Philipp Middendorf
2 years ago
parent
fb679d351a
commit
93332c2779
@ -0,0 +1,43 @@ |
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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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@ -0,0 +1,226 @@ |
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{ lib |
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, stdenv |
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, fetchurl |
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, fetchFromGitHub |
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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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, slurm |
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, unzip |
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, makeWrapper |
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, meson |
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, git |
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, ninja |
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, eigen |
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, pkg-config |
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, wrapGAppsHook |
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, flex |
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, bison |
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, doxygen |
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, opencl-headers |
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, ncurses |
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, msgpack |
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, fftw |
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, zeromq |
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, ocl-icd |
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, gtk3 |
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, gdk-pixbuf |
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, argp-standalone |
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, memorymappingHook |
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, withGui ? true |
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, withBitshuffle ? true |
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}: |
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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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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}_${version}.orig.tar.gz"; |
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sha256 = "1rfvjliny29vy5bdi6rrjaw9hhhhh72pw536xwvqipqcjlylf2r8"; |
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}; |
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nativeBuildInputs = [ gfortran m4 ]; |
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buildInputs = [ hdf5 gsl ]; |
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configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ]; |
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# libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility. |
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# We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a |
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# preprocessor flag. |
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preBuild = '' |
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makeFlagsArray+=(CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"$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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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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}; |
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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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mosflm = |
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let |
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version = "7.4.0"; |
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src = |
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if stdenv.isDarwin then |
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fetchurl |
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{ |
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url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-osx-64-noX11.zip"; |
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sha256 = "1da5wimv3kl8bccp49j69vh8gi28cn7axg59lrmb38s68c618h7j"; |
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} |
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else |
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fetchurl { |
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url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-linux-64-noX11.zip"; |
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sha256 = "1rqh3nprxfmnyihllw31nb8i3wfhybmsic6y7z6wn4rafyv3w4fk"; |
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}; |
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mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11"; |
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in |
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stdenv.mkDerivation rec { |
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pname = "mosflm"; |
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inherit version src; |
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dontBuild = true; |
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nativeBuildInputs = [ unzip makeWrapper ]; |
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sourceRoot = "."; |
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# mosflm statically links against its own libccp4, which as the syminfo.lib environment variable problem. |
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# Here, we circumvent it by creating a little wrapper script that calls mosflm after setting the SYMINFO variable. |
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installPhase = '' |
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mkdir -p $out/bin |
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cp ${mosflmBinary} $out/bin/mosflm-raw |
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makeWrapper $out/bin/mosflm-raw $out/bin/mosflm --set SYMINFO ${libccp4}/share/syminfo.lib --add-flags -n |
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''; |
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}; |
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xgandalf = stdenv.mkDerivation rec { |
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pname = "xgandalf"; |
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version = "c15afa2381d5f87d4aefcc8181a15b4a6fd3a955"; |
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src = fetchurl { |
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url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz"; |
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sha256 = "11i1w57a3rpnb4x5y4n8d3iffn5m9w1zydl69syzljdk3aqg2pv8"; |
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}; |
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nativeBuildInputs = [ meson pkg-config ninja ]; |
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buildInputs = [ eigen ]; |
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}; |
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pinkIndexer = stdenv.mkDerivation rec { |
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pname = "pinkindexer"; |
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version = "8a828788f8272a89d484b00afbd2500c2c1ff974"; |
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src = fetchurl { |
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url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz"; |
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sha256 = "1mkgf1xd91ay0z0632kzxm0z3wcxf0cayjvs6a3znds72dkhfsyh"; |
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}; |
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nativeBuildInputs = [ meson pkg-config ninja ]; |
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buildInputs = [ eigen ]; |
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}; |
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fdip = stdenv.mkDerivation rec { |
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pname = "fdip"; |
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version = "29da626f17f66d5c0780fc59b1eafb7c85b81dd6"; |
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src = fetchurl { |
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url = "https://gitlab.desy.de/philipp.middendorf/fdip/-/archive/${version}/fdip-${version}.tar.gz"; |
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sha256 = "184l76r4fgznq54rnhgjk7dg41kqdl0d1da02vr5y4cs2fyqppky"; |
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}; |
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nativeBuildInputs = [ meson ninja pkg-config ]; |
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buildInputs = [ eigen ]; |
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}; |
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hdf5-external-filter-plugins = stdenv.mkDerivation rec { |
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pname = "HDF5-External-Filter-Plugins"; |
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version = "0.1.0"; |
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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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}; |
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nativeBuildInputs = [ cmake ]; |
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buildInputs = [ hdf5 lz4 bzip2 ]; |
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cmakeFlags = [ |
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"-DENABLE_BITSHUFFLE_PLUGIN=yes" |
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"-DENABLE_LZ4_PLUGIN=yes" |
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"-DENABLE_BZIP2_PLUGIN=yes" |
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]; |
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}; |
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in |
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stdenv.mkDerivation rec { |
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pname = "crystfel"; |
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version = "0.10.1"; |
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src = fetchurl { |
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url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz"; |
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sha256 = "0i9d5ggalic7alj97dxjdys7010kxhm2cb4lwakvigl023j8ms79"; |
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}; |
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nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers ] |
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++ lib.optionals withGui [ wrapGAppsHook ]; |
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buildInputs = [ |
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hdf5 |
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gsl |
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ncurses |
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msgpack |
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fftw |
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fdip |
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zeromq |
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ocl-icd |
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libccp4 |
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mosflm |
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pinkIndexer |
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xgandalf |
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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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memorymappingHook |
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] |
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# slurm is not available for Darwin; when it is, remove the condition |
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++ lib.optionals (!stdenv.isDarwin) [ slurm ] |
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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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patches = [ ./link-to-argp-standalone-if-needed.patch ]; |
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# CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but |
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# we'd have to do that for every CrystFEL executable (indexamajig, crystfel, partialator). Better to just |
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# hard-code mosflm's path once. |
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postPatch = '' |
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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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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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''; |
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meta = with lib; { |
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description = "Data processing for serial crystallography"; |
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longDescription = '' |
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CrystFEL is a suite of programs for processing (and simulating) Bragg diffraction data from "serial crystallography" experiments, often (but not always) performed using an X-ray Free-Electron Laser. Compared to rotation data, some of the particular characteristics of such data which call for a specialised software suite are: |
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- The sliced, rather than integrated, measurement of intensity data. Many, if not all reflections are partially integrated. |
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- Many patterns (thousands) are required - high throughput is needed. |
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- The crystal orientations in each pattern are random and uncorrelated. |
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- Merging into lower symmetry point groups may require the resolution of indexing ambiguities.''; |
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homepage = "https://www.desy.de/~twhite/crystfel/"; |
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changelog = "https://www.desy.de/~twhite/crystfel/changes.html"; |
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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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}; |
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} |
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@ -0,0 +1,30 @@ |
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diff --git a/ccp4/csymlib.c b/ccp4/csymlib.c
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index 76bc70b..7a0c5dc 100644
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--- a/ccp4/csymlib.c
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+++ b/ccp4/csymlib.c
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@@ -137,24 +137,7 @@ CCP4SPG *ccp4spg_load_spacegroup(const int numspg, const int ccp4numspg,
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}
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/* Open the symop file: */
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- if (!(symopfile = getenv("SYMINFO"))) {
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- if (debug)
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- printf("Environment variable SYMINFO not set ... guessing location of symmetry file. \n");
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- if (!(ccp4dir = getenv("CLIBD"))) {
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- printf("Environment variable CLIBD not set ... big trouble! \n");
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- return NULL;
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- }
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-
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- symopfile = ccp4_utils_malloc((strlen(ccp4dir)+22)*sizeof(char));
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- strcpy(symopfile,ccp4_utils_joinfilenames(ccp4dir,"syminfo.lib"));
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- symopfile[strlen(ccp4dir)+21] = '\0';
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- ccp4printf(1," SYMINFO file set to %s \n",symopfile);
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- } else {
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- if (debug) {
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- ccp4printf(1,"\n Spacegroup information obtained from library file: \n");
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- ccp4printf(1," Logical Name: SYMINFO Filename: %s\n\n",symopfile);
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- }
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- }
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+ symopfile = NIX_PROVIDED_SYMOP_FILE;
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filein = fopen(symopfile,"r");
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if (!filein) {
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@ -0,0 +1,26 @@ |
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diff --git a/meson.build b/meson.build
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index efc9002b..070f37e4 100644
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--- a/meson.build
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+++ b/meson.build
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@@ -34,6 +34,12 @@ if slurmdep.found()
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conf_data.set10('HAVE_SLURM', 1)
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endif
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+if build_machine.system() == 'darwin' or build_machine.system() == 'freebsd' or not cc.links('#include <argp.h>\nstatic error_t parse_opt (int key, char *arg, struct argp_state *state) { argp_usage(state); return 0; }; void main() {}')
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+ argpdep = cc.find_library('argp')
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+else
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+ argpdep = dependency('', required : false)
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+endif
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+
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# Find HDF5 using inbuilt Meson methods. Requires Meson >= 0.50.0
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hdf5dep = dependency('hdf5', language: 'c', required: true)
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@@ -180,7 +186,7 @@ if zmqdep.found()
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endif
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executable('indexamajig', indexamajig_sources,
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- dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep],
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+ dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep, argpdep],
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install: true,
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install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib')
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