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@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@ntu.edu.twmailto:r06222015@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@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users

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@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_B...

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@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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@ntu.edu.twmailto:r06222015@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@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users

Dear Zach, It seems that none parameter file in https://bitbucket.org/zach_etienne/wvuthorns_diagnostics/src/a7dfd31684ba/Me... 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@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://blackholesathome.net

On Tue, Jul 17, 2018 at 9:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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_B...

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@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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@ntu.edu.twmailto:r06222015@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@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users

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@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://blackholesathome.net

On Tue, Jul 17, 2018 at 10:18 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@ntu.edu.tw> wrote: Dear Zach, It seems that none parameter file in https://bitbucket.org/zach_etienne/wvuthorns_diagnostics/src/a7dfd31684ba/Me... 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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 9:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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_B...

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@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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@ntu.edu.twmailto:r06222015@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@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users

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__tracks__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@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://blackholesathome.net

On Wed, Jul 18, 2018 at 2:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 10:18 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@ntu.edu.tw> wrote: Dear Zach, It seems that none parameter file in https://bitbucket.org/zach_etienne/wvuthorns_diagnostics/src/a7dfd31684ba/Me... 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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 9:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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_B...

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@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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@ntu.edu.twmailto:r06222015@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@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users

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@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 teleconhttp://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://blackholesathome.net

On Thu, Jul 19, 2018 at 9:30 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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__tracks__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@gmail.commailto:zachetie@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://blackholesathome.net

On Wed, Jul 18, 2018 at 2:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 10:18 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@ntu.edu.tw> wrote: Dear Zach, It seems that none parameter file in https://bitbucket.org/zach_etienne/wvuthorns_diagnostics/src/a7dfd31684ba/Me... 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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 9:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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_B...

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@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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@ntu.edu.twmailto:r06222015@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@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users

Dear Zach,

After I disabled TerminationTrigger, the code runs well without further problem.

Thank you a lot !

Best regards,

Chia-Hui

________________________________ 寄件者: Zach Etienne zachetie@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://blackholesathome.net

On Thu, Jul 19, 2018 at 2:36 PM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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 teleconhttp://whenisgood.net/pfjbm3c whenisgood.nethttp://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://blackholesathome.net

On Thu, Jul 19, 2018 at 9:30 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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__tracks__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@gmail.commailto:zachetie@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://blackholesathome.net

On Wed, Jul 18, 2018 at 2:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 10:18 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@ntu.edu.tw> wrote: Dear Zach, It seems that none parameter file in https://bitbucket.org/zach_etienne/wvuthorns_diagnostics/src/a7dfd31684ba/Me... 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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 9:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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_B...

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@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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@ntu.edu.twmailto:r06222015@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@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users

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@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://blackholesathome.net

On Thu, Jul 19, 2018 at 2:36 PM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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 teleconhttp://whenisgood.net/pfjbm3c whenisgood.nethttp://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://blackholesathome.net

On Thu, Jul 19, 2018 at 9:30 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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__tracks__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@gmail.commailto:zachetie@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://blackholesathome.net

On Wed, Jul 18, 2018 at 2:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 10:18 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@ntu.edu.tw> wrote: Dear Zach, It seems that none parameter file in https://bitbucket.org/zach_etienne/wvuthorns_diagnostics/src/a7dfd31684ba/Me... 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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 9:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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_B...

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@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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@ntu.edu.twmailto:r06222015@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@einsteintoolkit.orgmailto:Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users

Dear Zach, I think I have misunderstood CarpetIOHDF5::out2D_every = 256 and CarpetIOHDF5::out_every = 512 because my simulation was until iter=330 so I expected there are some .h5 files. And I also successfully made checkpoints after running more than the checkpoint_every_walltime_hours. After continuing the simulation I finally got the desired files. Thank you a lot for your detailed information.

Best regards, Chia-Hui ________________________________ 寄件者: Zach Etienne zachetie@gmail.com 寄件日期: 2018年7月23日 下午 08:54:14 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,

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://blackholesathome.net

On Mon, Jul 23, 2018 at 7:39 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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://blackholesathome.net

On Thu, Jul 19, 2018 at 2:36 PM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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 teleconhttp://whenisgood.net/pfjbm3c whenisgood.nethttp://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://blackholesathome.net

On Thu, Jul 19, 2018 at 9:30 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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__tracks__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@gmail.commailto:zachetie@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://blackholesathome.net

On Wed, Jul 18, 2018 at 2:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 10:18 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@ntu.edu.tw> wrote: Dear Zach, It seems that none parameter file in https://bitbucket.org/zach_etienne/wvuthorns_diagnostics/src/a7dfd31684ba/Me... 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@gmail.commailto:zachetie@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://blackholesathome.net

On Tue, Jul 17, 2018 at 9:26 AM, 林家暉 <r06222015@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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_B...

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@ntu.edu.twmailto:r06222015@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@gmail.commailto:zachetie@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@ntu.edu.twmailto:r06222015@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

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