Users November 2018

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14 participants
19 discussions

Re: [Users] Summatiobyparts compilation failure on ARA cluster (latest ET release)
by Andrea Endrizzi 17 Nov '18

17 Nov '18

Hi all, Thanks for the tip, I'll try it on Monday! (I just moved and I have no internet at the new apartment)! Bests, Andrea On 17 Nov 2018 00:47, "Peter Diener" <diener(a)cct.lsu.edu> wrote: Hi Andrea, Roland pointed out in a separate e-mail that in your optionlist, you set FPP = fpp. I didn't notice that earlier. It is very likely that setting FPP = cpp instead will fix your problem. This is used in all option files in simfactory. Cheers, Peter On Friday 2018-11-16 15:20, Peter Diener wrote: Date: Fri, 16 Nov 2018 15:20:56 > From: Peter Diener <diener(a)cct.lsu.edu> > To: Roland Haas <rhaas(a)illinois.edu> > > Cc: Erik Schnetter <schnetter(a)protonmail.com>, > Andrea Endrizzi <aendrizzi7(a)gmail.com>, > Einstein Toolkit Users <users(a)einsteintoolkit.org> > Subject: Re: [Users] Summatiobyparts compilation failure on ARA cluster > (latest > ET release) > > hi Roland, > > FPPFLAGS=-traditional > > was included in the optionlist that Andrea attached to the e-mail. > > Cheers, > > Peter > > On Friday 2018-11-16 15:17, Roland Haas wrote: > > Date: Fri, 16 Nov 2018 15:17:08 >> From: Roland Haas <rhaas(a)illinois.edu> >> To: Peter Diener <diener(a)cct.lsu.edu> >> Cc: Erik Schnetter <schnetter(a)protonmail.com>, >> Andrea Endrizzi <aendrizzi7(a)gmail.com>, >> Einstein Toolkit Users <users(a)einsteintoolkit.org> >> Subject: Re: [Users] Summatiobyparts compilation failure on ARA cluster >> (latest >> ET release) >> >> Hello all, >> >> this is just a blind guess but I have seen various strange Fortan >> compiler errors if one forgets to include "-traditional" in the FPPFLAGS >> options in the option list. >> >> If you do not set FPPFLAGS at all then you should be good since the >> default includes it, however if you eg have >> >> FPPFLAGS=-DFOO >> >> then you have to change it to be >> >> FPPFLAGS=-DFOO -traditional >> >> Yours, >> Roland >> >> Hi Andrea, >>> >>> The error message points to line 11 in the source file, which is the >>> line that contains >>> >>> DECLARE_CCTK_FUNCTIONS >>> >>> This is expanded by a C-preprocessor before being handed of to the >>> compiler. >>> >>> The preprocessed file can be found in the directory: >>> >>> /home/wa65fop/CS_Wu/THC_ZM1/Cactus/configs/<your config >>> name>/build/SummationByParts >>> >>> and is named Derivatives_2_1.f90. >>> >>> It seems like the C-preprocessor is not expanding >>> "DECLARE_CCTK_FUNCTIONS" correctly and that the preprocessed file >>> contains a line like: >>> >>> end interface & interface >>> >>> which is clearly not valid fortran. Can you check your preprocessed file >>> and verify that this is indeed present? >>> >>> I don't see anything obviously wrong with your preprocessor flags, but >>> why is there a >>> -I/opt/intel/compilers_and_libraries_2018.0.128/linux/mpi/ >>> intel64/include >>> in your CPPFLAGS in you options file? >>> >>> Cheers, >>> >>> Peter >>> >>> On Friday 2018-11-16 11:08, Erik Schnetter wrote: >>> >>> Date: Fri, 16 Nov 2018 11:08:48 >>>> From: Erik Schnetter <schnetter(a)protonmail.com> >>>> To: Andrea Endrizzi <aendrizzi7(a)gmail.com> >>>> Cc: Einstein Toolkit Users <users(a)einsteintoolkit.org> >>>> Subject: Re: [Users] Summatiobyparts compilation failure on ARA cluster >>>> (latest >>>> ET release) >>>> >>>> Andrea >>>> >>>> The error message quotes a line that is not and should not be present >>>> in the source code. I wonder whether maybe your source file has >>>> somehow become corrupted? >>>> >>>> Can you attach the file >>>> /home/wa65fop/CS_Wu/THC_ZM1/Cactus/arrangements/CactusNumeri >>>> cal/SummationByParts/src/Derivatives_2_1.F90 >>>> from your source tree, as well as the preprecessed file >>>> /home/wa65fop/CS_Wu/THC_ZM1/Cactus/configs/whiskyTHC_ZM1/bui >>>> ld/SummationByParts/Derivatives_2_1.f90? >>>> >>>> -erik >>>> >>>> On Nov 16, 2018, at 1:51 , Andrea Endrizzi <aendrizzi7(a)gmail.com> >>>>> wrote: >>>>> >>>>> Good morning, >>>>> I was trying to compile ET on ARA cluster, specifically with the >>>>> latest intel compilers (2018, Update 3). All the C/C++ code compiled >>>>> nicely, but when reaching the SummationByParts thorn, the file >>>>> Derivatives_2_1.F90 failed (attached is a .txt of the error). I never >>>>> saw this kind of error before when compiling previous versions of ET, >>>>> but it seems to complain about syntax in a file that looked ok when I >>>>> opened the source. Could it be related to the compiler/the compiler's >>>>> flags I'm using? If that may be the case, I also attach the .cfg file >>>>> I'm using (architecture of the nodes is Skylake). I am currently >>>>> trying to build with a previous version, to check whether it is >>>>> version-related or just a problem on my side. >>>>> >>>>> Thanks already for your attention! >>>>> >>>>> Best regards, >>>>> >>>>> Andrea Endrizzi >>>>> <error_report_summationbyparts.txt><ara-skl-icc_v0.1.cfg> >>>>> >>>> >>>> -- >>>> Erik Schnetter <schnetter(a)protonmail.com> >>>> http://www.perimeterinstitute.ca/personal/eschnetter/ >>>> >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> Users mailing list >>> Users(a)einsteintoolkit.org >>> http://lists.einsteintoolkit.org/mailman/listinfo/users >>> >> >> >> >> -- >> My email is as private as my paper mail. I therefore support encrypting >> and signing email messages. Get my PGP key from http://keys.gnupg.net. >> >> > >

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Summatiobyparts compilation failure on ARA cluster (latest ET release)
by Andrea Endrizzi 16 Nov '18

16 Nov '18

Good morning, I was trying to compile ET on ARA cluster, specifically with the latest intel compilers (2018, Update 3). All the C/C++ code compiled nicely, but when reaching the SummationByParts thorn, the file Derivatives_2_1.F90 failed (attached is a .txt of the error). I never saw this kind of error before when compiling previous versions of ET, but it seems to complain about syntax in a file that looked ok when I opened the source. Could it be related to the compiler/the compiler's flags I'm using? If that may be the case, I also attach the .cfg file I'm using (architecture of the nodes is Skylake). I am currently trying to build with a previous version, to check whether it is version-related or just a problem on my side. Thanks already for your attention! Best regards, Andrea Endrizzi

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Baryonic mass
by Theodoros Soultanis 12 Nov '18

12 Nov '18

Good morning, It would be greatly appreciated if you could give me some feedback regarding the following topic. I would like know whether it is possible to calculate the total baryonic mass of the given system during the evolution within the ET ( maybe there is a module which I was not able to find) or I have to compute it externally. Thank you. Sincerely, Theodoros Soultanis

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No meeting Monday, Nov 12 2018
by Roland Haas 11 Nov '18

11 Nov '18

Hello all, due to supercomputing 2018 we will skip Monday's ET call. Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net.

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problems about accretion disk of binary neutron star
by 黃世杰 08 Nov '18

08 Nov '18

Dear all, I want to add energy into the accretion disk of the binary neutron star merger in gallery code(https://einsteintoolkit.org/gallery/bns/index.html)and calculate the accretion rate (dM/dt) do I need to add some other thorn into the simulation, or could just modify the parameter file of the gallery code? Thank you Gratefully, Jie

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Trac
by Steven R. Brandt 08 Nov '18

08 Nov '18

We have a solution for our Trac woes--and Christmas isn't even here yet. If you wish to have access to Trac, and currently do not have such, please email Richard Raether, CC'd above, and he will create an external user CCT account for you. With this account, you will be able to login to Trac, create tickets, and otherwise have fun. --Steve

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cctk_alignment
by Steven R. Brandt 07 Nov '18

07 Nov '18

I'm debugging a modification to Cactus, and something I've done has tripped an assertion error when running the RK2-central.par test. The message is: cactus_sim: /home/sbrandt/et-tester/Cactus/configs/sim/build/TestMoL/Init.c:40: TestMoL_InitVars: Assertion `cctki0_ialn>0' failed. The variable cctki0_ialn seems to get filled in from cctkGH->cctk_alignment, which is (as far as I can see) only set in mode.cc by carpet. The test in question, however, uses PUGH. Valgrind confirms that just before the assertion error, I am tripping a conditional depends on uninitialized value error. However, I don't see this same problem when running with the unmodified Cactus source--so somehow I've broken something relating to this infrastructure. How and where is cctk_alignment supposed to get set when running PUGH? What should its value be? Thanks. --Steve

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Hydro_RNSID Inherits from GRHydro
by Zach Etienne 05 Nov '18

05 Nov '18

Hello, Hydro_RNSID inherits from GRHydro, which goes against the usual policy that initial data thorns depend only on HydroBase / ADMBase. Is there a plan to fix this? Is a fix even difficult? -Zach * * * Zachariah Etienne Assistant Professor of Mathematics West Virginia University *https://math.wvu.edu/~zetienne/ <https://math.wvu.edu/~zetienne/>* https://blackholesathome.net

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meeting minutes for 2018-11-05
by Roland Haas 05 Nov '18

05 Nov '18

Present: Roland, Antoni, Bill, Bruno, Chris, Federico Cipoletta, Hassan Khalvati, Steve, Zach LORENE2: * switch thornlist to have LORENE2 as the default WVUThorns: * postpone to after SC BNS gallery example * postpone to after SC Possible Carpet memory leak * Steve looked at this with Valgrind * Roland pointed out that Carpet does not (as far as he knows) Trac to bitbucket transfer: * can transfer user name properly * still stuck with creating many tickets (ticket 13 is the one that gets stuck) Restmass computation * Federico added capabilities to Hydro_Analaysis to compute rest mass * tested with a TOV star and GRHydro and IllinoisGRMHD * asked to create pull request on bitbucket Yours, Roland -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .

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Users November 2018