[Users] error after activating IllinoisGRMHD and VolumeIntegrals_GRMHD
Zach Etienne
zachetie at gmail.com
Thu Jul 19 15:41:38 CDT 2018
Dear Chia-Hui,
I noticed at the bottom of your .out file the following line:
> INFO (TerminationTrigger): Remaining wallclock time for your job is
57.5667 minutes. Triggering termination...
It appears that for some reason, TerminationTrigger is terminating your
run. I updated the .par files to properly document the relevant
TerminationTrigger parameters. You could also try disabling
TerminationTrigger completely, as this should prevent the code from
terminating.
-Zach
* * *
Zachariah Etienne
Assistant Professor of Mathematics
West Virginia University
*https://math.wvu.edu/~zetienne/ <https://math.wvu.edu/~zetienne/>*
https://blackholesathome.net
On Thu, Jul 19, 2018 at 2:36 PM, 林家暉 <r06222015 at ntu.edu.tw> wrote:
> Dear Zach,
> Thank a lot for your updating. The previous errors are solved. However the
> code exits after 3 minutes running. The attached files are the
> corresponding .err and .out files. I am not sure whether it is caused by ML_BSSN
> parameters.
> Also thanks for inviting me to the IllinoisGRMHD Working Group telecon. I
> would like to attend and I have selected possible time.
>
> Best regards,
> Chia-Hui
> ------------------------------
> *寄件者:* Zach Etienne <zachetie at gmail.com>
> *寄件日期:* 2018年7月20日 上午 01:31:50
> *收件者:* 林家暉
> *副本:* Einstein Toolkit Users
> *主旨:* Re: [Users] error after activating IllinoisGRMHD and
> VolumeIntegrals_GRMHD
>
> Dear Chia-Hui,
>
> Thank you for your report! I just updated the parameter files to fix these
> issues (sorry, I should've checked earlier), and they seem to run fine now
> when using the latest Einstein Toolkit release, ET_2018_02. There may be
> some remaining warnings about ML_BSSN parameters, but these may be safely
> ignored.
>
> Please consider attending the next IllinoisGRMHD Working Group telecon
> next Thursday or Friday; respond to http://whenisgood.net/pfjbm3c if you
> are interesting in attending.
> WhenIsGood: July 2018 IllinoisGRMHD telecon
> <http://whenisgood.net/pfjbm3c>
> whenisgood.net
> Plan the time to have your meeting or event by co-ordinating availability
> with all the particpants using this fuss-free online tool.
>
>
> -Zach
>
> * * *
> Zachariah Etienne
> Assistant Professor of Mathematics
> West Virginia University
> *https://math.wvu.edu/~zetienne/ <https://math.wvu.edu/~zetienne/>*
> https://blackholesathome.net
>
> On Thu, Jul 19, 2018 at 9:30 AM, 林家暉 <r06222015 at ntu.edu.tw> wrote:
>
>> Dear Zach,
>> Thank you for updating the parameter file. But I have several questions :
>> 1.It seems some name of parameters should be changed,
>> from VolumeIntegrals_GRMHD::volintegral_inside_sphere__center_x_initial
>> to VolumeIntegrals_GRMHD::volintegral_sphere__center_x_initial
>> and
>> from VolumeIntegrals_vacuum::volintegral_inside_sphere__trac
>> ks__amr_centre
>> to VolumeIntegrals_vacuum::amr_centre__tracks__volintegral_inside_sphere
>>
>> 2. There is an error message for this parameter IllinoisGRMHD::Symmetry
>> = 0:
>>
>> in thorn IllinoisGRMHD, file nsns_test.par:78:
>> -> Invalid assignment: Attempting to set a variable of type KEYWORD with (INT)0
>>
>>
>> I tried to change 0 to "no", another error message appeared:
>>
>> ParameterSetKeyword: Unable to set keyword 'IllinoisGRMHD::Symmetry', new
>> value 'no' is not in any active range
>>
>> 3.For parameter IOUtil::checkpoint_dir= ABEoutput_directory-$parfile
>>
>> There is an error message:
>>
>> in thorn IOUtil, file nsns_test.par:388:
>> -> Unknown add operator: -
>> Interpreting as literal string with value 'ABEoutput_directory-nsns_test'
>>
>> I met obove problems when I executed the code.How could I modify?
>> Thank you very much.
>>
>> Best regards,
>> Chia-Hui
>>
>> ------------------------------
>> *寄件者:* Zach Etienne <zachetie at gmail.com>
>> *寄件日期:* 2018年7月18日 下午 09:07:46
>>
>> *收件者:* 林家暉
>> *副本:* Einstein Toolkit Users
>> *主旨:* Re: [Users] error after activating IllinoisGRMHD and
>> VolumeIntegrals_GRMHD
>>
>> Dear Chia-Hui,
>>
>> Thanks so much for sending the error message. Based on the file you sent,
>> I was able to push a few bugfixes to the WVUThorns_Diagnostics arrangement.
>>
>> I also updated the example parameter files and moved them to a new
>> location:
>> wvuthorns_diagnostics/NSNS_parameter_files
>>
>> You'll find that nsns_test.par has been updated as well.
>>
>> Please grab the latest wvuthorns_diagnostics git repo. I'd suggest
>> comparing the updated nsns_test.par to the version you sent me and
>> modifying as needed so that your neutron stars are properly centered
>> (you'll need to replace +/- "20.319527" with the locations of the neutron
>> stars in your initial data).
>>
>> Thanks again, and let me know if you run into further troubles.
>>
>> -Zach
>>
>> * * *
>> Zachariah Etienne
>> Assistant Professor of Mathematics
>> West Virginia University
>> *https://math.wvu.edu/~zetienne/ <https://math.wvu.edu/~zetienne/>*
>> https://blackholesathome.net
>>
>> On Wed, Jul 18, 2018 at 2:26 AM, 林家暉 <r06222015 at ntu.edu.tw> wrote:
>>
>>> Dear Zach,
>>> I modified nsns_test.par as the attached file by replacing
>>> VolumeIntegrals with VolumeIntegrals_GRMHD and remove the line using centeroflapse
>>> which is for VolumeIntegrals_vacuum. Then I got the error message as
>>> the attached file.What else should I modify?
>>> By the way , my ETK version is ET_2018_02.
>>> On the other hand,I am still trying to use illinoisGRMHD in the gallery
>>> example (nsnstohmns.par),but not yet success. I haven't come up with ideal
>>> how to make it compatible with IllinoisGRMHD.
>>> Thanks,
>>> Best regards,
>>> Chia-Hui
>>> ------------------------------
>>> *寄件者:* Zach Etienne <zachetie at gmail.com>
>>> *寄件日期:* 2018年7月18日 上午 03:17:53
>>>
>>> *收件者:* 林家暉
>>> *副本:* Einstein Toolkit Users
>>> *主旨:* Re: [Users] error after activating IllinoisGRMHD and
>>> VolumeIntegrals_GRMHD
>>>
>>> Dear Chia-Hui,
>>> > Does this mean that I should update the parameter file in order to use
>>> them ?
>>>
>>> Yes, though this should be simple. I would expect that simply replacing
>>> all references to VolumeIntegrals by references to VolumeIntegrals_GRMHD
>>> will fix the problem.
>>>
>>> > I have already produced some initial data by LORENE.
>>>
>>> Great to hear. You will need to modify the parameter file so that the
>>> AMR grid structures are properly centered on each neutron star initially.
>>>
>>> > Can I consult for your suggestion that which method would be more
>>> efficient and proper without tracking problem? Or there are other possible
>>> solution?
>>>
>>> I am unsure what advice would be best. You have told me is that the code
>>> exits unexpectedly. To help diagnose, I will need to know the exact version
>>> of the ETK you are using and the error message.
>>>
>>> -Zach
>>>
>>> * * *
>>> Zachariah Etienne
>>> Assistant Professor of Mathematics
>>> West Virginia University
>>> *https://math.wvu.edu/~zetienne/ <https://math.wvu.edu/~zetienne/>*
>>> https://blackholesathome.net
>>>
>>> On Tue, Jul 17, 2018 at 10:18 AM, 林家暉 <r06222015 at ntu.edu.tw> wrote:
>>>
>>>> Dear Zach,
>>>> It seems that none parameter file in https://bitbucket.org/zach_
>>>> etienne/wvuthorns_diagnostics/src/a7dfd31684ba/Meudon_Bin_NS
>>>> -modified/par/?at=master uses VolumeIntegrals_GRMHD but use VolumeIntegrals
>>>> instead. Does this mean that I should update the parameter file in order to
>>>> use them ?
>>>> My main goal is to simulate binary neutron star with unequal mass,
>>>> and I have already produced some initial data by LORENE. It seems now I
>>>> have two options. First is to modify (update) one of the parameter files
>>>> above(e.g. nsns_test.par ) and second is significantly modify
>>>> nsnstohmns.par in the gallery. Can I consult for your suggestion that
>>>> which method would be more efficient and proper without tracking problem?
>>>> Or there are other possible solution?
>>>>
>>>> Thank you.
>>>> Best regards,
>>>> Chia-Hui
>>>> ------------------------------
>>>> *寄件者:* Zach Etienne <zachetie at gmail.com>
>>>> *寄件日期:* 2018年7月17日 下午 09:53:20
>>>>
>>>> *收件者:* 林家暉
>>>> *副本:* Einstein Toolkit Users
>>>> *主旨:* Re: [Users] error after activating IllinoisGRMHD and
>>>> VolumeIntegrals_GRMHD
>>>>
>>>> Dear Chia-Hui,
>>>>
>>>> > Is there a thorn called VolumeIntegrals ?
>>>>
>>>> No, there isn't, and this *might* be evidence that the parameter file
>>>> you chose is outdated (try to find one that depends on
>>>> VolumeIntegrals_GRMHD): the old "VolumeIntegrals" thorn was split into the
>>>> VolumeIntegrals_GRMHD and VolumeIntegrals_vacuum thorns. The former can use
>>>> IllinoisGRMHD gridfunctions and the latter can use McLachlan gridfunctions.
>>>> VolumeIntegrals_GRMHD is used to find the center of masses of the
>>>> neutron stars so their motion can be tracked by the AMR grids.
>>>>
>>>> > And I am curious about: what is the main difference between the
>>>> parameter file (nsnstohmns.par) in the gallery example and nsns_test.par ?
>>>>
>>>> The nsns_test.par is designed to evolve the "Missing Link" case (
>>>> https://arxiv.org/abs/1101.4298), which is probably different than the
>>>> gallery example. To run this case, you'll need to use the LORENE initial
>>>> data file here (credit: Meudon group; you can find this case on the LORENE
>>>> website -- https://lorene.obspm.fr/ -- as well, but you'll need to
>>>> hunt for it):
>>>> http://math.wvu.edu/~zetienne/resu.d
>>>>
>>>> -Zach
>>>>
>>>> * * *
>>>> Zachariah Etienne
>>>> Assistant Professor of Mathematics
>>>> West Virginia University
>>>> *https://math.wvu.edu/~zetienne/ <https://math.wvu.edu/~zetienne/>*
>>>> https://blackholesathome.net
>>>>
>>>> On Tue, Jul 17, 2018 at 9:26 AM, 林家暉 <r06222015 at ntu.edu.tw> wrote:
>>>>
>>>>> Dear Zach,
>>>>>
>>>>> Sorry for late reply. I have tried one of the parameter file you
>>>>> mentioned ( nsns_test.par ). I have a question for this file that the
>>>>> thorn VolumeIntegrals should be activated but I can only find VolumeIntegrals_GRMHD
>>>>> and VolumeIntegrals_vacuum. After I tried both thorns, I chose
>>>>> VolumeIntegrals_GRMHD(that is, I change all VolumeIntegrals into VolumeIntegrals_GRMHD
>>>>> in the nsns_test.par).However the code stopped after several minutes
>>>>> running. So what I want to ask is: Is there a thorn called VolumeIntegrals ?
>>>>> Since I cannot find after searching and I think it is the reason
>>>>> terminating the code.
>>>>>
>>>>> And I am curious about: what is the main difference between the
>>>>> parameter file (nsnstohmns.par) in the gallery example and nsns_test.par
>>>>> ?
>>>>>
>>>>>
>>>>> Thank you.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Chia-Hui
>>>>> ------------------------------
>>>>> *寄件者:* Zach Etienne <zachetie at gmail.com>
>>>>> *寄件日期:* 2018年7月14日 上午 02:41:24
>>>>>
>>>>> *收件者:* 林家暉
>>>>> *副本:* Einstein Toolkit Users
>>>>> *主旨:* Re: [Users] error after activating IllinoisGRMHD and
>>>>> VolumeIntegrals_GRMHD
>>>>>
>>>>> Hi Chia-Hui,
>>>>>
>>>>> If you really want to use VolumeIntegrals_GRMHD, you are more than
>>>>> welcome to do so. However, the parameter file you are using from the
>>>>> examples gallery will need to be significantly modified to be compatible
>>>>> with IllinoisGRMHD. My immediate thought (which may be correct or
>>>>> incorrect) is that it is attempting to initialize both GRHydro and
>>>>> IllinoisGRMHD simultaneously.
>>>>>
>>>>> If you want to use IllinoisGRMHD, the easiest route would be to start
>>>>> with a parameter file in the following wvuthorns_diagnostics directory:
>>>>> https://bitbucket.org/zach_etienne/wvuthorns_diagnostics/src
>>>>> /master/Meudon_Bin_NS-modified/par/
>>>>>
>>>>> I haven't had time yet to fully set up a gallery example for this BNS
>>>>> case, so beware: you may need to modify the parameter file a bit to make it
>>>>> work properly. I'm hoping to schedule the next IllinoisGRMHD Working Group
>>>>> telecon in the next few weeks, so please stay tuned if you are interested.
>>>>>
>>>>> -Zach
>>>>>
>>>>> * * *
>>>>> Zachariah Etienne
>>>>> Assistant Professor of Mathematics
>>>>> West Virginia University
>>>>> http://math.wvu.edu/~zetienne/
>>>>> http://blackholesathome.net
>>>>>
>>>>> On Fri, Jul 13, 2018 at 11:50 AM, 林家暉 <r06222015 at ntu.edu.tw> wrote:
>>>>>
>>>>>> Dear Zach,
>>>>>> Becasue if I only activate VolumeIntegrals_GRMHD but not IllinoisGRMHD
>>>>>> , there will be following error in the .out file:
>>>>>>
>>>>>> Error: Implementation 'ILLINOISGRMHD' not activated.
>>>>>> This implementation is required by activated thorn(s):
>>>>>> VolumeIntegrals_GRMHD (implementing VolumeIntegrals_GRMHD)
>>>>>> This implementation is provided by compiled thorn(s):
>>>>>> IllinoisGRMHD
>>>>>> Add a thorn providing this implementation to the ActiveThorns
>>>>>> parameter.
>>>>>> Activation failed - 1 errors in activation sequence
>>>>>>
>>>>>> It seems it is required to activate IllinoisGRMHD in order to use
>>>>>> VolumeIntegrals_GRMHD.
>>>>>>
>>>>>> Thanks,
>>>>>> Chia-Hui
>>>>>> ------------------------------
>>>>>> *寄件者:* Zach Etienne <zachetie at gmail.com>
>>>>>> *寄件日期:* 2018年7月13日 下午 09:04:30
>>>>>> *收件者:* 林家暉
>>>>>> *副本:* Einstein Toolkit Users
>>>>>> *主旨:* Re: [Users] error after activating IllinoisGRMHD and
>>>>>> VolumeIntegrals_GRMHD
>>>>>>
>>>>>> Hi Chia-Hui,
>>>>>>
>>>>>> Is there a reason you are using IllinoisGRMHD for this particular
>>>>>> example? The example was written for GRHydro.
>>>>>>
>>>>>> -Zach
>>>>>>
>>>>>> * * *
>>>>>> Zachariah Etienne
>>>>>> Assistant Professor of Mathematics
>>>>>> West Virginia University
>>>>>> http://math.wvu.edu/~zetienne/
>>>>>> http://blackholesathome.net
>>>>>>
>>>>>> On Thu, Jul 12, 2018 at 11:35 PM, 林家暉 <r06222015 at ntu.edu.tw> wrote:
>>>>>>
>>>>>>> Dear whom it may concern,
>>>>>>> I tried to solve the tracking problem of unequal mass binary neutron
>>>>>>> (http://einsteintoolkit.org/gallery/bns/index.html ) star by using
>>>>>>> the thorn WVUThorns_Diagnostics / VolumeIntegrals_GRMHD . Therefore
>>>>>>> I activate both IllinoisGRMHD and VolumeIntegrals_GRMHD. However I
>>>>>>> met the error which showed in both .err file and .out file.
>>>>>>>
>>>>>>> In .err file:
>>>>>>> Thu Jul 12 08:03:04 2018: [unset]:_pmi_alps_init:alps_get_placement_info
>>>>>>> returned with error -1
>>>>>>> Thu Jul 12 08:03:04 2018: [unset]:_pmi_init:_pmi_alps_init returned
>>>>>>> -1
>>>>>>>
>>>>>>> In .out file:
>>>>>>> INFO (IllinoisGRMHD): Font fix failed!
>>>>>>> INFO (IllinoisGRMHD): i,j,k = 78 31 41, stats.failure_checker =
>>>>>>> 10000 x,y,z = -1.800000e+01 -7.593750e+00 1.068750e+01 , index=574610 st_i
>>>>>>> = -nan -nan -nan, rhostar = 2.902693e+243, Bi = 0.000000e+00 0.000000e+00
>>>>>>> 0.000000e+00, gij = 1.295702e+00 0.000000e+00 0.000000e+00 1.295702e+00
>>>>>>> 0.000000e+00 1.295702e+00, Psi6 = 1.474883e+00
>>>>>>> INFO (IllinoisGRMHD): Couldn't find root from: -nan 2.902693e+243
>>>>>>> -nan -nan -nan, rhob approx=1.968084e+243, rho_b_atm=1.000000e+200,
>>>>>>> Bx=0.000000e+00, By=0.000000e+00, Bz=0.000000e+00, gij_phys=1.295702e+00
>>>>>>> 0.000000e+00 0.000000e+00 1.295702e+00 0.000000e+00 1.295702e+00,
>>>>>>> alpha=8.746533e-01
>>>>>>>
>>>>>>> I am not sure what these error exactly mean and how to solve it.
>>>>>>>
>>>>>>> Thanks.
>>>>>>> Chia-Hui
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Users mailing list
>>>>>>> Users at einsteintoolkit.org
>>>>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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