[Mesa-users] Help regarding NuDocker and mesa old version
Falk Herwig
fherwig at uvic.ca
Mon Aug 22 16:38:13 UTC 2022
Hello Abhijan,
Glad to hear that you got the NuDocker to work. The intriguing thing about the NuDocker environment is that if you are using the same docker image, which should be
nugrid/nudome 16.0 96669ee42b2a 3 years ago 2.08GB
atlas:MESA $ docker pull nugrid/nudome:16.0
16.0: Pulling from nugrid/nudome
Digest: sha256:29c0928ebba4b20dbb229c554e818c7920ae6a4e72f69329cf450bb2da4b113e
Status: Image is up to date for nugrid/nudome:16.0
docker.io/nugrid/nudome:16.0
And if you are using the same mesa source package, I am using
atlas:MESA $ md5sum mesa-r9575.zip
69c263292e87fcaa4b1cfa7033f03d55 mesa-r9575.zip
(Check the md5sum that you have the same)
Then there is no way conceivable to me how we can have a different outcome, if you have really correctly unpacked the zip file and have indeed mounted your mesa source tree on the host files system correctly into the docker container. Just to make sure again, here is the command I use on my laptop:
./bin/start_and_login.sh mesa-r9575 nugrid/nudome:16.0 /Volumes/Astro/MESA/mesa-r9575
That command is launched from the root directory of the NuDocker git repo, and in this example the mesa source tree for r9575 is located in /Volumes/Astro/MESA/mesa-r9575
on the host system.
With this setup I get when compiling the main source tree the usual success message:
************************************************
************************************************
MESA installation was successful
************************************************
************************************************
And then moving on to the binary/test_suite/double_bh case just works fine:
user at mesa-r9575:~/mesa/binary/test_suite/double_bh$ ./rn
DATE: 2022-08-22
TIME: 16:30:03
read inlist_project
read inlist_extra
version_number 9575
^Cuser at mesa-r9575:~/mesa/binary/test_suite/double_bh$ ./rn
DATE: 2022-08-22
TIME: 16:30:21
read inlist_project
read inlist_extra
version_number 9575
new_rotation_flag T
new_surface_rotation_v 0 5.0000000000000000D+01 5.9612211423488179D-06
set_uniform_initial_composition
initial_h1 6.9999999999999996D-01
I am not able to help beyond this. It simply has to work.
I can offer one more solution to get you past your current bottle neck. Our research platform https://astrohub.uvic.ca offers a “Public/Outreach” Hub based on a similar Docker technology compared to NuDocker. Just as in NuDocker a number of previous mesa versions we have used are precompiled and ready to be used there, r9575 being one of them. I just checked, and the double_bh test suite problem works just fine there.
If you send me your github user name I could give you temporary access so that you can run some tests on the Astrohub platform. If you do find this useful and work benefiting from this ends up in a paper we ask that you acknowledge Astrohub and let us know.
Best, Falk.
> On Aug 19, 2022, at 11:05 PM, ABHIJNAN KAR 20064 <abhijnank20 at iiserbpr.ac.in> wrote:
>
> By error, i mean : mesa/const has been built, tested, and exported. These kind of messages came with eacgh package but there was no final message saying mesa installation was successful.The installation stopped at eos data : /home/user/mesa/eos
> installing mesa eos data.
>
> create eosDT_data
> bzip2 -d eosDT_data.tar.bz2
> bzip2: Input file eosDT_data.tar.bz2 has 1 other link.
> May be due to this the the final compilation in any test_suite is not happening.
>
>> On 20-Aug-2022, at 2:14 AM, ABHIJNAN KAR 20064 <abhijnank20 at iiserbpr.ac.in> wrote:
>>
>> Yeah, the initial install of mesa was without error.All the packages were successfully built and the successful installation message was there.Ans this is the unchanged test suite directory.But still while doing ./mk , this is showing the same error.
>>
>>> On 20-Aug-2022, at 12:07 AM, Falk Herwig <fherwig at uvic.ca> wrote:
>>>
>>> Is the standard unchanged test suite directory of the newly downloaded source
>>> Tree ? And in the Mesa root directory the initial install of mesa completed without error?
>>>
>>>> On Aug 19, 2022, at 11:07, ABHIJNAN KAR 20064 <abhijnank20 at iiserbpr.ac.in> wrote:
>>>>
>>>> Thanks for your reply!Yes, it worked.The crlibm is now successfully installed after downloading fresh mesa-r9575.But still while running double_bh, it is showing 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
>>>> ../src/run_star_extras.f:25:10:
>>>>
>>>> use star_lib
>>>> 1
>>>> Fatal Error: Can't open module file 'star_lib.mod' for reading at (1): No such file or directory
>>>> compilation terminated.
>>>> ../../../../binary/work_standard_makefile_binary:33: recipe for target 'run_star_extras.o' failed
>>>> make: *** [run_star_extras.o] Error 1
>>>>
>>>> FAILED
>>>>
>>>>
>>>>> On 19-Aug-2022, at 9:29 PM, Falk Herwig <fherwig at uvic.ca> wrote:
>>>>>
>>>>> Hi Abhijnan,
>>>>> You should add as you did in your direct message to me that you had troubles compiling mesa in the first place. So if you don’t have mesa compiled correctly in the first place you can’t expect any of the test suite cases to compile.
>>>>>
>>>>> Yesterday you mailed me:
>>>>>
>>>>>> Thanks for the reply!It has been fixed.However, it gives the message like following:
>>>>>> mesa/utils has been built, tested, and exported.
>>>>>>
>>>>>> ************************************************
>>>>>>
>>>>>> /home/user/mesa/crlibm
>>>>>> building crlibm package.
>>>>>>
>>>>>> gzip: crlibm-1.0beta4_unzip.tar.gz has 1 other link -- unchanged
>>>>>> tar: crlibm-1.0beta4_unzip.tar: Cannot open: No such file or directory
>>>>>> tar: Error is not recoverable: exiting now
>>>>>> mv: cannot stat 'crlibm-1.0beta4': No such file or directory
>>>>>> ./build_and_test_parallel: line 43: cd: crlibm: No such file or directory
>>>>>> make: ../makefile_crlibm: No such file or directory
>>>>>> make: *** No rule to make target '../makefile_crlibm'. Stop.
>>>>>> make: *** No targets specified and no makefile found. Stop.
>>>>>>
>>>>>> /home/user/mesa/crlibm
>>>>>> ./build_and_test FAILED
>>>>>>
>>>>>>
>>>>>> /home/user/mesa/crlibm
>>>>>> ./build_and_test FAILED
>>>>>
>>>>>
>>>>> Now, fortunately since we are now in the NuDocker system we can exclude any system/OS differences. It looks from the above to me as if you are not having a complete source tree. I looks as if the entire crlib dir is missing. Here is what the content of my r9575 source tree looks like:
>>>>> user at mesa-r9575:~/mesa/crlibm$ pwd
>>>>> /home/user/mesa/crlibm
>>>>> user at mesa-r9575:~/mesa/crlibm$ ls
>>>>> README ck crlibm-1.0beta4.tar.gz i1 makefile_crlibm test
>>>>> build_and_test clean crlibm_private.c i1p mk
>>>>> build_and_test_mic_native crlibm de_Dinechin_et_at_2007.pdf install private
>>>>> build_and_test_parallel crlibm-1.0beta3.pdf export make public
>>>>> It looks your r9575 source tree is corrupted, maybe from previous compilation or whatever. I suggest you download and unpack a fresh r97575 an place that in the same location you are mounting as mesa source into your Docker instance and start with a fresh compile of mesa itself before moving on to a test-suite case.
>>>>>
>>>>> If you unpack the r9575 zip archive it will have the crlib dir with the source tar.gz archive:
>>>>> atlas:tmp $ ls mesa-r9575/crlibm
>>>>> README clean export makefile_crlibm
>>>>> build_and_test crlibm-1.0beta3.pdf i1 mk
>>>>> build_and_test_mic_native crlibm-1.0beta4.tar.gz i1p private/
>>>>> build_and_test_parallel crlibm_private.c install public/
>>>>> ck de_Dinechin_et_at_2007.pdf make/ test/
>>>>> atlas:tmp $
>>>>>
>>>>> then doing inside ~/mesa the usual ./install command will give the usual:
>>>>> ************************************************
>>>>> ************************************************
>>>>> ************************************************
>>>>>
>>>>> MESA installation was successful
>>>>>
>>>>> ************************************************
>>>>> ************************************************
>>>>> ************************************************
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> user at mesa-r9575:~/mesa$
>>>>>
>>>>>
>>>>>
>>>>> Then you can move on to your specific test-suite case, and it has to work:
>>>>> user at mesa-r9575:~/mesa/binary/test_suite/double_bh$ ./mk
>>>>> 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
>>>>> 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_binary_extras.f
>>>>> 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 ../../../../binary/job/run_binary.f
>>>>> 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/binary_run.f
>>>>> gfortran -fopenmp -o ../binary run_star_extras.o run_binary_extras.o run_binary.o binary_run.o -L../../../../lib -lbinary -lstar -lionization -latm -lcolors -lmlt -lnet -leos -lkap -lrates -lneu -lchem -linterp_2d -linterp_1d -lnum -lf2crlibm -lcrlibm -lmtx -lconst -lutils -lmesaklu `mesasdk_lapack_link` `mesasdk_blas_link` `mesasdk_pgplot_link` -lz
>>>>> user at mesa-r9575:~/mesa/binary/test_suite/double_bh$ ./rn
>>>>> DATE: 2022-08-19
>>>>> TIME: 15:56:50
>>>>>
>>>>>
>>>>> read inlist_project
>>>>> read inlist_extra
>>>>> version_number 9575
>>>>> new_rotation_flag T
>>>>> new_surface_rotation_v 0 5.0000000000000000D+01 5.9612211423488179D-06
>>>>>
>>>>> Good luck,
>>>>> Falk
>>>>>
>>>>>
>>>>>> On Aug 19, 2022, at 4:24 AM, ABHIJNAN KAR 20064 <abhijnank20 at iiserbpr.ac.in <mailto:abhijnank20 at iiserbpr.ac.in>> wrote:
>>>>>>
>>>>>> Hi Mesa Users,
>>>>>> I am running a mesa old version of r9575 and I have to reproduce the results of a paper.I have successfully installed NuDocker.I have to run the inlists in test_suite of binary module using NuDocker.So, the problem i am encountering is that during ./mk command in test_suite of binary module in mesa-r9575 it is showing error as follows:
>>>>>> 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
>>>>>> ../src/run_star_extras.f:25:10:
>>>>>>
>>>>>> use star_lib
>>>>>> 1
>>>>>> Fatal Error: Can't open module file 'star_lib.mod' for reading at (1): No such file or directory
>>>>>> compilation terminated.
>>>>>> ../../../../binary/work_standard_makefile_binary:33: recipe for target 'run_star_extras.o' failed
>>>>>> make: *** [run_star_extras.o] Error 1
>>>>>>
>>>>>> FAILED
>>>>>> What to do next?
>>>>>> 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
>>>>>>
>>>>>
>>>>
>>>> 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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