Merge pull request #218968 from pmiddend/crystfel-aarch64
CrystFEL: support aarch64-linux and HDF5 on Darwin
This commit is contained in:
Weijia Wang
GitHub
commit
7b57f59155
3 changed files with 44 additions and 62 deletions
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@ -1,43 +0,0 @@
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Description: Fixing argument mismatches in Fortran code, addressing #957430.
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Author: Andrius Merkys <merkys@debian.org>
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Forwarded: ccp4-dev@dl.ac.uk
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--- a/fortran/pack_f.f
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+++ b/fortran/pack_f.f
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@@ -106,7 +106,7 @@
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endif
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10 continue
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filnarray(len(filn) + 1) = 0
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- call pack_wordimage_f(data, x, y, filnarray)
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+ call pack_longimage_f(data, x, y, filnarray)
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return
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end
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@@ -138,7 +138,7 @@
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endif
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10 continue
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filnarray(len(filn) + 1) = 0
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- call v2pack_wordimage_f(data, x, y, filnarray)
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+ call v2pack_longimage_f(data, x, y, filnarray)
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return
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end
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--- a/fortran/lgglib.f
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+++ b/fortran/lgglib.f
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@@ -1236,7 +1236,7 @@
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B3(2) = XYZ(2) * CELL(2)
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B3(3) = XYZ(3) * CELL(3)
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C
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- CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
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+ CALL matmult(3,3,3,1,ORTH,B3,XYZ)
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END
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c
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c
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@@ -1274,7 +1274,7 @@
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B3(1) = XYZ(1)
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B3(2) = XYZ(2)
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B3(3) = XYZ(3)
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- CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
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+ CALL matmult(3,3,3,1,ORTH,B3,XYZ)
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END
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character*80 function getnam(filnam)
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character*(*) filnam
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@ -3,10 +3,10 @@
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, fetchurl
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, fetchFromGitHub
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, fetchpatch
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, fetchzip
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, cmake
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, lz4
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, bzip2
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, gfortran
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, m4
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, hdf5
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, gsl
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@ -38,14 +38,12 @@
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let
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libccp4 = stdenv.mkDerivation rec {
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pname = "libccp4";
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version = "6.5.1";
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version = "8.0.0";
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src = fetchurl {
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# Original mirror, now times out
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# url = "ftp://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
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url = "https://deb.debian.org/debian/pool/main/libc/${pname}/${pname}_${version}.orig.tar.gz";
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sha256 = "1rfvjliny29vy5bdi6rrjaw9hhhhh72pw536xwvqipqcjlylf2r8";
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url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
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hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";
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};
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nativeBuildInputs = [ gfortran m4 ];
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nativeBuildInputs = [ meson ninja ];
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buildInputs = [ hdf5 gsl ];
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configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ];
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@ -53,16 +51,22 @@ let
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# libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility.
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# We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a
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# preprocessor flag.
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preBuild = ''
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makeFlagsArray+=(CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"')
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export NIX_LDFLAGS="-L${gfortran.cc}/lib64 -L${gfortran.cc}/lib $NIX_LDFLAGS";
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'';
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makeFlags = [ "CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"" ];
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env.NIX_CFLAGS_COMPILE = "-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/ccp4/syminfo.lib\"";
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patches = [
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./libccp4-use-hardcoded-syminfo-lib.patch
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./0002-fix-ftbfs-with-gcc-10.patch
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];
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postPatch =
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let
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mesonPatch = fetchzip {
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url = "https://wrapdb.mesonbuild.com/v2/libccp4c_8.0.0-1/get_patch#somefile.zip";
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hash = "sha256-ohskfKh+972Pl56KtwAeWwHtAaAFNpCzz5vZBAI/vdU=";
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};
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in
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''
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cp ${mesonPatch}/meson.build .
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'';
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};
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# This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult
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# since the build process is very hard-coded for a specific machine, architecture, and libraries.
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@ -145,10 +149,17 @@ let
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src = fetchFromGitHub {
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owner = "nexusformat";
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repo = pname;
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rev = "d469f175e5273c1d488e71a6134f84088f57d39c";
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sha256 = "1jrzzh75i68ad1yrim7s1nx9wy0s49ghkziahs71mm5azprm6gh9";
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rev = "49e3b65eca772bca77af13ba047d8b577673afba";
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hash = "sha256-bEzfWdZuHmb0PDzCqy8Dey4tLtq+4coO0sT0GzqrTYI=";
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};
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patches = [
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(fetchpatch {
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url = "https://github.com/spanezz/HDF5-External-Filter-Plugins/commit/6b337fe36da97a3ef72354393687ce3386c0709d.patch";
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hash = "sha256-wnBEdL/MjEyRHPwaVtuhzY+DW1AFeaUQUmIXh+JaRHo=";
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})
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];
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nativeBuildInputs = [ cmake ];
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buildInputs = [ hdf5 lz4 bzip2 ];
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@ -184,13 +195,14 @@ stdenv.mkDerivation rec {
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] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]
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++ lib.optionals stdenv.isDarwin [
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argp-standalone
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] ++ lib.optionals (stdenv.isDarwin && !stdenv.isAarch64) [
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memorymappingHook
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]
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# hdf5-external-filter-plugins doesn't link on Darwin
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++ lib.optionals (withBitshuffle && !stdenv.isDarwin) [ hdf5-external-filter-plugins ];
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++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ];
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patches = [
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./link-to-argp-standalone-if-needed.patch
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./disable-fmemopen-on-aarch64-darwin.patch
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(fetchpatch {
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url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff";
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hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc=";
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@ -204,7 +216,7 @@ stdenv.mkDerivation rec {
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sed -i -e 's#execlp("mosflm"#execl("${mosflm}/bin/mosflm"#' libcrystfel/src/indexers/mosflm.c;
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'';
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postInstall = lib.optionalString (withBitshuffle && !stdenv.isDarwin) ''
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postInstall = lib.optionalString withBitshuffle ''
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for file in $out/bin/*; do
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wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins
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done
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@ -224,7 +236,7 @@ stdenv.mkDerivation rec {
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downloadPage = "https://www.desy.de/~twhite/crystfel/download.html";
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license = licenses.gpl3Plus;
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maintainers = with maintainers; [ pmiddend ];
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platforms = [ "x86_64-linux" "x86_64-darwin" ];
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platforms = platforms.unix;
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};
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}
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@ -0,0 +1,13 @@
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diff --git a/libcrystfel/src/image-cbf.c b/libcrystfel/src/image-cbf.c
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index b8f09a1f..f8a15c1b 100644
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--- a/libcrystfel/src/image-cbf.c
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+++ b/libcrystfel/src/image-cbf.c
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@@ -287,7 +287,7 @@ static float *read_cbf_data(const char *filename, int gz, int *w, int *h)
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} else {
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- #ifdef HAVE_ZLIB
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+ #if defined(HAVE_ZLIB) && !(defined(__aarch64__) && defined(__APPLE__))
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gzFile gzfh;
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int len_read;
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size_t len;
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