CrystFEL: init at 0.10.1

This commit is contained in:
Philipp Middendorf 2021-11-26 12:29:18 +01:00
parent fb679d351a
commit 93332c2779
5 changed files with 329 additions and 0 deletions

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@ -0,0 +1,43 @@
Description: Fixing argument mismatches in Fortran code, addressing #957430.
Author: Andrius Merkys <merkys@debian.org>
Forwarded: ccp4-dev@dl.ac.uk
--- a/fortran/pack_f.f
+++ b/fortran/pack_f.f
@@ -106,7 +106,7 @@
endif
10 continue
filnarray(len(filn) + 1) = 0
- call pack_wordimage_f(data, x, y, filnarray)
+ call pack_longimage_f(data, x, y, filnarray)
return
end
@@ -138,7 +138,7 @@
endif
10 continue
filnarray(len(filn) + 1) = 0
- call v2pack_wordimage_f(data, x, y, filnarray)
+ call v2pack_longimage_f(data, x, y, filnarray)
return
end
--- a/fortran/lgglib.f
+++ b/fortran/lgglib.f
@@ -1236,7 +1236,7 @@
B3(2) = XYZ(2) * CELL(2)
B3(3) = XYZ(3) * CELL(3)
C
- CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
+ CALL matmult(3,3,3,1,ORTH,B3,XYZ)
END
c
c
@@ -1274,7 +1274,7 @@
B3(1) = XYZ(1)
B3(2) = XYZ(2)
B3(3) = XYZ(3)
- CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
+ CALL matmult(3,3,3,1,ORTH,B3,XYZ)
END
character*80 function getnam(filnam)
character*(*) filnam

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@ -0,0 +1,226 @@
{ lib
, stdenv
, fetchurl
, fetchFromGitHub
, cmake
, lz4
, bzip2
, gfortran
, m4
, hdf5
, gsl
, slurm
, unzip
, makeWrapper
, meson
, git
, ninja
, eigen
, pkg-config
, wrapGAppsHook
, flex
, bison
, doxygen
, opencl-headers
, ncurses
, msgpack
, fftw
, zeromq
, ocl-icd
, gtk3
, gdk-pixbuf
, argp-standalone
, memorymappingHook
, withGui ? true
, withBitshuffle ? true
}:
let
libccp4 = stdenv.mkDerivation rec {
pname = "libccp4";
version = "6.5.1";
src = fetchurl {
# Original mirror, now times out
# url = "ftp://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
url = "https://deb.debian.org/debian/pool/main/libc/${pname}/${pname}_${version}.orig.tar.gz";
sha256 = "1rfvjliny29vy5bdi6rrjaw9hhhhh72pw536xwvqipqcjlylf2r8";
};
nativeBuildInputs = [ gfortran m4 ];
buildInputs = [ hdf5 gsl ];
configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ];
# libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility.
# We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a
# preprocessor flag.
preBuild = ''
makeFlagsArray+=(CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"$out/share/syminfo.lib\"')
export NIX_LDFLAGS="-L${gfortran.cc}/lib64 -L${gfortran.cc}/lib $NIX_LDFLAGS";
'';
makeFlags = [ "CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"" ];
patches = [
./libccp4-use-hardcoded-syminfo-lib.patch
./0002-fix-ftbfs-with-gcc-10.patch
];
};
# This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult
# since the build process is very hard-coded for a specific machine, architecture, and libraries.
mosflm =
let
version = "7.4.0";
src =
if stdenv.isDarwin then
fetchurl
{
url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-osx-64-noX11.zip";
sha256 = "1da5wimv3kl8bccp49j69vh8gi28cn7axg59lrmb38s68c618h7j";
}
else
fetchurl {
url = "https://www.mrc-lmb.cam.ac.uk/mosflm/mosflm/ver${builtins.replaceStrings [ "." ] [ "" ] version}/pre-built/mosflm-linux-64-noX11.zip";
sha256 = "1rqh3nprxfmnyihllw31nb8i3wfhybmsic6y7z6wn4rafyv3w4fk";
};
mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11";
in
stdenv.mkDerivation rec {
pname = "mosflm";
inherit version src;
dontBuild = true;
nativeBuildInputs = [ unzip makeWrapper ];
sourceRoot = ".";
# mosflm statically links against its own libccp4, which as the syminfo.lib environment variable problem.
# Here, we circumvent it by creating a little wrapper script that calls mosflm after setting the SYMINFO variable.
installPhase = ''
mkdir -p $out/bin
cp ${mosflmBinary} $out/bin/mosflm-raw
makeWrapper $out/bin/mosflm-raw $out/bin/mosflm --set SYMINFO ${libccp4}/share/syminfo.lib --add-flags -n
'';
};
xgandalf = stdenv.mkDerivation rec {
pname = "xgandalf";
version = "c15afa2381d5f87d4aefcc8181a15b4a6fd3a955";
src = fetchurl {
url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
sha256 = "11i1w57a3rpnb4x5y4n8d3iffn5m9w1zydl69syzljdk3aqg2pv8";
};
nativeBuildInputs = [ meson pkg-config ninja ];
buildInputs = [ eigen ];
};
pinkIndexer = stdenv.mkDerivation rec {
pname = "pinkindexer";
version = "8a828788f8272a89d484b00afbd2500c2c1ff974";
src = fetchurl {
url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
sha256 = "1mkgf1xd91ay0z0632kzxm0z3wcxf0cayjvs6a3znds72dkhfsyh";
};
nativeBuildInputs = [ meson pkg-config ninja ];
buildInputs = [ eigen ];
};
fdip = stdenv.mkDerivation rec {
pname = "fdip";
version = "29da626f17f66d5c0780fc59b1eafb7c85b81dd6";
src = fetchurl {
url = "https://gitlab.desy.de/philipp.middendorf/fdip/-/archive/${version}/fdip-${version}.tar.gz";
sha256 = "184l76r4fgznq54rnhgjk7dg41kqdl0d1da02vr5y4cs2fyqppky";
};
nativeBuildInputs = [ meson ninja pkg-config ];
buildInputs = [ eigen ];
};
hdf5-external-filter-plugins = stdenv.mkDerivation rec {
pname = "HDF5-External-Filter-Plugins";
version = "0.1.0";
src = fetchFromGitHub {
owner = "nexusformat";
repo = pname;
rev = "d469f175e5273c1d488e71a6134f84088f57d39c";
sha256 = "1jrzzh75i68ad1yrim7s1nx9wy0s49ghkziahs71mm5azprm6gh9";
};
nativeBuildInputs = [ cmake ];
buildInputs = [ hdf5 lz4 bzip2 ];
cmakeFlags = [
"-DENABLE_BITSHUFFLE_PLUGIN=yes"
"-DENABLE_LZ4_PLUGIN=yes"
"-DENABLE_BZIP2_PLUGIN=yes"
];
};
in
stdenv.mkDerivation rec {
pname = "crystfel";
version = "0.10.1";
src = fetchurl {
url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz";
sha256 = "0i9d5ggalic7alj97dxjdys7010kxhm2cb4lwakvigl023j8ms79";
};
nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers ]
++ lib.optionals withGui [ wrapGAppsHook ];
buildInputs = [
hdf5
gsl
ncurses
msgpack
fftw
fdip
zeromq
ocl-icd
libccp4
mosflm
pinkIndexer
xgandalf
] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]
++ lib.optionals stdenv.isDarwin [
argp-standalone
memorymappingHook
]
# slurm is not available for Darwin; when it is, remove the condition
++ lib.optionals (!stdenv.isDarwin) [ slurm ]
# hdf5-external-filter-plugins doesn't link on Darwin
++ lib.optionals (withBitshuffle && !stdenv.isDarwin) [ hdf5-external-filter-plugins ];
patches = [ ./link-to-argp-standalone-if-needed.patch ];
# CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but
# we'd have to do that for every CrystFEL executable (indexamajig, crystfel, partialator). Better to just
# hard-code mosflm's path once.
postPatch = ''
sed -i -e 's#execlp("mosflm"#execl("${mosflm}/bin/mosflm"#' libcrystfel/src/indexers/mosflm.c;
'';
postInstall = lib.optionalString (withBitshuffle && !stdenv.isDarwin) ''
for file in $out/bin/*; do
wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins
done
'';
meta = with lib; {
description = "Data processing for serial crystallography";
longDescription = ''
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:
- The sliced, rather than integrated, measurement of intensity data. Many, if not all reflections are partially integrated.
- Many patterns (thousands) are required - high throughput is needed.
- The crystal orientations in each pattern are random and uncorrelated.
- Merging into lower symmetry point groups may require the resolution of indexing ambiguities.'';
homepage = "https://www.desy.de/~twhite/crystfel/";
changelog = "https://www.desy.de/~twhite/crystfel/changes.html";
downloadPage = "https://www.desy.de/~twhite/crystfel/download.html";
license = licenses.gpl3Plus;
maintainers = with maintainers; [ pmiddend ];
platforms = [ "x86_64-linux" "x86_64-darwin" ];
};
}

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@ -0,0 +1,30 @@
diff --git a/ccp4/csymlib.c b/ccp4/csymlib.c
index 76bc70b..7a0c5dc 100644
--- a/ccp4/csymlib.c
+++ b/ccp4/csymlib.c
@@ -137,24 +137,7 @@ CCP4SPG *ccp4spg_load_spacegroup(const int numspg, const int ccp4numspg,
}
/* Open the symop file: */
- if (!(symopfile = getenv("SYMINFO"))) {
- if (debug)
- printf("Environment variable SYMINFO not set ... guessing location of symmetry file. \n");
- if (!(ccp4dir = getenv("CLIBD"))) {
- printf("Environment variable CLIBD not set ... big trouble! \n");
- return NULL;
- }
-
- symopfile = ccp4_utils_malloc((strlen(ccp4dir)+22)*sizeof(char));
- strcpy(symopfile,ccp4_utils_joinfilenames(ccp4dir,"syminfo.lib"));
- symopfile[strlen(ccp4dir)+21] = '\0';
- ccp4printf(1," SYMINFO file set to %s \n",symopfile);
- } else {
- if (debug) {
- ccp4printf(1,"\n Spacegroup information obtained from library file: \n");
- ccp4printf(1," Logical Name: SYMINFO Filename: %s\n\n",symopfile);
- }
- }
+ symopfile = NIX_PROVIDED_SYMOP_FILE;
filein = fopen(symopfile,"r");
if (!filein) {

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@ -0,0 +1,26 @@
diff --git a/meson.build b/meson.build
index efc9002b..070f37e4 100644
--- a/meson.build
+++ b/meson.build
@@ -34,6 +34,12 @@ if slurmdep.found()
conf_data.set10('HAVE_SLURM', 1)
endif
+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() {}')
+ argpdep = cc.find_library('argp')
+else
+ argpdep = dependency('', required : false)
+endif
+
# Find HDF5 using inbuilt Meson methods. Requires Meson >= 0.50.0
hdf5dep = dependency('hdf5', language: 'c', required: true)
@@ -180,7 +186,7 @@ if zmqdep.found()
endif
executable('indexamajig', indexamajig_sources,
- dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep],
+ dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep, argpdep],
install: true,
install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib')

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@ -1910,6 +1910,10 @@ with pkgs;
checkip = callPackage ../tools/networking/checkip { };
crystfel = callPackage ../applications/science/physics/crystfel { };
crystfel-headless = callPackage ../applications/science/physics/crystfel { withGui = false; };
ec2-api-tools = callPackage ../tools/virtualization/ec2-api-tools { };
ec2-ami-tools = callPackage ../tools/virtualization/ec2-ami-tools { };