[Mesa-users] Error while installing old version of mesa

Falk Herwig fherwig at uvic.ca
Wed Aug 17 18:00:37 UTC 2022 

It does not say anywhere in the instructions that you should set MESA_DIR environment variable. These are set inside the Docker already. When you are in the Docker at there terminal prompt it is as if you are on a different computer. Do `ls` and see `mesa` and `mesa_sdk` dir. Just follow the instructions. It say `cd mesa` and then build the code, that’s it. 

Since you have messed with the environment variable you will have to reset them to the defaults, like
user at mesa-r9575:~/mesa$ source ~/.bash_aliases 

Or you stop and remove he Docker container and then just do:

atlas:NuDocker $ ./bin/start_and_login.sh mesa-r9575 nugrid/nudome:16.0 /your/path/to/where/your/mesa/mesa-r9575
user at mesa-r9575:~$ ls    
mesa  mesasdk
user at mesa-r9575:~$ cd mesa
user at mesa-r9575:~/mesa$ ./install


Note that whatever YOUR dir /your/path/to/where/your/mesa/mesa-r9575
Is will appear inside the Docker container as ~/mesa

Unless you mount additional host folders you will not have any further access to anything on the host machine.

F

> On Aug 17, 2022, at 1:36 AM, ABHIJNAN KAR 20064 <abhijnank20 at iiserbpr.ac.in> wrote:
> 
> Hi,
> My docker is working but the problem is somehow it is now giving bash shell and i can’t install MESA as the last step of mesa installation is giving error.Also when i enter cd Mesa or cd binary it is not working too.Can you please help it?I mailed you the commands in previous mails.It would be extremely helpful if you could do it.
> 
>> On 16-Aug-2022, at 2:36 PM, ABHIJNAN KAR 20064 <abhijnank20 at iiserbpr.ac.in> wrote:
>> 
>> This is the whole command after starting docker.
>> user at mesa-r9575:~$ export MESA_DIR=/Users/abhijnankar/Downloads/mesa-r9575 
>> user at mesa-r9575:~$ export OMP_NUM_THREADS=8
>> user at mesa-r9575:~$ export MESASDK_ROOT=/Applications/mesasdk
>> user at mesa-r9575:~$ source $MESASDK_ROOT/bin/mesasdk_init.sh
>> bash: /Applications/mesasdk/bin/mesasdk_init.sh: No such file or directory
>> user at mesa-r9575:~$ source $MESASDK_ROOT/bin/mesasdk_init.sh
>> bash: /Applications/mesasdk/bin/mesasdk_init.sh: No such file or directory
>> user at mesa-r9575:~$ 
>> In the last step of the mesa installation it is giving that error.How to fix it?
>> 
>>> On 16-Aug-2022, at 5:50 AM, Falk Herwig <fherwig at uvic.ca> wrote:
>>> 
>>> Hi Abhijnan, 
>>> 
>>> This is easy to fix. I think you have skipped the step 3 in the Quickinstall notes:
>>> 
>>> 
>>> 3. Download
>>>  und unpack an old mesa version, assuming mesa-r5329 in these instructions
>>> 
>>> You need to have the mesa source tree of the version already downloaded in some accessible location of your file hierarchy. You copy/pasted the command from an example in which the MESA source tree is located in "/Volumes/Astro/L/CODE/MESA/mesa-r9575”. But you can only use that path name if the source tree dir "mesa-r9575” is located in “"/Volumes/Astro/L/CODE/MESA/“. This is very unlikely. So, instead make sure you do step 3 in the instructions and then use YOUR path name to the mesa source tree dir as the last argument. 
>>> 
>>> Thanks for asking the question, I have updated the Quickstart instruction to make this more clear.
>>> 
>>> Once you have this going you may want to explore the slightly advanced option to mount a second directory from you host where you can have your work space and run dirs on the host. 
>>> 
>>> 
>>> If you are entirely new to docker you may want to consider this: 
>>> By now you will probably have a few docker containers running which you may want to stop and remove before attempting to start again. Do 
>>>  $ docker ps -a
>>> CONTAINER ID   IMAGE                COMMAND       CREATED          STATUS                     PORTS     NAMES
>>> 3649632649b4   nugrid/nudome:16.0   "/bin/bash"   43 minutes ago   Exited (0) 4 minutes ago             mesa-r9575
>>> 
>>> To see your active docker containers. Do docker stop xxxx where xxxx is the container name or ID, to stop the container if status is not yet “exited". Then do docker rm xxxx to remove the container.
>>> 
>>> 
>>> Let me know how it goes. 
>>> Best, Falk.
>>> 
>>> 
>>> 
>>> 
>>>> On Aug 15, 2022, at 11:39 AM, ABHIJNAN KAR 20064 <abhijnank20 at iiserbpr.ac.in <mailto:abhijnank20 at iiserbpr.ac.in>> wrote:
>>>> 
>>>> Hi,
>>>> Thanks for your reply!The host system is mac os.And I am using docker for apple silicon.I used the code : bin/start_and_login.sh mesa-r9575 nugrid/nudome:16.0 /Volumes/Astro/L/CODE/MESA/mesa-r9575 
>>>> The docker was successfully installed as docker run hello-world command gave successful installation message.
>>>> The final output of NuGrid was :
>>>> WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
>>>> docker: Error response from daemon: error while creating mount source path '/host_mnt/Volumes/Astro/L/CODE/MESA/mesa-r9575': mkdir /host_mnt/Volumes/Astro: operation not permitted.
>>>> 
>>>>> On 16-Aug-2022, at 12:03 AM, Falk Herwig <fherwig at uvic.ca <mailto:fherwig at uvic.ca>> wrote:
>>>>> 
>>>>> I’m happy to help you and walk you through and the back. But I need more information. What host system are you using? Have you verified dockers working as specified in the documentation? What command exactly have you launched?
>>>>> F
>>>>> 
>>>>>> On Aug 15, 2022, at 11:19, ABHIJNAN KAR 20064 <abhijnank20 at iiserbpr.ac.in <mailto:abhijnank20 at iiserbpr.ac.in>> wrote:
>>>>>> 
>>>>>>  Hi,
>>>>>> I installed docker.Then I went to NuDocker directory and ran the command as mentioned in github for mesa9575.But it is showing following error: docker: Error response from daemon: error while creating mount source path '/host_mnt/Volumes/Astro/L/CODE/MESA/mesa-r9575': mkdir /host_mnt/Volumes/Astro: operation not permitted.
>>>>>> 
>>>>>>> On 14-Aug-2022, at 8:20 PM, Falk Herwig <fherwig at uvic.ca <mailto:fherwig at uvic.ca>> wrote:
>>>>>>> 
>>>>>>> Use NuDocker
>>>>>>> 
>>>>>>> https://github.com/NuGrid/NuDocker <https://github.com/NuGrid/NuDocker>
>>>>>>> 
>>>>>>> Falk
>>>>>>> 
>>>>>>>> On Aug 14, 2022, at 06:43, ABHIJNAN KAR 20064 <abhijnank20 at iiserbpr.ac.in <mailto:abhijnank20 at iiserbpr.ac.in>> wrote:
>>>>>>>> 
>>>>>>>>  Hi,
>>>>>>>> I am trying to install Mesa version of 9575 to reproduce result of a paper.I have also installed sdk for that version.But while doing ./mk in binary_both_stars it is showing the following error:
>>>>>>>> gfortran -Wno-uninitialized -fno-range-check -fmax-errors=12  -fprotect-parens -fno-sign-zero -fbacktrace -ggdb -finit-real=snan -fopenmp -fbounds-check -Wuninitialized -Warray-bounds  -ffree-form -x f95-cpp-input -I../../../../include  -c ../src/run_star_extras.f
>>>>>>>> f951: Warning: Nonexistent include directory '../../../../include' [-Wmissing-include-dirs]
>>>>>>>> ../src/run_star_extras.f:230: Error: Can't open included file 'formats'
>>>>>>>> make: *** [run_star_extras.o] Error 1
>>>>>>>> 
>>>>>>>> FAILED
>>>>>>>> Any help will be appreciated.
>>>>>>>> Regards,
>>>>>>>> Abhijnan Kar(He/his/him)
>>>>>>>> BS-MS,IISER Berhampur
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> mesa-users at lists.mesastar.org <mailto:mesa-users at lists.mesastar.org>
>>>>>>>> https://lists.mesastar.org/mailman/listinfo/mesa-users <https://lists.mesastar.org/mailman/listinfo/mesa-users>
>>>>>>>> 
>>>>>> 
>>>>>> Regards,
>>>>>> Abhijnan Kar(He/his/him)
>>>>>> BS-MS,IISER Berhampur
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>> 
>>>> Regards,
>>>> Abhijnan Kar(He/his/him)
>>>> BS-MS,IISER Berhampur
>>> 
>> 
>> Regards,
>> Abhijnan Kar(He/his/him)
>> BS-MS,IISER Berhampur
>> 
>> 
>> 
>> 
>> 
>> 
> 
> Regards,
> Abhijnan Kar(He/his/him)
> BS-MS,IISER Berhampur
> 
> 
> 
> 
> 
> 

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