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meeting minutes for 2018-12-03
by Steven R. Brandt 03 Dec '18

03 Dec '18

Present: Steve, Peter, Zach, Samuel, Antoni Ramos, Bill (taking minutes) LORENE2: * no Roland, no report (see below) WVUThorns: * Zach reported. He has a small-ish but not well understood LORENE2 initial data from his collaborator, has permissions to use it. * Working with Josh Faber (RIT) who is using LORENE2 for binary NS mergers, will have another small initial data set from him. * Discussion of a possible problem in LORENE2, a bug, that may make it incorrect. In the translation from French to English a subroutine was not translated. Also the LORENE1 initial data may not be useful in LORENE2. * Because of this Zach and Steve recommend proceeding with caution. Last week the conclusion had been to replace LORENE1 with LORENE2...now not recommended until this is understood/explored further. BNS gallery example: * no progress TRAC update: * Migration to BitBucket * no report ET Infrastructure Presentations: * Will be next week, 10 December 2018 during the phone meeting. * As listed in the minutes for 2018-11-26, the nominal agenda/topics and presenters are: * website: Steve * wiki: Steve * trac: Steve * svn: Steve / Peter * Jenkins: Roland * mailing lists: Steve * tutorial server: Roland * repos on bitbucket: Roland * repos on github: Roland * release process: Steve / Roland

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Compiling ET Using PGI
by Christopher Ramirez 29 Nov '18

29 Nov '18

Hello, I've been getting the following errors when trying to compile using PGI compilers and am wondering if were any additional steps needed to compile successfully. COMPILING arrangements/CactusBase/Boundary/src/ScalarBoundary.c PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cGH.h: 41) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cGH.h: 41) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cGH.h: 42) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cGH.h: 42) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cGH.h: 45) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cGH.h: 45) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cGH.h: 71) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cGH.h: 71) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Coord.h: 29) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Coord.h: 29) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Coord.h: 30) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Coord.h: 30) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Coord.h: 60) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Coord.h: 60) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Coord.h: 61) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Coord.h: 61) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Coord.h: 67) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Coord.h: 67) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Coord.h: 68) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Coord.h: 68) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Misc.h: 43) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Misc.h: 43) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Interp.h: 39) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Interp.h: 39) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Interp.h: 40) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Interp.h: 40) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Interp.h: 76) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Interp.h: 76) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/cctk_Interp.h: 77) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/cctk_Interp.h: 77) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/util_Table.h: 216) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/util_Table.h: 216) PGC-S-0040-Illegal use of symbol, CCTK_COMPLEX16 (/home/ramirez/Cactus/src/include/util_Table.h: 228) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/util_Table.h: 228) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/util_Table.h: 301) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/util_Table.h: 301) PGC-S-0040-Illegal use of symbol, CCTK_COMPLEX16 (/home/ramirez/Cactus/src/include/util_Table.h: 321) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/util_Table.h: 321) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/util_Table.h: 381) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/util_Table.h: 381) PGC-S-0040-Illegal use of symbol, CCTK_COMPLEX16 (/home/ramirez/Cactus/src/include/util_Table.h: 393) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/util_Table.h: 393) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/src/include/util_Table.h: 467) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/util_Table.h: 467) PGC-S-0040-Illegal use of symbol, CCTK_COMPLEX16 (/home/ramirez/Cactus/src/include/util_Table.h: 487) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/src/include/util_Table.h: 487) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/arrangements/CactusBase/Boundary/src/Boundary.h: 40) PGC-W-0156-Type not specified, 'int' assumed (/home/ramirez/Cactus/arrangements/CactusBase/Boundary/src/Boundary.h: 40) PGC-S-0040-Illegal use of symbol, CCTK_REAL8 (/home/ramirez/Cactus/arrangements/CactusBase/Boundary/src/Boundary.h: 42) PGC-F-0008-Error limit exceeded (/home/ramirez/Cactus/arrangements/CactusBase/Boundary/src/Boundary.h: 42) PGC/x86-64 Linux 17.10-0: compilation aborted make[3]: *** [ScalarBoundary.c.o] Error 2 make[2]: *** [make.checked] Error 2

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postdoc positions at SISSA
by Witek, Helvi 29 Nov '18

29 Nov '18

Dear all, the group at SISSA invites applications for Postdoc positions. Enrico Barausse contacted me since he is looking for outstanding candidates with a background in numerical relativity, so I hope you don't mind me advertising his position. You can find more information here: https://hyperspace.uni-frankfurt.de/2018/10/30/postdoctoral-positions-in-gr… Best wishes, Helvi =========================================== Dr. Helvi Witek Royal Society University Research Fellow Theoretical Particle Physics and Cosmology Department of Physics King's College London ===========================================

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meeting minutes for 2018-11-26
by Roland Haas 26 Nov '18

26 Nov '18

Present: Roland, Chris, Helvi, Peter, Bill, Zach, Steve memory leaks: * Roland described the current status in https://trac.einsteintoolkit.org/ticket/2194 ET tutorial server: * new server using Kubernetes and docker images is being worked on * Steve, Roland and Craig to get together to finish up things BNS gallery example: * no progress last week ET infrastructure presentations: * website: Steve * wiki: Steve * trac: Steve * svn: Steve / Peter * Jenkins: Roland * mailing lists: Steve * tutorial server: Roland * repos on bitbucket: Roland * repos on github: Roland * release process: Steve / Roland trac to bitbucket transition: * same as last week, have a working took, need to spend time to get username translation correctly * Roland estimates the amount of time needed to make the transition is something like 1/2 day of coding plus a couple days / week of busywork getting the username translation right WVUThorns: * Zach is working on getting small file size LORENE ID file permissions * there was a discussion on how to mark parfiles etc. that are only usable as tests (low res, dodgy science). Adding log output at runtime is less likely to be seen than eg a comment in the parfile. This comment should be standardized if possible. Can also add explicit comments where the parfiles differ from LORENE2: * make default in thornlist Proca / Lean: * Helvi writing docs now * Miguel updated test suites * responded to Peter's comments next release: * need name of famous scientist * current list is here: https://docs.einsteintoolkit.org/et-docs/Release_Details There are no unanswered questions on the mailing list we are aware of. 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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environmental variables in Cactus configuration files
by Miguel Zilhão 22 Nov '18

22 Nov '18

hi all, i'm compiling ET on a local cluster that uses the module system. on this system, once one does "module load <...>", the respective path is added to an environmental variable. for instance, doing $ module load HDF5 sets the environmental variable $EBROOTHDF5: $ echo $EBROOTHDF5 /home/share/easybuild/software/HDF5/1.8.20-GCC-7.3.0-2.30-generic so i was trying to use these in my configuration file, by adding the lines HDF5_DIR = $EBROOTHDF5 HDF5_LIB_DIRS = ${EBROOTHDF5}/lib HDF5_INC_DIRS = ${EBROOTHDF5}/include etc, to it. however, these environmental variables don't seem to be correctly expanded, as i get things like the following: Running configuration script for thorn HDF5: Additional requested language support: Fortran WARNING in HDF5 configuration: None of H5pubconf.h H5pubconf-64.h H5pubconf-32.h found in ${EBROOTHDF5}/lib ${EBROOTHDF5}/include Automatic detection of szip/zlib compression not possible Finished running configuration script for thorn HDF5. but if i look into the folder ${EBROOTHDF5}/include, these files are clearly there. the compilation later fails because of this. when i specify the full path explicitly in the config file: HDF5_INC_DIRS = /home/share/easybuild/software/HDF5/1.8.20-GCC-7.3.0-2.30-generic/include i get no such warnings, and the code proceeds to compile just fine. is this the expected behaviour? shouldn't the environmental variables be correctly expanded? if not, what would be the typical procedure to compile the code on systems with such module tools? thanks, Miguel

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meeting minutes for 2018-11-19
by Roland Haas 19 Nov '18

19 Nov '18

Present: Steve, Miguel, Roland, Sam, Peter, Bill, Helvi, Antoni, Zach * tasks for next Einstein Toolkit relelase trac listing: ** LORENE2, should be enable in thornlist to compile, Zac wanted to provide a small data set to load it ** WVU Thorns, Zach will try and spend time for test file creation as well as making VolumeIntegrals thorn work with pure HydroBaser ** Gallery Example, Peter will look into it, has had no time last week ** Memory leak, Roland is running with his custom memory checker to find out of a single routine allocates more and more memory as the simulation progresses * Trac migration: ** have progress ** can import all 2000 tickets ** need more work to translate user names and attachment names * Tutorial server ** will move to NCSA Nebula ** Roland to talk to Craig Willis about user authentication. We do not expect very many users, but a steady stream. * Date for ET infrastructure presentation: Steve, Roland, Peter to present the ET infrastructure on Dec 10th We expect to have low attendance for the Nov 26th call (Monday after Thanksgiving) but will have a 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://pgp.mit.edu .

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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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