[Mesa-users] [EXTERNAL] Re: PGPLOT does not work on my new system, no visual output from MESA while running a test suite
Jared Goldberg
jgoldberg at flatironinstitute.org
Sun Jul 30 21:51:53 UTC 2023
Hi Bill,
Excellent! Glad it’s working!
For posterity: in general, when starting from a new test suite case, it is a good idea to look at the rn script in a text editor and see which inlists it points to, and in what order. In many cases, a set of inlists are chained together to guide the stellar model through different phases of evolution.
While it’s often necessary for only one inlist to contain pgstar_flag =.true. (e.g. inlist_project in $MESA_DIR/star/work/), when running multiple inlists in a sequence, that line needs to appear somewhere in one of the inlists corresponding to each “step” of the run in order for pgstar to remain active.
Cheers,
~Jared
> On Jul 30, 2023, at 11:59 AM, Danchi, William C. (GSFC-6600) <william.c.danchi at nasa.gov> wrote:
>
> Hi Frank & Jared,
>
> After uncommenting "!pgstar_flag = .true." on ALL the inlists in that directory, and using the xterm window, suddenly the PGPLOT window has magically appeared.
>
> I think the misunderstanding was that ALL the inlists had to be uncommented. I am not sure why using the xterm window would matter, but in any case, things seem to be working OK now. I will also try to run out of a regular terminal window.
>
> Many thanks for your help!
>
> Regards,
>
> Bill
>
>
>
> -----------
> Dr. William C. Danchi
> Senior Astrophysicist
> NASA Goddard Space Flight Center
> Astrophysics Science Division, Code 660
> Greenbelt, MD 20771
>
> Phone: 301-286-4586
> FAX: 301-286-1752
>
>
>
> On 7/30/23, 10:59 AM, "Francis Timmes" <fxt44 at mac.com <mailto:fxt44 at mac.com>> wrote:
>
>
> CAUTION: This email originated from outside of NASA. Please take care when clicking links or opening attachments. Use the "Report Message" button to report suspicious messages to the NASA SOC.
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> hi bill,
>
>
> don't move applications or change $PATH.
>
>
> 1) double click on xquartz to open it. you can check that it is working by choosing "Terminal" under "Applications" in the xquartz menu bar.
>
>
> 2) uncomment "!pgstar_flag = .true." in the 1M_pre_ms_to_wd inlists. run it and you should see a pgstar xwindow.
>
>
> fxt
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>> On Jul 29, 2023, at 12:47 PM, Danchi, William C. (GSFC-6600) via Mesa-users <mesa-users at lists.mesastar.org <mailto:mesa-users at lists.mesastar.org>> wrote:
>>
>> Hi Frank and Jared,
>>
>> The way the student's laptop was fixed sounds like something that couls work for mine.
>>
>> On my laptop, Xquartz.app is installed on the "Utilities" folder of the Applications folder. I assume the $PATH is set OK since the regular terminal app is located there, as are other things. X11 binaries are also located in /opt/X11/bin.
>>
>> Also, I did try to run MESA with the ./rn in the folder I mentioned. I have not tried anything in the work folder, only the test_suite folder.
>>
>> I think the problem may be that the $PATH looks for X11 in /opt/X11/bin, which is in the path. I added /Applications/Utilities to the path, but so far no joy. Should I remove the reference to /opt/X11/bin, leave /Applications/Utilities unchanged and reboot?
>>
>> Currently, X11 starts up when I reboot, but maybe not from the location where MESA star is looking.
>>
>> Here is what I get when I echo $PATH :
>>
>> wdanchi% echo $PATH
>> /Users/wdanchi/anaconda3/bin:/Applications/mesasdk/bin:/opt/local/bin:/opt/local/sbin:/Applications/Utilities:/opt/X11/bin:/bin:/usr/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/Users/wdanchi/software/vplanet/bin
>>
>> Let me know if this might fix the problem, or I should move Xquartz.app somewhere else?
>>
>> Thanks,
>>
>> Bill
>>
>>
>> -----------
>> Dr. William C. Danchi
>> Senior Astrophysicist
>> NASA Goddard Space Flight Center
>> Astrophysics Science Division, Code 660
>> Greenbelt, MD 20771
>>
>> Phone: 301-286-4586
>> FAX: 301-286-1752
>>
>>
>>
>> On 7/29/23, 1:32 PM, "Francis Timmes" <fxt44 at mac.com <mailto:fxt44 at mac.com> <mailto:fxt44 at mac.com <mailto:fxt44 at mac.com>>> wrote:
>>
>>
>> CAUTION: This email originated from outside of NASA. Please take care when clicking links or opening attachments. Use the "Report Message" button to report suspicious messages to the NASA SOC.
>>
>>
>>
>>
>>
>>
>>
>>
>> hi jared,
>>
>>
>>> ... with the xwindows server already open ...
>>
>>
>> ok, yes, lately i've been having to start xquartz myself after a restart. in the past, xquartz would open itself when pgstar first called. i figured the change was a security feature - i had to start xquartz, not another program. both intel and m1.
>>
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>> fxt
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>>>> On Jul 29, 2023, at 10:16 AM, Jared Goldberg <jgoldberg at flatironinstitute.org <mailto:jgoldberg at flatironinstitute.org> <mailto:jgoldberg at flatironinstitute.org <mailto:jgoldberg at flatironinstitute.org>>> wrote:
>>>
>>> Does pgstar ever work? E.g. when you run from $MESA_DIR/star/work/ instead of a test_suite case? Or are you finding the problem specific to the test_suite?
>>>
>>> A student I’m working with ran into a similar issue affecting all of MESA running on a clean (wiped but refurbished) mac (though not on an M2 chip). For some reason the xquartz installation was not talking to the Mac/the Mac was not actually finding the installation or launching an xwindows server with ./rn
>>>
>>> I don’t exactly what caused the issue, but I can share the steps we took that ended up working:
>>>
>>> The first thing we did was ensure that xquartz was installed properly in the Applications folder and that the $PATH variable pointed there.
>>>
>>> We then rebooted the laptop.
>>>
>>> Then we manually opened an Xquartz terminal (rather than the regular terminal) and tried running Mesa from that terminal. We figured if a pgplot/xwindows window didn’t pop up in xwindows client, then that would be very suspicious. At that point, the pgplot window did pop up, and then with the xwindows server already open, we ran MESA from a normal terminal, which “magically” worked, and we haven’t had the problem since.
>>>
>>> Perhaps you’re running into a different issue, but I figured I’ll share in case it’s helpful!
>>>
>>> Cheers,
>>> ~Jared
>>>
>>>
>>>> On Jul 29, 2023, at 12:52 PM, Danchi, William C. (GSFC-6600) via Mesa-users <mesa-users at lists.mesastar.org <mailto:mesa-users at lists.mesastar.org> <mailto:mesa-users at lists.mesastar.org <mailto:mesa-users at lists.mesastar.org>>> wrote:
>>>>
>>>> Hi Frank,
>>>>
>>>> I tried the suggestion, but unfortunately nothing has changed. Could there be a problem with the pgplot library and xwindow server files in the SDK that are supposed to linked when you do the "./mk" in the directory you are working in? I am working in the 1M_pre_ms_to_wd, directory of the test suite, as mentioned before.
>>>>
>>>> I can send more information if needed. Let me know what is needed to finish debugging this problem.
>>>>
>>>> Thanks,
>>>>
>>>> Bill
>>>> -----------
>>>> Dr. William C. Danchi
>>>> Senior Astrophysicist
>>>> NASA Goddard Space Flight Center
>>>> Astrophysics Science Division, Code 660
>>>> Greenbelt, MD 20771
>>>>
>>>> Phone: 301-286-4586
>>>> FAX: 301-286-1752
>>>>
>>>>
>>>>
>>>> On 7/29/23, 11:59 AM, "Francis Timmes" <fxt44 at mac.com <mailto:fxt44 at mac.com> <mailto:fxt44 at mac.com <mailto:fxt44 at mac.com>> <mailto:fxt44 at mac.com <mailto:fxt44 at mac.com> <mailto:fxt44 at mac.com <mailto:fxt44 at mac.com>>>> wrote:
>>>>
>>>>
>>>> CAUTION: This email originated from outside of NASA. Please take care when clicking links or opening attachments. Use the "Report Message" button to report suspicious messages to the NASA SOC.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> hi bill,
>>>>
>>>>
>>>> one has to activate pgstar in an inlist. for example, in inlist_start one finds
>>>>
>>>>
>>>> !pgstar_flag = .true.
>>>>
>>>>
>>>> uncomment and do the same for the other inlists where one wants pgstar output.
>>>>
>>>>
>>>> fxt
>>>>
>>>>
>>>>
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>>>>
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>>>>> On Jul 29, 2023, at 6:40 AM, Danchi, William C. (GSFC-6600) via Mesa-users <mesa-users at lists.mesastar.org <mailto:mesa-users at lists.mesastar.org> <mailto:mesa-users at lists.mesastar.org <mailto:mesa-users at lists.mesastar.org>> <mailto:mesa-users at lists.mesastar.org <mailto:mesa-users at lists.mesastar.org> <mailto:mesa-users at lists.mesastar.org <mailto:mesa-users at lists.mesastar.org>>>> wrote:
>>>>>
>>>>> Hi mesa_users,
>>>>> I installed MESA on a new M2 Max based Mac laptop, running Ventura 13.5. I installed Xquartz, Xcode, MESA_SDK, etc. All the installations worked as expected with no errors.
>>>>> However, I try running a test suite such as 1M_pre_ms_to_wd, but I get no PGPLOT output. The code runs fine and produces the expected output at each time step, but without the visual display of the progress.
>>>>> If this has happened to any of you, and you have a solution, that would be great.
>>>>> Many thanks,
>>>>>
>>>>> Bill Danchi
>>>>> -----------
>>>>> Dr. William C. Danchi
>>>>> Senior Astrophysicist
>>>>> NASA Goddard Space Flight Center
>>>>> Astrophysics Science Division, Code 660
>>>>> Greenbelt, MD 20771
>>>>>
>>>>> Phone: 301-286-4586
>>>>> FAX: 301-286-1752
>>>>> _______________________________________________
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