September 2024 - Trac - lists.einsteintoolkit.org

#2826: NRPyEllipticET documentation file uses extra LaTeX package
by Roland Haas 05 Sep '24

05 Sep '24

#2826: NRPyEllipticET documentation file uses extra LaTeX package Reporter: Roland Haas Status: new Milestone: Version: Type: bug Priority: major Component: Using extra packages $`listing` in this case$ breaks the `<config>-ThornGuide` target which builds a single PDF file with all documentation $[http://einsteintoolkit.org/usersguide/UsersGuide.html#x1-34000B3.3](http://einsteintoolkit.org/usersguide/UsersGuide.html#x1-34000B3.3)$. The only packages that may be used $and they don’t need a `\usepackage`$ are those already required by `cactus.sty`: ``` $ grep RequirePackage repos/flesh/doc/latex/cactus.sty \RequirePackage[utf8]{inputenc} \RequirePackage{fancyhdr} \RequirePackage{graphicx} \RequirePackage{latexsym} \RequirePackage{amssymb} \RequirePackage{amsmath} \RequirePackage{ifthen} \RequirePackage{calc} \RequirePackage{thumbpdf} \RequirePackage{hyperref} ``` ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2826/nrpyellipticet-do…

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#2825: GRHayL documentation files uses extra LaTeX package
by Roland Haas 05 Sep '24

05 Sep '24

#2825: GRHayL documentation files uses extra LaTeX package Reporter: Roland Haas Status: new Milestone: Version: Type: bug Priority: major Component: Using extra packages $`xspace` in this case$ breaks the `<config>-ThornGuide` target which builds a single PDF file with all documentation $[http://einsteintoolkit.org/usersguide/UsersGuide.html#x1-34000B3.3](http://einsteintoolkit.org/usersguide/UsersGuide.html#x1-34000B3.3)$. The only packages that may be used $and they don’t need a `\usepackage`$ are those already required by `cactus.sty`: ``` $ grep RequirePackage repos/flesh/doc/latex/cactus.sty \RequirePackage[utf8]{inputenc} \RequirePackage{fancyhdr} \RequirePackage{graphicx} \RequirePackage{latexsym} \RequirePackage{amssymb} \RequirePackage{amsmath} \RequirePackage{ifthen} \RequirePackage{calc} \RequirePackage{thumbpdf} \RequirePackage{hyperref} ``` ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2825/grhayl-documentat…

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#2824: CarpetX documentation file uses extra LaTeX package
by Roland Haas 05 Sep '24

05 Sep '24

#2824: CarpetX documentation file uses extra LaTeX package Reporter: Roland Haas Status: new Milestone: Version: Type: bug Priority: minor Component: Using extra packages $`listing` in this case$ breaks the `<config>-ThornGuide` target which builds a single PDF file with all documentation $[http://einsteintoolkit.org/usersguide/UsersGuide.html#x1-34000B3.3](http://einsteintoolkit.org/usersguide/UsersGuide.html#x1-34000B3.3)$. The only packages that may be used $and they don’t need a `\usepackage`$ are those already required by `cactus.sty`: ``` $ grep RequirePackage repos/flesh/doc/latex/cactus.sty \RequirePackage[utf8]{inputenc} \RequirePackage{fancyhdr} \RequirePackage{graphicx} \RequirePackage{latexsym} \RequirePackage{amssymb} \RequirePackage{amsmath} \RequirePackage{ifthen} \RequirePackage{calc} \RequirePackage{thumbpdf} \RequirePackage{hyperref} ``` ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2824/carpetx-documenta…

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#2823: Include TOVola: An enhanced TOV solver with Tabulated EOS support
by David Boyer 05 Sep '24

05 Sep '24

#2823: Include TOVola: An enhanced TOV solver with Tabulated EOS support Reporter: David Boyer Status: new Milestone: Version: Type: enhancement Priority: major Component: EinsteinToolkit thorn TOVola is an enhanced TOV solver that has support of multiple different EOS types $Simple and Piecewise Polytrope, and **Tabulated EOS**$ through the use of the GRHayLib thorn. It also has access to two different ODE methods through the use of GSL’s ODE solver $RK4\(5$ and DP7$8$\), but more methods can be added in the future if there is a desire, as long as it is a GSL compatible method. ‌ To be used in the GRHayL announcement paper, currently in prep. ‌ Here is the github link: [https://github.com/dboyer7/TOVola](https://github.com/dboyer7/TOVola) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2823/include-tovola-an…

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#2822: work around full paths used by pkg-config in `-l` options
by Steven R. Brandt 05 Sep '24

05 Sep '24

#2822: work around full paths used by pkg-config in `-l` options Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: minor Component: Comment (by Steven R. Brandt): This change looks good… should it be a PR? -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2822/work-around-full-…

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#2822: work around full paths used by pkg-config in `-l` options
by Roland Haas 05 Sep '24

05 Sep '24

#2822: work around full paths used by pkg-config in `-l` options Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: minor Component: Changes (by Roland Haas): title: work around full paths used by pkg-config in `-l` options (was support full paths to libraries in LIBS variables) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2822/work-around-full-…

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#2817: update ExternalLibraries-libjpeg to version 9f
by Roland Haas 05 Sep '24

05 Sep '24

#2817: update ExternalLibraries-libjpeg to version 9f Reporter: Roland Haas Status: resolved Milestone: Version: Type: enhancement Priority: major Component: EinsteinToolkit thorn Changes (by Roland Haas): status: resolved (was open) Comment (by Roland Haas): Thank you. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2817/update-externalli…

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#2817: update ExternalLibraries-libjpeg to version 9f
by Roland Haas 05 Sep '24

05 Sep '24

#2817: update ExternalLibraries-libjpeg to version 9f Reporter: Roland Haas Status: open Milestone: Version: Type: enhancement Priority: major Component: EinsteinToolkit thorn Comment (by Roland Haas): Applied as git hash [04d84a6](https://github.com/EinsteinToolkit/ExternalLibraries-libjpeg/commi… "libjpeg: add docs for INC\_DIRS and LIB\_DIRS" of [ExternalLibraries-libjpeg](https://github.com/EinsteinToolkit/ExternalLibra… -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2817/update-externalli…

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#2817: update ExternalLibraries-libjpeg to version 9f
by Leonardo Werneck 05 Sep '24

05 Sep '24

#2817: update ExternalLibraries-libjpeg to version 9f Reporter: Roland Haas Status: open Milestone: Version: Type: enhancement Priority: major Component: EinsteinToolkit thorn Comment (by Leonardo Werneck): Please apply. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2817/update-externalli…

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#2822: support full paths to libraries in LIBS variables
by Roland Haas 05 Sep '24

05 Sep '24

#2822: support full paths to libraries in LIBS variables Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: minor Component: Comment (by Roland Haas): @{5bae587b96242d2e2b6110a4} says that this also can be $for hdf5 with homebrew$ be avoid by not passing the `--static` flag to `pkg-config`. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2822/support-full-path…

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#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl
by Roland Haas 05 Sep '24

05 Sep '24

#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl Reporter: Roland Haas Status: resolved Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn Changes (by Roland Haas): status: resolved (was open) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2819/setmask_spherical…

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#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl
by Roland Haas 05 Sep '24

05 Sep '24

#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn Comment (by Roland Haas): Applied as git hash [01d568f](https://bitbucket.org/einsteintoolkit/einsteinutils/commits/01d568… "SetMask\_SphericalSurface: support padded grid arrays" of [einsteinutils](https://bitbucket.org/einsteintoolkit/einsteinutils) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2819/setmask_spherical…

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#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl
by Roland Haas 05 Sep '24

05 Sep '24

#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn Comment (by Roland Haas): Thank you. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2819/setmask_spherical…

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#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl
by Leonardo Werneck 05 Sep '24

05 Sep '24

#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn Comment (by Leonardo Werneck): Please apply. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2819/setmask_spherical…

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#2822: support full paths to libraries in LIBS variables
by Roland Haas 04 Sep '24

04 Sep '24

#2822: support full paths to libraries in LIBS variables Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: minor Component: Changes (by Roland Haas): On macOS using Homebrew `pkg-config` for HDF5 returns full library paths instead of `-lLIBNAME` stanzas: ``` rhaas@gdd6l52n-ofc Cactus % pkg-config --libs-only-l --static hdf5 -lhdf5 -lm -ldl -l/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd -l/opt/homebrew/lib/libsz.dylib ``` This happens only for static linking. This causes g\+\+ to fail at link time: ``` rhaas@gdd6l52n-ofc Cactus % g++-14 `pkg-config --libs-only-L hdf5` `pkg-config --libs-only-l --static hdf5` dummy.c ld: library '/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd' not found collect2: error: ld returned 1 exit status ``` This seems like bug in the pkg-config file $\`/opt/homebrew/Cellar/hdf5/1.14.3\_1/lib/pkgconfig/hdf5.pc\`$ supplied by HomeBrew: ``` rhaas@gdd6l52n-ofc Cactus % cat /opt/homebrew/Cellar/hdf5/1.14.3_1/lib/pkgconfig/hdf5.pc prefix=/opt/homebrew/Cellar/hdf5/1.14.3_1 exec_prefix=${prefix} libdir=${exec_prefix}/lib includedir=${prefix}/include Name: hdf5 Description: HDF5 (Hierarchical Data Format 5) Software Library Version: 1.14.3 Cflags: -I${includedir} Libs: -L${libdir} -lhdf5 Requires: Libs.private: -lhdf5 -lm -ldl -l/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd -l/opt/homebrew/lib/libsz.dylib -l/opt/homebrew/lib/libsz.dylib Requires.private: ``` Correct would be to not use `-l` with the full path $at least it will link$: ``` g++-14 `pkg-config --libs-only-L hdf5` dummy.c /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd ``` Right now we have no way of handling full paths in LIBS files though git hash [cb3a8731](https://bitbucket.org/cactuscode/cactus/commits/cb3a873135a303223… "Cactus: New pseudo-flag `-file=`" of [cactus](https://bitbucket.org/cactuscode/cactus) proposes some $partial$ solution. This would require changes in all ExternalLibraries though $that may need to pass `LIBS` to their own `configure`$. Another solution might be $in `bash_utils.sh`$ to detect full paths in `-l` entries and split into a `-L` and a `-l` entry. This assumes knowledge of the library prefix $usually `lib`$ and extension $`.a`, `.so`, `.dylib`, `.dll`$. A workaround for HDF5 is to self-compile HDF5 using `HDF5_DIR=BUILD`. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2822/support-full-path…

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#2822: support full paths to libraries in LIBS variables
by Roland Haas 04 Sep '24

04 Sep '24

#2822: support full paths to libraries in LIBS variables Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: minor Component: Changes (by Roland Haas): status: open (was new) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2822/support-full-path…

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#2822: support full paths to libraries in LIBS variables
by Roland Haas 04 Sep '24

04 Sep '24

#2822: support full paths to libraries in LIBS variables Reporter: Roland Haas Status: new Milestone: Version: Type: bug Priority: minor Component: Comment (by Roland Haas): A possible workaround in `bash_utils.sh` is ```shell # NOTE: This breaks if pkg-config returns quotes strings, i.e., path names # with strings in them. It doesn't seems to happen in practice. # If it does: let us know what pkg-config prints in that case, and we # can try to fix it. local INC_DIRS=$($PKGCONFIG --cflags-only-I "$STATIC" "$LIBNAME" | perl -pe 's/(^| )+-I/\1/g') local LIB_DIRS=$($PKGCONFIG --libs-only-L "$STATIC" "$LIBNAME" | perl -pe 's/(^| )+-L/\1/g') local LIBS="" local ALLLIBS=$($PKGCONFIG --libs-only-l "$STATIC" "$LIBNAME" | perl -pe 's/(^| )+-l/\1/g') for lib in $ALLLIBS; do if [ "${lib%/*}" != "$lib" ] ; then LIB_DIRS="$LIB_DIRS ${lib%/*}" lib=${lib##*/lib} lib=${lib%.*} fi LIBS="$LIBS $lib" done ``` ‌ -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2822/support-full-path…

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#2822: support full paths to libraries in LIBS variables
by Roland Haas 04 Sep '24

04 Sep '24

#2822: support full paths to libraries in LIBS variables Reporter: Roland Haas Status: new Milestone: Version: Type: bug Priority: minor Component: On macOS using Homebrew `pkg-config` for HDF5 returns full library paths instead of `-lLIBNAME` stanzas: ``` rhaas@gdd6l52n-ofc Cactus % pkg-config --libs-only-l --static hdf5 -lhdf5 -lm -ldl -l/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd -l/opt/homebrew/lib/libsz.dylib ``` This happens only for static linking. This causes g\+\+ to fail at link time: ``` rhaas@gdd6l52n-ofc Cactus % g++ `pkg-config --libs-only-L hdf5` `pkg-config --libs-only-l --static hdf5` dummy.c clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] ld: library '/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd' not found ``` This seems like bug in the pkg-config file $\`/opt/homebrew/Cellar/hdf5/1.14.3\_1/lib/pkgconfig/hdf5.pc\`$ supplied by HomeBrew: ``` rhaas@gdd6l52n-ofc Cactus % cat /opt/homebrew/Cellar/hdf5/1.14.3_1/lib/pkgconfig/hdf5.pc prefix=/opt/homebrew/Cellar/hdf5/1.14.3_1 exec_prefix=${prefix} libdir=${exec_prefix}/lib includedir=${prefix}/include Name: hdf5 Description: HDF5 (Hierarchical Data Format 5) Software Library Version: 1.14.3 Cflags: -I${includedir} Libs: -L${libdir} -lhdf5 Requires: Libs.private: -lhdf5 -lm -ldl -l/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd -l/opt/homebrew/lib/libsz.dylib -l/opt/homebrew/lib/libsz.dylib Requires.private: ``` Correct would be to not use `-l` with the full path $at least it will link$: ``` g++ `pkg-config --libs-only-L hdf5` dummy.c /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/lib/libz.tbd ``` Right now we have no way of handling full paths in LIBS files though git hash [cb3a8731](https://bitbucket.org/cactuscode/cactus/commits/cb3a873135a303223… "Cactus: New pseudo-flag `-file=`" of [cactus](https://bitbucket.org/cactuscode/cactus) proposes some $partial$ solution. This would require changes in all ExternalLibraries though $that may need to pass `LIBS` to their own `configure`$. Another solution might be $in `bash_utils.sh`$ to detect full paths in `-l` entries and split into a `-L` and a `-l` entry. This assumes knowledge of the library prefix $usually `lib`$ and extension $`.a`, `.so`, `.dylib`, `.dll`$. A workaround for HDF5 is to self-compile HDF5 using `HDF5_DIR=BUILD`. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2822/support-full-path…

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#2821: update PETSc to 3.21.5
by Roland Haas 03 Sep '24

03 Sep '24

#2821: update PETSc to 3.21.5 Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn Comment (by Roland Haas): Please review. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2821/update-petsc-to-3…

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#2821: update PETSc to 3.21.5
by Roland Haas 03 Sep '24

03 Sep '24

#2821: update PETSc to 3.21.5 Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn Changes (by Roland Haas): status: open (was new) -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2821/update-petsc-to-3…

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#2821: update PETSc to 3.21.5
by Roland Haas 03 Sep '24

03 Sep '24

#2821: update PETSc to 3.21.5 Reporter: Roland Haas Status: new Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn Comment (by Roland Haas): Pull request is here: [https://github.com/EinsteinToolkit/ExternalLibraries-PETSc/pull/3](https://… -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2821/update-petsc-to-3…

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#2821: update PETSc to 3.21.5
by Roland Haas 03 Sep '24

03 Sep '24

#2821: update PETSc to 3.21.5 Reporter: Roland Haas Status: new Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn ExernalLibraries/PETSc fails to compile for me with gcc-14 and required both an update $to 3.12.5$ and change in how it is compiled to make its own `configure.py` pass. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2821/update-petsc-to-3…

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#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl
by Roland Haas 03 Sep '24

03 Sep '24

#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn Comment (by Roland Haas): Please review. -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2819/setmask_spherical…

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#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl
by Roland Haas 03 Sep '24

03 Sep '24

#2819: SetMask_SphericalSurface uses LoopControl's LC_LOOP but does not require LoopControl Reporter: Roland Haas Status: open Milestone: Version: Type: bug Priority: major Component: EinsteinToolkit thorn Comment (by Roland Haas): Pull request is here: [https://bitbucket.org/einsteintoolkit/einsteinutils/pull-requests/4](https:… -- Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2819/setmask_spherical…

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