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[OpenFOAM plus] [v1606+] On Mac: "Error response from daemon: Mounts denied:"

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Old   December 8, 2016, 15:21
Default [OpenFOAM plus] [v1606+] On Mac: "Error response from daemon: Mounts denied:"
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Adam Dershowitz
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I have not been having any luck getting OpenFOAM to run with Docker for Mac. I just did a fresh install of Docker for Mac (this is no longer in beta).
$docker info shows that that docker is running.

Here is the first problem:
Code:
$docker-machine ssh default $HOME/installMacOpenFOAM+ $HOME
Host does not exist: "default"
Since, that wasn’t working, I decided to try following the linux instructions from the same page. That leads to more progress:

Code:
$./installMacOpenFOAM+ 
********************************************************* 
Following Docker containers are present on your system:
********************************************************* 
CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES
**************************************** 
            
Creating Docker OpenFOAM+ container of_v1606_plus
Unable to find image 'openfoamplus/of_v1606plus_centos66:latest' locally
latest: Pulling from openfoamplus/of_v1606plus_centos66
44c8556c2421: Pull complete 
Digest: sha256:f2520d671e93d5a692c42fef7a8b4caa8d0a2c39d540a13664a9c5ac0d414a32
Status: Downloaded newer image for openfoamplus/of_v1606plus_centos66:latest
238ace393942096a8aa85444385dd7088d761cf3a4d3383a7fc3f863485b122d
docker: Error response from daemon: Mounts denied: 
The path /etc/sudoers.d
is not shared from OS X and is not known to Docker.
You can configure shared paths from Docker -> Preferences... -> File Sharing.
See https://docs.docker.com/docker-for-m...fs/#namespaces for more info.
..
Container of_v1606_plus was created.
**************************************************
Run the ./startMacOpenFoam+  script to launch container
**************************************************
So it did download:

Code:
$ docker images
REPOSITORY                           TAG                 IMAGE ID            CREATED             SIZE
openfoamplus/of_v1606plus_centos66   latest              19ebf385cb00        5 months ago        2.297 GB
But, I still can’t then run it. It seems that there is a permissions issue:
Code:
$ ./startMacOpenFOAM+ 
Error response from daemon: Mounts denied: 
The path /etc/sudoers.d
is not shared from OS X and is not known to Docker.
You can configure shared paths from Docker -> Preferences... -> File Sharing.
See https://docs.docker.com/docker-for-m...fs/#namespaces for more info.
.
Error: failed to start containers: of_v1606_plus
You cannot attach to a stopped container, start it first
I did also try to add /etc to Docker->Preferences->File Sharing but it complains that “the path /etc is reserved by Docker”

Any guidance would be greatly appreciated.

--Adam

Last edited by wyldckat; December 27, 2016 at 12:24. Reason: Added [CODE][/CODE] markers
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Old   December 27, 2016, 12:42
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Quick answer: My guess is that the following description in the section "Frequently Asked Questions (FAQs)": http://www.openfoam.com/download/ins...y.php#x5-16000 - is related to the issue you're getting:
Quote:
If you receive an error message about not being able to contact the Docker daemon check that
  • the Docker daemon is started at boot time
  • the user account is in the group ‘docker’
Specially the user account having to be in the correct group.


On the other hand, have you tried following these instructions: https://docs.docker.com/engine/getst...r-installation - namely section "Step 3: Verify your installation"?
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Old   December 27, 2016, 16:39
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Pawan Ghildiyal
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Hi
With new docker-toolbox version in Mac, there is some issue . Either you can try to install previous version docker-toolbox i.e 1.12 or try new docker which run natively in Mac.
However it will require some different script . I will share these script tomorrow.

(Also you can try to uninstall all virtualbox and docker toolbox and then again reinstall all and run scripts. This is how it worked for some user as reported )

Thanks
Pawan
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Last edited by pgh; December 28, 2016 at 10:00.
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Old   December 30, 2016, 10:51
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nasir musa yakubu
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Hi,

I got openFOAM working on my mac yesterday using docker beta. however fot soem reason it stopped working today and i keep gettign the foloowing error message:


Quote:
nasirs-Mac-Pro:~ nasiryakubu$ ./startOpenFOAM+
non-network local connections being added to access control list
Error response from daemon: Mounts denied:
The path /etc/sudoers.d
is not shared from OS X and is not known to Docker.
You can configure shared paths from Docker -> Preferences... -> File Sharing.
See https://docs.docker.com/docker-for-m...fs/#namespaces for more info.
.
Error: failed to start containers: of_v1612_plus
Error response from daemon: Container 82f0d732a7b11838f1e3926595d173238c357f68ac26837613 50553521127f2e is not running
nasirs-Mac-Pro:~ nasiryakubu$
would appreciate some help on this.

will really appreciate your script.

Kind regards
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Old   January 4, 2017, 12:02
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Hi
With new release i.e OpenFOAM-v612+ , one can run openfoam using native docker i.e without using virtual box. Try the new docker and use script in the path and see whether it solve your problem
http://openfoam.com/download/install-binary-mac.php

Thanks
PGH
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Old   January 12, 2017, 22:58
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nasir musa yakubu
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Thanks for the response Pawan, for some reason I couldn't download those files new years eve. so I ended up suing the ubuntu version but now OpenFOAM is working. However, for some strange reason the su - password is not the same as my mac admin user password, which means I can't use yum install to make custom libraries.

I would appreciate some spill of know how on this issue.

Thanks
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Old   January 12, 2017, 23:46
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nasir musa yakubu
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all resolved now I did install the custom libraries using yum. however, I couldn't run the case as a root user for some reason.

thanks
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Old   January 13, 2017, 05:05
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Hi nasir
The files are uploaded afterwards i.e for mac . Are you using docker still or some unbuntu in virtual box ? Sorry this is not clear.
Also you cannot run mpi using root (it is not advisable . If you have to use then use some other argument with it . See error message and it will show what argument you need to add )

Thanks
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Old   January 13, 2017, 08:41
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nasir musa yakubu
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Hello Pawan,

this issue has now been resolved i am using the docker on Mac and found the details of the root log in in the installMacOpenfoam script.

however, I have tried to compile some custom scripts, i have used "wmake" and also tried using "yum install make". installation seems to complete but when i rum my openfoam case, it says it cannot read the custom libraries. i checked it seems like its been compiled just maybe in a different location.

please have a look at the outcome:

Code:
nasirs-Mac-Pro:~ nasiryakubu$ ./startMacOpenFOAM+ 
of_v1612_plus
[ofuser@23dd556b0781 ~]$ ls
OpenFOAM  workingDir
[ofuser@23dd556b0781 ~]$ cd OpenFOAM/
[ofuser@23dd556b0781 OpenFOAM]$ ls
ofuser-v1612+
[ofuser@23dd556b0781 OpenFOAM]$ cd ofuser-v1612+/
[ofuser@23dd556b0781 ofuser-v1612+]$ ls
platforms
[ofuser@23dd556b0781 ofuser-v1612+]$ cd platforms/
[ofuser@23dd556b0781 platforms]$ ls
linux64GccDPInt32Opt
[ofuser@23dd556b0781 platforms]$ cd linux64GccDPInt32Opt/
[ofuser@23dd556b0781 linux64GccDPInt32Opt]$ ls
bin  lib
[ofuser@23dd556b0781 linux64GccDPInt32Opt]$ cd bin/
[ofuser@23dd556b0781 bin]$ ls
polyDualMeshMod
[ofuser@23dd556b0781 bin]$ cd ..
[ofuser@23dd556b0781 linux64GccDPInt32Opt]$ cd lib/
[ofuser@23dd556b0781 lib]$ ls
libfieldFunctionObjectsMod.so
[ofuser@23dd556b0781 lib]$
Thank you very much

Kind regards
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Old   January 13, 2017, 10:18
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Hi ...
Ok I think i understand the issue . But to confirm first Can you go inside workingDir and do ls and post the output . This is for me to confirm ,

Thanks
Pawan
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Old   January 13, 2017, 10:20
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nasir musa yakubu
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Hi Pawan,

thanks for your response.

have a look

Applications Dropbox Public installMacOpenFOAM+
Applications (Parallels) Library chtMRF_bes_v4 polyDualMeshMod
Desktop Movies chtMRF_bes_v4.tar.gz polyDualMeshMod.tar.gz
Documents Music fieldFunctionObjectsMod startMacOpenFOAM+
Downloads Pictures fieldFunctionObjectsMod_v1612p.tar.gz untitled.geo.opt

kind request
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Old   January 13, 2017, 11:32
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Hi Nasir
Try following
1) Delete OpenFOAM directory i.e in your home area . One which is in parallel to workingDir
2) Now go inside workingDir and create a OpenFOAM directory .
3) Go one directory up i.e above workingDir
and make symbolic link
ln -s workingDir/OpenFOAM OpenFOAM

Now compile your application and try to run your case. Let me know if it works

Thanks
Pawan
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Old   January 13, 2017, 11:56
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nasir musa yakubu
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Hello Pawan,

Thank you very much for your prompt reply. however, I am new to docker and for some reason, I cannot even locate the folder that stores those directors. I only see them when I run ./startMacOpenFoam+ and using the ofuser profile.

also, i don't know what codes to use when trying to delete the OpenFOAM directory.

i tried rm -OpenFOAM but it doesn't work either

I would appreciate some guidance on this.

Thanks
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Old   January 13, 2017, 12:39
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Hi Nasir
Let's get a brief about working of openfoam in Mac using docker
There is image i.e centos image which has OpenFOAM and ofuser in it which docker support in Mac . Now inside docker based centos image , the environment is same as linux . Now we have mounted your user directory i.e your home area to workingDir.
Now to access OpenFOAM inside this image, we need to create and run container.

1. when you run startMacOpenFOAM+ script , it start container and login as ofuser .
2. if you run command ls , then you can see folder i.e in your case as
workingDir OpenFOAM
3. run rm -rf OpenFOAM
4 cd workingDir
5. mkdir OpenFOAM
6. cd /home/ofuser
7. ln -s workingDir/OpenFOAM OpenFOAM

I hope i answered your queries
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Old   January 13, 2017, 17:55
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Hello Pawan,

Thank you very much, I think it works now but I am not able to run the simulation yet. Thanks for your help. I am trying to compile the "libfiniteVolumeCustomFields.so" however it's giving me 1 error message but can't figure out what the error message is. Fortunately it works perfectly on ubuntu 1604 openfoam v1612+ And v4.0.x.

Kind regards
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Old   January 14, 2017, 05:59
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ok.. It will be good if you can send error message .
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Old   January 14, 2017, 07:49
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Hello Pawan,

Thank you very much for your reply.

when i run:

Quote:
wmake libso,
i get the following:

Quote:
mkdir: cannot create directory `/home/ofuser/OpenFOAM': File exists
make: *** [/home/ofuser/OpenFOAM/ofuser-v1612+/platforms/linux64GccDPInt32Opt/lib/libfiniteVolumeCustomFields.so] Error 1
[ofuser@23dd556b0781 finiteVolumeCustomFields4x]$
however, as a root user i end up with the following:


Quote:
[root@23dd556b0781 finiteVolumeCustomFields4x]# wclean libso
wclean libso .
[root@23dd556b0781 finiteVolumeCustomFields4x]# wmake libso
wmake libso .
/opt/OpenFOAM/ThirdParty-v1612+/platforms/linux64/gcc-4.8.5/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.8.5/cc1: error while loading shared libraries: libmpc.so.3: cannot open shared object file: No such file or directory
/opt/OpenFOAM/ThirdParty-v1612+/platforms/linux64/gcc-4.8.5/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.8.5/cc1: error while loading shared libraries: libmpc.so.3: cannot open shared object file: No such file or directory
make: *** [Make/linux64GccDPInt32Opt/sourceFiles] Error 1
wmake error: file 'Make/linux64GccDPInt32Opt/sourceFiles' could not be created in /home/ofuser/workingDir/finiteVolumeCustomFields4x
[root@23dd556b0781 finiteVolumeCustomFields4x]# cd
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