Users July 2021

users@lists.einsteintoolkit.org

20 participants
38 discussions

Can't build on Mac OS Catalina
by Murray Wolinsky 28 Jul '21

28 Jul '21

Hi All, I'm unable to build the Einstein Toolkit on Mac OS Catalina. Has anyone done so -- and do you have suggestions? When I try to run ./simfactory/bin/sim build -j2 --thornlist ../ einsteintoolkit.th I get the following error: Cactus requires a C++11 compiler -- check your C++ compiler and C++ compiler flags I know that the Mac makes it very difficult to use gcc instead of clang, but AFAICS I'm using the Homebrew gcc-11 compiler (Homebrew GCC 11.1.0_1) 11.1.0) and setting the options and flags properly in both the files OptionsList and generic-11.cfg : Setting CC to 'gcc-11' Setting CXX to 'g++-11' Setting CXXFLAGS to '-g -std=gnu++11' etc. Do I need to set environment variables? Is there some other toolkit file I should l modify? I appreciate any help anyone can provide! Thanks in advance! Murray ____________________________________________________________ This is the output from the above sim command: ~/et/Cactus ❯ ./simfactory/bin/sim build -j2 --thornlist ../ einsteintoolkit.th base 3.8.3 11:58:06 Using configuration: sim Reconfiguring sim Writing configuration to: /Users/murray/et/Cactus/configs/sim/OptionList Cactus - version: 4.10.0 Reconfiguring sim. Using configuration options from configure line Setting fds to '3,4 -j --' End of options from configure line Adding configuration options from '/Users/murray/et/Cactus/configs/sim/OptionList'... Setting VERSION to '2021-07-27' Setting CPP to 'cpp-11' Setting CC to 'gcc-11' Setting CXX to 'g++-11' Setting FPP to 'cpp-11' Setting F90 to 'gfortran-11' Setting LIBS to 'gfortran' Setting LIBDIRS to '/usr/local/Cellar/gcc/11.1.0_1/lib/gcc/11/ /usr/local/lib/' Setting CPPFLAGS to '-g -std=gnu++11' Setting FPPFLAGS to '-traditional' Setting CFLAGS to '-g -std=gnu99' Setting CXXFLAGS to '-g -std=gnu++11' Setting F90FLAGS to '-g -fcray-pointer -ffixed-line-length-none' Setting LDFLAGS to '-rdynamic -I/usr/local/lib/gfortran' Setting DEBUG to 'no' Setting CPP_DEBUG_FLAGS to '' Setting C_DEBUG_FLAGS to '' Setting CXX_DEBUG_FLAGS to '' Setting OPTIMISE to 'yes' Setting CPP_OPTIMISE_FLAGS to '' Setting C_OPTIMISE_FLAGS to '-O2' Setting CXX_OPTIMISE_FLAGS to '-O2' Setting F90_OPTIMISE_FLAGS to '-O2' Setting PROFILE to 'no' Setting CPP_PROFILE_FLAGS to '' Setting C_PROFILE_FLAGS to '-pg' Setting CXX_PROFILE_FLAGS to '-pg' Setting F90_PROFILE_FLAGS to '-pg' Setting WARN to 'yes' Setting CPP_WARN_FLAGS to '-Wall' Setting C_WARN_FLAGS to '-Wall' Setting CXX_WARN_FLAGS to '-Wall' Setting F90_WARN_FLAGS to '-Wall' Setting OPENMP to 'yes' Setting CPP_OPENMP_FLAGS to '-fopenmp' Setting FPP_OPENMP_FLAGS to '-D_OPENMP' Setting C_OPENMP_FLAGS to '-fopenmp' Setting CXX_OPENMP_FLAGS to '-fopenmp' Setting F90_OPENMP_FLAGS to '-fopenmp' Setting VECTORISE to 'yes' Setting VECTORISE_ALIGNED_ARRAYS to 'no' Setting VECTORISE_INLINE to 'yes' Setting PTHREADS_DIR to 'NO_BUILD' End of options from '/Users/murray/et/Cactus/configs/sim/OptionList'. creating cache ./config.cache checking host system type... x86_64-apple-darwin19.6.0 checking for mawk... no checking for gawk... no checking for nawk... no checking for awk... awk checking whether make sets ${MAKE}... yes checking whether the C compiler (gcc-11 -g -std=gnu99 -rdynamic -I/usr/local/lib/gfortran) works... yes checking whether the C compiler (gcc-11 -g -std=gnu99 -rdynamic -I/usr/local/lib/gfortran) is a cross-compiler... no checking whether we are using GNU C... yes checking whether the C++ compiler (g++-11 -g -std=gnu++11 -rdynamic -I/usr/local/lib/gfortran) works... yes checking whether the C++ compiler (g++-11 -g -std=gnu++11 -rdynamic -I/usr/local/lib/gfortran) is a cross-compiler... no checking whether we are using GNU C++... yes checking for nvcc... no checking for ranlib... ranlib checking for perl... perl checking for gtar... no checking for tar... tar checking for xargs... xargs checking for gzip... gzip checking for gpatch... no checking for patch... patch checking for git... git checking for ar... ar checking for mkdir... mkdir checking for bash... /bin/sh checking whether the Fortran compiler (gfortran-11 ) works... yes checking whether the Fortran compiler (gfortran-11 ) is a cross-compiler... no checking whether the Fortran compiler (gfortran-11 ) supports TYPE(*) for CCTK_PointerTo... yes checking how to run the C preprocessor... cpp-11 checking for ANSI C header files... no checking for C99 features... yes checking for M_PI... yes checking for C strdup... yes checking for C++ strdup... yes checking whether byte ordering is bigendian... no checking size of long long... 8 checking size of long int... 8 checking size of int... 4 checking size of short int... 2 checking size of long double... 16 checking size of double... 8 checking size of float... 4 checking size of char *... 8 checking for the null device... /dev/null checking for gethostbyname... yes checking whether mode_t is defined... yes checking for availability of gettimeofday timing... yes checking if gettimeofday needs timezone... yes checking for availability of getrusage timing... yes checking for availability of _ftime timing... no checking for time.h... yes checking for sys/time.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for string.h... yes checking for assert.h... yes checking for tgmath.h... yes checking for sys/stat.h... yes checking for getopt.h... yes checking for dirent.h... yes checking for c_asm.h... no checking for intrinsics.h... no checking for mach/mach_time.h... yes checking for regex.h... yes checking for sys/filio.h... yes checking for sys/ioctl.h... yes checking for sys/socket.h... yes checking for netinet/in.h... yes checking for netdb.h... yes checking for arpa/inet.h... yes checking for winsock2.h... no checking for crypt.h... no checking for signal.h... yes checking for malloc.h... no checking for sched.h... yes checking for execinfo.h... yes checking whether time.h and sys/time.h may both be included... yes checking whether socklen_t is defined... yes checking whether SOCKET is defined... no checking for hrtime_t... no checking for gethrtime... no checking for read_real_time... no checking for time_base_to_time... no checking for clock_gettime... yes checking for mach_absolute_time... yes checking for _rtc intrinsic... no checking for mallinfo... no checking for mallopt... no checking for malloc_info... no checking whether M_MMAP_THRESHOLD is defined... no checking for sched_getaffinity... no checking for getpid... yes checking if __int64 is defined... no checking if __int128 is defined... yes checking for vector... yes checking for vector.h... no checking if Intel compiler has broken restrict... no checking if compiler has broken omp collapse... no checking for getopt_long_only... yes checking for working const... yes checking for C inline... inline checking for C static inline... static inline checking for C restrict... restrict checking for C++ restrict... __restrict__ checking for C++ copysign... std::copysign checking for C++ fpclassify... std::fpclassify checking for C++ isfinite... std::isfinite checking for C++ isinf... std::isinf checking for C++ isnan... std::isnan checking for C++ isnormal... std::isnormal checking for C++ signbit... std::signbit checking for C _Pragma... yes checking for C data __attribute__((__common__))... yes checking for C+ data __attribute__((__common__))... yes checking for C function __attribute__((__noinline__))... yes checking for C++ function __attribute__((__noinline__))... yes checking for C++ member function __attribute__((__noinline__))... yes checking for C function __attribute__((__always_inline__))... yes checking for C++ function __attribute__((__always_inline__))... yes checking for C++ member function __attribute__((__always_inline__))... yes checking for C __attribute__((__unused__))... yes checking for C++ __attribute__((__unused__))... yes checking for C __attribute__((__aligned__(...)))... yes checking for C++ __attribute__((__aligned__(...)))... yes checking for C __attribute__((__cold__))... yes checking for C++ __attribute__((__cold__))... yes checking for C __attribute__((__hot__))... yes checking for C++ __attribute__((__hot__))... yes checking for C __attribute__((__format__(printf, 1, 2)))... yes checking for C++ __attribute__((__format__(printf, 1, 2)))... yes checking for C __attribute__((__noreturn__))... yes checking for C++ __attribute__((__noreturn__))... yes checking for C __attribute__((__nonnull__))... yes checking for C++ __attribute__((__nonnull__))... yes checking for C __attribute__((__returns_nonnull__))... yes checking for C++ __attribute__((__returns_nonnull__))... yes checking for C __builtin_expect... yes checking for C++ __builtin_expect... yes checking for C __builtin_trap... yes checking for C++ __builtin_trap... yes checking for C __builtin_unreachable... yes checking for C++ __builtin_unreachable... yes checking for C __builtin_assume_aligned... yes checking for C++ __builtin_assume_aligned... yes checking for C++ static_assert... yes checking for C++ auto specifier... yes checking for C++ lambda expressions... yes checking for C++ range-based for statements... no Cactus requires a C++11 compiler -- check your C++ compiler and C++ compiler flags

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Adding unofficial thorns to GetComponents script
by Konrad Topolski 28 Jul '21

28 Jul '21

Hi, Yesterday at the summer school we learnt in the comments that a Frankfurt-developed version of Kadath (ID solver) was made public recently - fuka. Great news too. I was trying to incorporate it into the GetComponents script - and the repos from: https://bitbucket.org/fukaws/ indeed land successfully in Cactus/repos. However, the symbolic links in arrangements directory are not being made the same way the rest of the ET thorns are. lrwxrwxrwx 1 topolski icm-users 21 07-28 12:30 fuka -> ../../repos/fuka/fuka lrwxrwxrwx 1 topolski icm-users 41 07-28 12:30 kadathimporter -> ../../repos /kadathimporter/kadathimporter lrwxrwxrwx 1 topolski icm-users 37 07-28 12:30 kadath_pizza -> ../../repos/kadath_pizza/kadath_pizza lrwxrwxrwx 1 topolski icm-users 35 07-28 12:30 kadaththorn -> ../../repos/kadaththorn/kadaththorn Trying to enter any of these results in "there is no such file or directory". Here's my thorn list part for GetComponents script: !TARGET = $ARR !TYPE = git !URL = https://bitbucket.org/fukaws/$2 !REPO_PATH = $2 !CHECKOUT = Kadath/fuka Kadath/kadath_pizza Kadath/kadathimporter Kadath/kadaththorn If I, however, place the thorns manually in arrangements/Kadath/, what I'm getting upon ./simfactory/bin/sim build okeanos_custom --machine=okeanos --optionlist=simfactory/mdb/optionlists/okeanos_custom.cfg --submitscript=okeanos.sub --runscript=okeanos.run --thornlist=../ einsteintoolkit_custom.th is: CST error in /lustre/tetyda/home/topolski/Cactus/lib/sbin/CST (at 317) -> Kadath/fuka - missing ccl file(s) CST error 2: -> Thorn 'kadath_pizza' requires the capability 'PizzaBase'. Please add a thorn that provides 'PizzaBase' to your ThornList or remove 'kadath_pizza' from it ! CST error 3: -> Thorn 'kadath_pizza' requires the capability 'PizzaIDBase'. Please add a thorn that provides 'PizzaIDBase' to your ThornList or remove 'kadath_pizza' from it ! CST error in /lustre/tetyda/home/topolski/Cactus/repos/flesh/lib/sbin/ interface_parser.pl (at 296) -> KADATH_PIZZA (thorn kadath_pizza) inherits from PizzaBase No thorn in your current ThornList implements PizzaBase Either remove kadath_pizza, or add a thorn to your ThornList implementing PizzaBase No thorns in arrangements directory implement PizzaBase CST error in /lustre/tetyda/home/topolski/Cactus/repos/flesh/lib/sbin/ interface_parser.pl (at 296) -> KADATH_PIZZA (thorn kadath_pizza) inherits from PizzaIDBase No thorn in your current ThornList implements PizzaIDBase Either remove kadath_pizza, or add a thorn to your ThornList implementing PizzaIDBase No thorns in arrangements directory implement PizzaIDBase Best regards Konrad Topolski

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North American Einstein Toolkit summer school day 2 recap
by workshop＠einsteintoolkit.org 27 Jul '21

27 Jul '21

Hello all, the second day of the virtual North American Einstein Toolkit Summer School 2021 was all about initial data: almost 120 participants learned about the theoretical foundation behind binary neutron star initial data codes (Joshua Faber), how to generate initial data using LORENE (Atul Kedia), and finally how to use LORENE initial data with the Einstein Toolkit (Bruno Giacomazzo). Gabriele Bozzola showcased kuibit a free and open-source Python library to analyze and visualize Einstein Toolkit simulations with a strong focus on accessible documentation and usability. Continuing a series of presentations around CarpetX, Erik Schnetter provided an update on the current status of the future CarpetX driver thorn for the Einstein Toolkit, based on AMReX. Erik also stuck around for the tutorial help session after the school ended and gave an ad-hoc tutorial on how the parts of a typical Einstein Toolkit parameter file for binary black hole simulations are set. All recordings and slides are now uploaded to the respective talk pages and collected in a YouTube playlist: https://youtube.com/playlist?list=PLRxi-yB7cTGfIPyQLSNulydOAPSPHN2Hc Please join us again tomorrow at 8:25 AM CDT via Zoom or via the YouTube stream at: https://go.illinois.edu/et2021uiuc for more interesting presentations and lightning talks. See the program https://einsteintoolkit.github.io/et2021uiuc/program.html for upcoming presentations and tutorials. Yours, the organizers

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North American Einstein Toolkit summer school day 1 recap
by workshop＠einsteintoolkit.org 26 Jul '21

26 Jul '21

Hello all, the first day of the virtual North American Einstein Toolkit Summer School 2021 is over and we were very happy to see so many particpants and exciting presentations. More than 130 participants joined Helvi Witek's lecture on Numerical Relativity, and more than 100 students took part in Steven R. Brandt's Introduction to the Einstein Toolkit. We heard a very interesting presentation by Donald Willcox about AMReX, the infrastructure behind the next generation mesh refinement driver for the Einstein Toolkit: CarpetX. Finally lightning talks by Santiago Jaraba, Thiago Assumpcao, and Hayley Macpherson rounded out the day's events. All recordings and slides are now uploaed to the respective talk pages and collected in a YouTube playlist: https://youtube.com/playlist?list=PLRxi-yB7cTGfIPyQLSNulydOAPSPHN2Hc Please join us again tommorow at 8:25 AM CDT via Zoom or via the YouTube stream at: https://go.illinois.edu/et2021uiuc for more interesting presentations and tutorials on the, now much larger, tutorial server. See the program https://einsteintoolkit.github.io/et2021uiuc/program.html for upcoming presentations and tutorials. Yours, the organizers

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Unexpected Hamiltonian constraint violation from refinement when using CCZ4
by CHEN, Kenneth 26 Jul '21

26 Jul '21

While using CCZ4 to simulate a single star, the Hamiltonian constraint violation initially came from the star surface as expected, but after some time, the violation was dominated by areas near corners of refinement levels (by Carpet) as shown in following figures, which were strange. Any suggestions? Thanks and regards, KZ [cid:dde3bc76-5092-4cf5-91c4-2e86b59e3dbd] [cid:f02f345c-bc52-4701-9d0c-66013d123c95] [cid:ea736a88-1566-4321-93c6-093fbd7bad35] [cid:9c6d9aca-98f3-4488-ae60-b927bd525ff4]

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sim error
by Tomas Andrade 23 Jul '21

23 Jul '21

Hi all, I'm encountering the same building error as described by Hamideh Hosseini on Fri, 16 Jul 2021 07:11:58 -0700 (sorry, can't seem to find a way to reply to that thread). The error is [test-vectors-4-SSE.cc.o] Error 1 make[2]: *** [make.checked] Error 2 make[1]: *** [/home/hhossei/Cactus/configs/sim/lib/libthorn_Vectors.a] Error 2 & Creating /home/hhossei/Cactus/configs/sim/lib/libthorn_Fortran.a make: *** [sim] Error 2 I'm working on a cluster with Linux Centos7. As suggested by Roland Haas on the previous thread, I attach the files make.log configs/sim/config-info configs/sim/config-data/config.log and configs/sim/config-data/make.config.defn Do you have any advice? Thank you! Tomas -- Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir informació confidencial o protegida legalment i s’adreça exclusivament a la persona o entitat destinatària. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver. Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener. This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account.

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Meeting Minutes 2021-07-22
by Gabella, William E 22 Jul '21

22 Jul '21

Present: Roland H, Bill G, Steve B, Yosef Z, David B, Atul K, Leonardo W, Indrani B, Bruno G, Chair: Roland H, Minutes: Bill G * AOB Steve, the tutorial server for the workshop next week is up and running, ETK1 https://etk1.cct.lsu.edu , see Steve for magic codes. Would like people to test it. Should be able to compile and run the toolkit...it is actually pre-compiled, so it finishes in a minute. Account and data will stay around for anythign we make before the workshop. Steve if you want ot use the tutorial server on your laptop in a container see, https://github.com/nds-org/jupyter-et/blob/master/tutorial-server/docker-co… . * ET summer school update [RH] Next Week! https://einsteintoolkit.github.io/et2021uiuc/ Roland, 280 registered participants. Most of the speakers have title and abstracts in. Sam Cupp is testing code, notebooks. Atul, How to run Lorene? Roland, a runtime question. Atul, runtime is 30 m to 1 hour, maybe have them do it the day before the class. Will be a pre-compiled version of Lorene too. Bruno, If you produce initial data, then we can visualize it on the tutorial server, easy if using Josh Faber's POWER. Bruno and Atul discuss some details of the workshop classes for BNS and Lorene, handling EOS, etc. * SPEC benchmark contribution [https://bitbucket.org/einsteintoolkit/tickets/issues/2470 task] [RH, SB] Roland, have to send email to the SPEC people...still needs to be sent. * Search for next ET release manager [RH] Next release is around November...maybe mid-November to avoid US Thanksgiving holiday. * [https://www.einsteintoolkit.org/tools/unanswered.php unanswered question on mailing list] Shamims' email, would like a BHNS initial data and other useful ET files. BHNS reader is NOT active in ET. Should close it by saying we do not have this. Bruno, we have a reader but it is private. Could make it public but without support. Steve, we should have this in the Toolkit. Kopolski's email about changing MPI ranks, looks like he is answered. Heel Kim, vectorization problem, looks like this is being answered. Heel Kim also investigates recon method for MHD code and WENO, this needs further investigation. Also the Mid-West Relativity meeting announcement, 11-13 November 2021. http://lists.einsteintoolkit.org/pipermail/users/2021-July/008066.html * [https://bitbucket.org/einsteintoolkit/tickets/issues?status=open&status=new… open tickets sorted by update time] Open Tickets: #2540 Hamiltonian violation, Carpet boundaries using CCZ4. * [https://bitbucket.org/einsteintoolkit/tickets/issues?status=new&status=open… tickets ready for review] All the usual ones. * AOB Aug 5th, Chair Yosef Z., and Minute taker Steve B. (week after school) -- ============================== William Gabella Research Assistant Professor Department of Physics and Astronomy Nashville, TN USA (o) 615-343-2713

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Einstein Toolkit Meeting Reminder
by users＠einsteintoolkit.org 21 Jul '21

21 Jul '21

Hello, Please consider joining the weekly Einstein Toolkit phone call at 9:00 am US central time on Thursdays. For details on how to connect and what agenda items are to be discussed, use the link below. https://docs.einsteintoolkit.org/et-docs/Main_Page#Weekly_Users_Call --The Maintainers

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Agenda for Thursday's Meeting
by users＠einsteintoolkit.org 19 Jul '21

19 Jul '21

Please update the Wiki with agenda items for Thursday's meeting. Thanks! https://docs.einsteintoolkit.org/et-docs/meeting_agenda --The Maintainers

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information on ET activities for "Welcome" talk at UIUC ET summer school
by Roland Haas 19 Jul '21

19 Jul '21

Hello all, I am drafting some few slides for the "Welcome to the school" 15 minutes presentation at the ET summer school on July 26th. I would ideally want to mention all the efforts in the Einstein Toolkt community, or at least as many as are feasible given space and time constraints. So if you have a 0.5 line description of something you would like me to advertise, and possibly a nice picture then that would be very nice for me to have. Items will be added first come, first serve until I run out of space on the slides. 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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