[Users] error after activating IllinoisGRMHD and VolumeIntegrals_GRMHD
Zach Etienne
zachetie at gmail.com
Mon Jul 23 07:54:14 CDT 2018
Dear Chia-Hui,
Regarding the HDF5 output:
The parameter file you sent has the following parameter set:
CarpetIOHDF5::out_every = 512
CarpetIOHDF5::checkpoint = "yes"
CarpetIOHDF5::compression_level = 0
CarpetIOHDF5::one_file_per_group = "yes"
CarpetIOHDF5::open_one_input_file_at_a_time = "yes"
CarpetIOHDF5::out2D_every = 256
CarpetIOHDF5::out2D_xy = "yes"
CarpetIOHDF5::out2D_xz = "no"
CarpetIOHDF5::out2D_yz = "no"
CarpetIOHDF5::out2D_xyplane_z = 0.0
CarpetIOHDF5::out2D_vars = "
IllinoisGRMHD::rho_b
IllinoisGRMHD::P
IllinoisGRMHD::vx
IllinoisGRMHD::vy
IllinoisGRMHD::vz
IllinoisGRMHD::Bx
IllinoisGRMHD::By
IllinoisGRMHD::Bz
ADMBase::curv
ADMBase::lapse
ADMBase::metric
ADMBase::shift
ML_ADMConstraints::ml_ham
"
This means that every 512 iterations, a 2D HDF5 output in the x-y plane
will be dumped to disk. IllinoisGRMHD::rho_b is the same as HydroBase::rho,
and IllinoisGRMHD will set HydroBase::rho with a cadence given by:
convert_to_HydroBase::convert_to_HydroBase_every = 8 # needed for particle
tracer.
Thus every 8 iterations, IllinoisGRMHD will set HydroBase::rho. However,
because of the setting
CarpetIOHDF5::one_file_per_group = "yes"
it will only rho_b in the file with other variables in its variable group.
According to IllinoisGRMHD/interface.ccl, this means that rho_b will be
output to a file with "grmhd_primitives_allbutBi" in its name.
> How can I continue the simulation ?
IOUtil::checkpoint_on_terminate = "yes"
Will only checkpoint if, for example TerminationTrigger is properly
enabled.
Further, your parameter file says:
IOUtil::checkpoint_every_walltime_hours = 3
Thus you should get a checkpoint after 3 hours of letting the job run.
-Zach
* * *
Zachariah Etienne
Assistant Professor of Mathematics
West Virginia University
*https://math.wvu.edu/~zetienne/ <https://math.wvu.edu/~zetienne/>*
https://blackholesathome.net
On Mon, Jul 23, 2018 at 7:39 AM, 林家暉 <r06222015 at ntu.edu.tw> wrote:
> Dear Zach,
>
> Sorry there is another question besides generating .h5 file in the
> previous email. I try to continue my simulation by checkpoint so I have
> IOUtil::checkpoint_on_terminate = "yes", but it seems no checkpoints
> being made. So even the restart id is 1 or 2 , the simulation stars from
> the beginning . How can I continue the simulation ? The attached file is
> the parameter file I use which is only a little bit different from the
> original one.
>
> Thanks a lot.
>
>
> 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 04:41:38
>
> *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,
>
> 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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