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 <[email protected]> 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 <[email protected]> > *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 <[email protected]> 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 <[email protected]> >> *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 <[email protected]> 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 <[email protected]> >>> *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 <[email protected]> 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 <[email protected]> >>>> *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 <[email protected]> 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 <[email protected]> >>>>> *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 <[email protected]> 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 <[email protected]> >>>>>> *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 <[email protected]> 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 <[email protected]> >>>>>>> *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 <[email protected]> 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 >>>>>>>> [email protected] >>>>>>>> http://lists.einsteintoolkit.org/mailman/listinfo/users >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
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