dealii installation Mac OS 10.15.5 (Catalina)

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Deepak Kukrety

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Jun 22, 2020, 7:05:06 PM6/22/20
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Dear All, 

I recently updated deal ii, but I am unable to run the programs. The main problem appears as a set of warnings when starting to "make": 


I tried to make run, despite these warnings and get the following errors: 


bash-3.2$ make run 

[ 66%] Built target step-1

Scanning dependencies of target run

[100%] Run step-1 with Debug configuration

dyld: malformed mach-o: load commands size (33848) > 32768

make[3]: *** [CMakeFiles/run] Abort trap: 6

make[2]: *** [CMakeFiles/run.dir/all] Error 2

make[1]: *** [CMakeFiles/run.dir/rule] Error 2

make: *** [run] Error 2



I have tried re-installing, going back to an older version of make, but I seem stuck with this problem. 


Any help will be highly appreciated. 


Regards 

Deepak






David Wells

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Jun 23, 2020, 11:30:53 AM6/23/20
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Hi Deepak,

This is a known issue with the current version of the mac bundle - it doesn't work with Catalina. We are in the process of fixing this. For now, unfortunately, you will have to either use an older version of deal.II or compile it yourself.

Sorry,
David

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Deepak Kukrety

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Jun 24, 2020, 1:19:38 AM6/24/20
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Hi David, 

Thanks for confirming this. On a related note, may I ask which earlier version could be a safe bet to install? 

I don't understand the Mac OS or Linux environment too well, so please excuse me for asking - but when you say "compile yourself"  - what do you mean? and is there a documented "procedure" for compiling that I can follow? 

Regards 
Deepak




On Tuesday, 23 June 2020 23:30:53 UTC+8, David Wells wrote:
Hi Deepak,

This is a known issue with the current version of the mac bundle - it doesn't work with Catalina. We are in the process of fixing this. For now, unfortunately, you will have to either use an older version of deal.II or compile it yourself.

Sorry,
David

On Mon, Jun 22, 2020 at 7:05 PM Deepak Kukrety <deepak...@gmail.com> wrote:
Dear All, 

I recently updated deal ii, but I am unable to run the programs. The main problem appears as a set of warnings when starting to "make": 

ld: warning: directory not found for option '-L/Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/zlib-1.2.11-rqiqrujgg5aemhk7eqjk3asbaukff'

ld: warning: directory not found for option '-L/Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-x86_64/clang-11.0.3-apple/dealii-develop-rrf4rjxvntgbw2l44kbr6aoa4xnr4gsb/lib'


I tried to make run, despite these warnings and get the following errors: 


bash-3.2$ make run 

[ 66%] Built target step-1

Scanning dependencies of target run

[100%] Run step-1 with Debug configuration

dyld: malformed mach-o: load commands size (33848) > 32768

make[3]: *** [CMakeFiles/run] Abort trap: 6

make[2]: *** [CMakeFiles/run.dir/all] Error 2

make[1]: *** [CMakeFiles/run.dir/rule] Error 2

make: *** [run] Error 2



I have tried re-installing, going back to an older version of make, but I seem stuck with this problem. 


Any help will be highly appreciated. 


Regards 

Deepak






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David Wells

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Jun 25, 2020, 12:16:52 PM6/25/20
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Hi Deepak,

I think that we have now fixed our Mac packages, so at the moment I think the best answer would be to download the new version of the mac bundle for deal.II from our GitHub release page. I had exactly the same error as you did with the older version of the mac bundle and the new version fixed it for me, so I am optimistic that it will work for you too.

> I don't understand the Mac OS or Linux environment too well, so please excuse me for asking - but when you say "compile yourself"  - what do you mean? and is there a documented "procedure" for compiling that I can follow?

This is a completely reasonable question :) I meant that you should download the source code, configure your local copy for your machine, compile it, and install it. We have detailed instructions on how to do this on the web site:


Do you see what to do? Please post again if you still have questions.

Best,
David

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Deepak Kukrety

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Jun 27, 2020, 8:35:00 AM6/27/20
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Thanks for your reply, David. 

I reverted to 9.1.0 for the time being and it's working. I am intending to finish some coding assignments after which I intend to try and update to the latest version of deal.ii. This time, I will try to compile it from source code and will reach out again, if I run into problems. 

Regards 
Deepak


On Friday, 26 June 2020 00:16:52 UTC+8, David Wells wrote:
Hi Deepak,

I think that we have now fixed our Mac packages, so at the moment I think the best answer would be to download the new version of the mac bundle for deal.II from our GitHub release page. I had exactly the same error as you did with the older version of the mac bundle and the new version fixed it for me, so I am optimistic that it will work for you too.

> I don't understand the Mac OS or Linux environment too well, so please excuse me for asking - but when you say "compile yourself"  - what do you mean? and is there a documented "procedure" for compiling that I can follow?

This is a completely reasonable question :) I meant that you should download the source code, configure your local copy for your machine, compile it, and install it. We have detailed instructions on how to do this on the web site:


Do you see what to do? Please post again if you still have questions.

Best,
David

Deepak Kukrety

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Dec 5, 2020, 8:00:49 AM12/5/20
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Hi David,

Hope you are doing good. I recently changed my computer and tried to install deal ii. Installation seems OK, but I can't seem to execute the codes. Please see below the error message for step-1. Can you guide me to fix this:


Thanks in advance for your help. 
Regards 
Deepak 

On 27 Jun 2020, at 8:35 PM, Deepak Kukrety <deepak....@gmail.com> wrote:


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Wells, David

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Dec 7, 2020, 2:34:06 PM12/7/20
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Hi Deepak,

What version of the mac bundle are you using? We recently released a new version named

dealii-9.2.0-v3.dmg

which should resolve this problem (it is known to work with other Catalina installations). Is this the version you downloaded?

Best,
David
From: dea...@googlegroups.com <dea...@googlegroups.com> on behalf of Deepak Kukrety <deepak....@gmail.com>
Sent: Saturday, December 5, 2020 8:00 AM
To: dea...@googlegroups.com <dea...@googlegroups.com>
Subject: Re: [deal.II] dealii installation Mac OS 10.15.5 (Catalina)
 
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Deepak Kukrety

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Dec 8, 2020, 8:53:20 AM12/8/20
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Hi David

 

Yes, I am using this version but I changed my computer which is now a mac mini with apple M1 chip and Big Sur as OS. I wonder if there may be hardware computability issues with new M1 based mac or with latest OS.

 

Appreciate your help to resolve.

 

Regards

Deepak

Wells, David

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Dec 8, 2020, 9:04:10 AM12/8/20
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Hi Deepak,

You may be the first person to ever run deal.II on the new M1 Mac, congratulations :)

I don't have an M1 machine so I will have to make some educated guesses on how to fix this. Executing the mac bundle directly won't work since its compiled for a different architecture. Executing it with rosetta2 should work, but I don't know precisely how to do this: Something like

rosetta2 ./step-1

Might work. Can you give that a try?

Best,
David
Sent: Tuesday, December 8, 2020 8:52 AM

Praveen C

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Dec 8, 2020, 9:10:06 AM12/8/20
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I think this should work

arch -x86_64 ./step-1

Deepak Kukrety

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Dec 8, 2020, 6:54:50 PM12/8/20
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Dear Praveen & David,

 

Thanks but I may need little more direction in trying to make this run. I deeply appreciate your help.

 

Regards

Deepak

 

 

From: "dea...@googlegroups.com" <dea...@googlegroups.com> on behalf of Praveen C <cpra...@gmail.com>
Reply to: "dea...@googlegroups.com" <dea...@googlegroups.com>
Date: Tuesday, 8 December 2020 at 10:10 PM
To: "Deal. II Googlegroup" <dea...@googlegroups.com>
Subject: Re: [deal.II] dealii installation Mac OS 10.15.5 (Catalina)

 

I think this should work

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thodo...@gmail.com

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Dec 21, 2020, 11:26:34 AM12/21/20
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Dear all 

I have downloaded deal.II.9.2.0-v3.dmg and installed on MacBook Pro (Catalina, Xcode 12.3). In terminal I use : module load dealii and everything went well. 

Initially there was a problem with the compiler path in the CMakeCache.txt which I fixed it. Then when I tried to compile and run my code I received the following message 

dyld: Library not loaded: @rpath/libmuelu-adapters.13.dylib

Reason: image not found

The folder /Applications/deal.II.app/Contents/Resources/Libraries/lib is on my $DYLD_LIBRARY_PATH so I was wondering what is happening ?
Any suggestions?

Many Thanks

Thodoros
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