog asking if you are sure about opening the app, and giving you some instruction on how to allow deal.II to run on your system.

L.

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[Alberto Salvadori]

Dear community,

Luca in particular

I have installed the package for Mac OS Catalina that was pointed out. 

In running the examples I noticed some unexpected errors

Illegal instruction: 4

See below.

Needless to say, the very same error comes out in running my own code.

Any help is appreciated

Perhaps you may also address me on this: when running my old deal.ii 8.5.1 version, it does not work anymore.

The application just does not open and if I attempt at running via command line, I get this:

/Applications/deal.II-8.5.1.app/Contents/Resources/opt/openmpi-1.10.2/bin/mpirun -np 4 ./m4_code ../input/SE_trivial_battery_m

dyld: Library not loaded: /Applications/deal.II.app/Contents/Resources/opt/openmpi-1.10.2/lib/libopen-rte.12.dylib

  Referenced from: /Applications/deal.II-8.5.1.app/Contents/Resources/opt/openmpi-1.10.2/bin/mpirun

  Reason: image not found

Abort trap: 6

tests-MacBook-Pro:Release albertosalvadori$ 

Any suggestions on how to sort this issue out?

Thank you,

Alberto

---

bash-3.2$ which cmake 

/Applications/deal.II.app/Contents/Resources/Libraries/bin/cmake

bash-3.2$ cmake -G 'Unix Makefiles' .

-- The C compiler identification is AppleClang 11.0.0.11000033

-- The CXX compiler identification is AppleClang 11.0.0.11000033

-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc

-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Detecting C compile features

-- Detecting C compile features - done

-- Check for working CXX compiler: /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-haswell/clang-11.0.0-apple/openmpi-3.1.4-qcsz2fblznqlgt3j4u7dctfjag4kapar/bin/mpic++

-- Check for working CXX compiler: /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-haswell/clang-11.0.0-apple/openmpi-3.1.4-qcsz2fblznqlgt3j4u7dctfjag4kapar/bin/mpic++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Autopilot invoked

###

#

#  Project  step-20  set up with  deal.II-9.1.1  found at

#      /Applications/deal.II.app/Contents/Resources/Libraries

#

#  CMAKE_BUILD_TYPE:          Debug

#

#  You can now run

#       $ make                - to compile and link the program

#       $ make run            - to (compile, link and) run the program

#

#       $ make sign           - to sign the executable with the supplied OSX developer key

#

#       $ make debug          - to switch the build type to 'Debug'

#       $ make release        - to switch the build type to 'Release'

#

#       $ make edit_cache     - to change (cached) configuration variables

#                               and rerun the configure and generate phases of CMake

#

#       $ make strip_comments - to strip the source files in this

#                               directory off their comments; this is irreversible

#       $ make clean          - to remove the generated executable as well as

#                               all intermediate compilation files

#       $ make runclean       - to remove all output generated by the program

#       $ make distclean      - to clean the directory from _all_ generated

#                               files (includes clean, runclean and the removal

#                               of the generated build system)

#       $ make info           - to view this message again

#

#  Have a nice day!

#

###

-- Configuring done

-- Generating done

-- Build files have been written to: /Users/albertosalvadori/Codes/dealii-9.1.1/deal.II/examples/step-20

bash-3.2$ make release

Scanning dependencies of target release

[100%] Switching CMAKE_BUILD_TYPE to Release

-- Autopilot invoked

-- Run   $ make info  to print a detailed help message

-- Configuring done

-- Generating done

-- Build files have been written to: /Users/albertosalvadori/Codes/dealii-9.1.1/deal.II/examples/step-20

***

*** Switched to Release mode. Now recompile with:  $ make

***

[100%] Built target release

bash-3.2$ make

Scanning dependencies of target step-20

[ 50%] Building CXX object CMakeFiles/step-20.dir/step-20.cc.o

[100%] Linking CXX executable step-20

[100%] Built target step-20

bash-3.2$ ./step-20 

Illegal instruction: 4

Alberto Salvadori
 Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/CB27B768-395C-4148-A540-C2886D241A06%40gmail.com.

Informativa sulla Privacy: http://www.unibs.it/node/8155

[luca.heltai]

I have not updated to the latest version yet. They changed clang, xcode, and a few other things. I’m assuming that the package I built on catalina is no longer functional.

I’ll get to it as quickly as I can.

In the mean time, can you try to see if you can install deal.II using spack?

L.

> To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/CABcATpd7eSGU6Fg%2Bx6RSGMUjdDNW32d-FCKRC%3DChxLqmqqzCuA%40mail.gmail.com.

[Ester Comellas]

Hi,

I got deal.II-9.1.1 to work on macOS Catalina using the link Luca provided. I'm running my parallel code using mpirun and everything works smoothly.

I don't recall the details, but I remember having some issues with XCode during the installation. I thought it had automatically updated correctly, but on closer inspection there was an error message (nothing an online search couldn't solve).

Ester

El dimarts, 3 desembre de 2019 11:08:57 UTC-5, luca.heltai va escriure:

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[Ester Comellas]

I'm also able to run step-20 succesfully, both in debug and release modes.

El dimarts, 3 desembre de 2019 11:33:40 UTC-5, Ester Comellas va escriure:

[Alberto Salvadori]

This is good, perhaps you can address how did you solved the issue. 

I honestly have not done anything fancy: 

1 - downloaded dealii-9.1.1-catalina-haswell-ro.dmg.zip
2 - drag and drop into applications

3 - open the deal.ii.app 

4 - the outcome in attachment.

I am using Xcode Version 11.2.1 (11B500), and macOS Catalina 10.15

Thank you!

[Ester Comellas]

Alberto,

I'm not sure what's the problem in your case. I can only tell you that, like you, I'm using macOS Catalina 10.15.1 and XCode 11.2.1 (11B500). I followed the instructions given here:

https://github.com/dealii/dealii/wiki/MacOSX

So, in addition to your steps 1-3, I also set up my bash profile as instructed in step 5. Also, not sure if it's relevant, but I'm using cmake version 3.15.3. 

I attach a screenshoot of my terminal showing a successful run of step-20.

Sorry I can't be of more help.

Ester

El dijous, 5 desembre de 2019 10:56:01 UTC-5, Alberto Salvadori va escriure:

[luca.heltai]

Alberto,

do you have 10.15.1, or 10.15? Did you also update XCode?

I’m currently building everything from scratch for 10.15.1, with XCode 11.2.1. This may be the issue.

I hope I’ll have a new package by tonight.

Best,
Luca.

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> <Screen Shot 2019-12-05 at 4.39.17 PM.png>

[luca.heltai]

Alberto,

this may be related to different hardware and different optimisation configurations.

What’s the output of:

spack arch

for you, in the deal.II terminal?

I get:

darwin-catalina-haswell

If you get something different, then maybe the problem is there. I don’t have a more recent mac (yet). It should arrive shortly, and then I should be able to fix it also for you, I think.

My initial suggestion still stands. I create the package using simply “spack install dealii”. Try the following (in your dealii terminal):

cd $SPACK_ROOT
# git pull origin develop # Optional, if you want the latest versions of all libraries
spack install dea...@9.1.1

This will take some time, but should succeed.

Luca.


> On 5 Dec 2019, at 16:56, Alberto Salvadori <alberto....@unibs.it> wrote:
>

[Alberto Salvadori]

Hi Luca

many thanks. I got this:

bash-3.2$ spack arch

shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted

shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted

shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted

shell-init: error retrieving current directory: getcwd: cannot access parent directories: Operation not permitted

darwin-catalina-ivybridge

Thank you, I will do as you suggest.

Alberto

Alberto Salvadori
 Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/597049E3-A96B-4F00-86AA-30192998D584%40gmail.com.

[luca.heltai]

Dear Alberto,

I’ve just finished uploading a new image:

https://github.com/dealii/dealii/releases/download/v9.1.1/dealii-9.1.1-clang-9.0.0.dmg

This one is built with clang-9.0.0 (embedded in the image), and mpich. It is still a temporary image, because symengine could not be installed (www.mpfr.org is down, and symengine depends on it), and neither could netcdf.

Can you see if this image works for you?

The examples are in the path

/Applications/deal.II.app/Contents/Resources/Libraries/share/deal.II/examples

I quickly checked step-40, and it compiled and run fine.

L.

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[Alberto Salvadori]

It works very well. Thank you so much, Luca.

Alberto

Alberto Salvadori
 Dipartimento di Ingegneria Meccanica e Industriale (DIMI)
 Universita` di Brescia, via Branze 43, 25123 Brescia
 Italy
 tel 030 3711239
 fax 030 3711312

e-mail:
 alberto....@unibs.it
web-page:
 http://m4lab.unibs.it/faculty.html

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/67CEBECC-D97A-4467-B4D6-660ACA2492F3%40gmail.com.