[med-svn] [Git][med-team/relion][debian/master] 9 commits: drop backup file from git
Andreas Beckmann (@anbe)
gitlab at salsa.debian.org
Fri Sep 23 23:44:04 BST 2022
Andreas Beckmann pushed to branch debian/master at Debian Med / relion
Commits:
4a976b0a by Andreas Beckmann at 2022-09-23T11:47:48+02:00
drop backup file from git
- - - - -
e6a91129 by Andreas Beckmann at 2022-09-23T15:50:03+02:00
cherry-pick fixes related to cub
- - - - -
44fa3ca8 by Andreas Beckmann at 2022-09-23T18:57:55+02:00
relion_maingui is gone
- - - - -
9edfb28e by Andreas Beckmann at 2022-09-23T19:02:03+02:00
simplify the configure/build/install overrides
- - - - -
d4978531 by Andreas Beckmann at 2022-09-23T19:32:29+02:00
fix paths in copyright file
- - - - -
7575eb73 by Andreas Beckmann at 2022-09-23T23:03:02+02:00
restore the relion (3.1.0-2) changelog entry
- - - - -
5ee542db by Andreas Beckmann at 2022-09-23T23:05:50+02:00
simplify lintian overrides
- - - - -
b88a7386 by Andreas Beckmann at 2022-09-23T23:10:47+02:00
drop superfluous ldconfig triggers
there are no more shared libraries
- - - - -
5984c176 by Andreas Beckmann at 2022-09-23T23:34:54+02:00
fix missing hardening flags
- - - - -
10 changed files:
- debian/changelog
- debian/copyright
- + debian/patches/0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch
- + debian/patches/series
- debian/relion-gui.lintian-overrides
- − debian/relion-gui.triggers
- debian/relion.lintian-overrides
- − debian/relion.triggers
- debian/rules
- − src/jaz/Gaussian_pyramid.h.bak
Changes:
=====================================
debian/changelog
=====================================
@@ -1,7 +1,13 @@
relion (3.1.3-2) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Enable uscan to create a sensible download name
+ [ Andreas Beckmann ]
+ * Cherry-pick upstream fixes related to cub. (Closes: #995224)
+ * Simplify debian/rules.
+ * Fix missing hardening flags.
+
-- Andreas Tille <tille at debian.org> Wed, 20 Oct 2021 09:02:12 +0200
relion (3.1.3-1) unstable; urgency=medium
@@ -29,6 +35,12 @@ relion (3.1.0-4) unstable; urgency=medium
relion (3.1.0-3) unstable; urgency=medium
+ * relion-cuda and relion-gui-cuda are now built by src:relion-cuda/contrib.
+
+ -- Roland Fehrenbacher <rfehren at debian.org> Thu, 01 Oct 2020 10:37:37 +0200
+
+relion (3.1.0-2) unstable; urgency=medium
+
* New upstream version 3.1.0
* Update to Standards-Version: 4.5.0
* Rename available binary packages, since MPI support is now default.
@@ -36,11 +48,13 @@ relion (3.1.0-3) unstable; urgency=medium
available.
* Dropped librelion* packages. No shared libraries are created by relion
anymore.
+ * Add versions with CUDA/GPU support (these are in the Debian contrib
+ archive area). They are named relion-cuda and relion-gui-cuda.
* Moved to dep14 layout to work directly with the upstream git repo (see
README.source in the source archive).
* Added a simple autopkgtest
- -- Roland Fehrenbacher <rfehren at debian.org> Thu, 01 Oct 2020 10:37:37 +0200
+ -- Roland Fehrenbacher <rfehren at debian.org> Tue, 29 Sep 2020 19:01:31 +0000
relion (1.4+dfsg-4) unstable; urgency=medium
=====================================
debian/copyright
=====================================
@@ -46,16 +46,16 @@ Files: src/acc/cuda/cub/agent/*
src/acc/cuda/cub/thread/*
src/acc/cuda/cub/util*
src/acc/cuda/cub/warp/*
- src/gpu-utils/cub/agent/*
- src/gpu-utils/cub/block/*
- src/gpu-utils/cub/cub.cuh
- src/gpu-utils/cub/device/*
- src/gpu-utils/cub/grid/*
- src/gpu-utils/cub/host/mutex.cuh
- src/gpu-utils/cub/iterator/*
- src/gpu-utils/cub/thread/*
- src/gpu-utils/cub/util*
- src/gpu-utils/cub/warp/*
+ src/gpu_utils/cub/agent/*
+ src/gpu_utils/cub/block/*
+ src/gpu_utils/cub/cub.cuh
+ src/gpu_utils/cub/device/*
+ src/gpu_utils/cub/grid/*
+ src/gpu_utils/cub/host/mutex.cuh
+ src/gpu_utils/cub/iterator/*
+ src/gpu_utils/cub/thread/*
+ src/gpu_utils/cub/util*
+ src/gpu_utils/cub/warp/*
Copyright: 2011, Duane Merrill.
2011-2016, NVIDIA CORPORATION.
2011-2017, NVIDIA CORPORATION.
=====================================
debian/patches/0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch
=====================================
@@ -0,0 +1,25 @@
+From 554e0ed993e5ac8a3fee4be7c5cf64a62216a8c7 Mon Sep 17 00:00:00 2001
+From: Takanori Nakane <nakane.t at gmail.com>
+Date: Tue, 9 Nov 2021 14:52:30 +0000
+Subject: [PATCH] Repair wrong comment sign (pointed out by Alexey Romanenko)
+
+---
+ src/acc/cuda/cuda_utils_cub.cuh | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/acc/cuda/cuda_utils_cub.cuh b/src/acc/cuda/cuda_utils_cub.cuh
+index 3e32fb86..cf6ede21 100644
+--- a/src/acc/cuda/cuda_utils_cub.cuh
++++ b/src/acc/cuda/cuda_utils_cub.cuh
+@@ -13,7 +13,7 @@
+ #undef CubLog
+ #endif
+
+-#define CUB_NS_QUALIFIER ::cub # for compatibility with CUDA 11.5
++#define CUB_NS_QUALIFIER ::cub // for compatibility with CUDA 11.5
+ #include "src/acc/cuda/cub/device/device_radix_sort.cuh"
+ #include "src/acc/cuda/cub/device/device_reduce.cuh"
+ #include "src/acc/cuda/cub/device/device_scan.cuh"
+--
+2.20.1
+
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch
=====================================
debian/relion-gui.lintian-overrides
=====================================
@@ -1 +1 @@
-relion-gui: no-manual-page
+no-manual-page
=====================================
debian/relion-gui.triggers deleted
=====================================
@@ -1 +0,0 @@
-activate-noawait ldconfig
=====================================
debian/relion.lintian-overrides
=====================================
@@ -1 +1 @@
-relion: no-manual-page
+no-manual-page
=====================================
debian/relion.triggers deleted
=====================================
@@ -1 +0,0 @@
-activate-noawait ldconfig
=====================================
debian/rules
=====================================
@@ -20,6 +20,9 @@ else
MPICXX := mpicxx.openmpi
endif
+CFLAGS += $(CPPFLAGS)
+CXXFLAGS += $(CPPFLAGS)
+
CONFIGURE_COMMON := cmake -DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" \
-DCMAKE_VERBOSE_MAKEFILE=ON \
@@ -30,27 +33,21 @@ CONFIGURE_COMMON := cmake -DCMAKE_INSTALL_PREFIX=/usr \
dh $@
override_dh_auto_configure:
-
-override_dh_auto_build:
mkdir $(CURDIR)/build
cd $(CURDIR)/build; \
- CC=gcc CXX=g++ $(CONFIGURE_COMMON) -DGUI=ON -DCUDA=OFF $(CURDIR);\
- make $(MAKE_-J); DESTDIR=$(CURDIR)/debian/tmp/cli make install
+ CC=gcc CXX=g++ $(CONFIGURE_COMMON) -DGUI=ON -DCUDA=OFF $(CURDIR)
+
+override_dh_auto_build:
+ $(MAKE) $(MAKE_-J) -C build
+
+override_dh_auto_install:
+ $(MAKE) -C build install DESTDIR=$(CURDIR)/debian/tmp/cli
mkdir -p $(CURDIR)/debian/tmp/gui/usr/bin
rm $(CURDIR)/debian/tmp/cli/usr/bin/*.csh # Useless ...
- for prog in relion relion_display relion_maingui relion_manualpick; do \
+ set -e; for prog in relion relion_display relion_manualpick; do \
mv $(CURDIR)/debian/tmp/cli/usr/bin/$$prog \
$(CURDIR)/debian/tmp/gui/usr/bin; done
-override_dh_prep:
- # We don't want debian/tmp to be removed again ...
- dh_prep -X debian/tmp
-
-override_dh_auto_install:
-
-override_dh_install-arch:
- dh_install -a
-
override_dh_clean:
dh_clean
-rm -rf build
=====================================
src/jaz/Gaussian_pyramid.h.bak deleted
=====================================
@@ -1,263 +0,0 @@
-/***************************************************************************
- *
- * Author: "Jasenko Zivanov"
- * MRC Laboratory of Molecular Biology
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 2 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * This complete copyright notice must be included in any revised version of the
- * source code. Additional authorship citations may be added, but existing
- * author citations must be preserved.
- ***************************************************************************/
-
-#ifndef GAUSSIAN_PYRAMID_H
-#define GAUSSIAN_PYRAMID_H
-
-#include <src/image.h>
-#include <src/jaz/filter_helper.h>
-#include <src/jaz/resampling_helper.h>
-#include <src/jaz/vtk_helper.h>
-#include <src/jaz/image_op.h>
-#include <vector>
-
-template <typename T>
-class GaussianPyramid
-{
- public:
-
- GaussianPyramid(const Image<T>& img, double sigma = 1.0, double cutoff = 2.5,
- int maxLev = -1, int initial = 3);
-
- double sigma, cutoff;
- int initial;
- std::vector<Image<T>> levels;
- std::vector<double> scales;
-
- T value(double x, double y, double s);
-
- std::vector<Image<T>> getUpsampled();
- Image<T> getUpsampledLevel(int i);
- Image<T> getInterpolated(double sig);
-
- static void test(const Image<T>& img);
- static void interpolationTest(const Image<T>& img);
-
-};
-
-template <typename T>
-GaussianPyramid<T>::GaussianPyramid(const Image<T>& img, double sigma, double cutoff, int maxLev, int initial)
-: sigma(sigma), cutoff(cutoff), initial(initial), levels(0), scales(0)
-{
- int w0 = img.data.xdim;
- int h0 = img.data.ydim;
-
- int w = w0;
- int h = h0;
-
- Image<T> curr = img;
- double currScale = 1.0;
- double currL0Var = 0.0;
- double wLast = w;
-
- if (PI * sigma < cutoff)
- {
- REPORT_ERROR("GaussianPyramid::GaussianPyramid: unable to shrink image levels - cutoff too large.\n");
- }
-
- levels.push_back(curr);
- scales.push_back(currScale);
-
- double dScale = PI * sigma / cutoff;
- int i = 0;
-
- for (int j = 0; j < initial; j++)
- {
- const double sig = (j+1)*sigma/(double)(initial+1);
-
- Image<T> filt;
- FilterHelper::separableGaussianXY(levels[0], filt, sig, 3*sigma, true);
-
- levels.push_back(filt);
- scales.push_back(1.0);
- }
-
- if (maxLev < 0) maxLev = floor(log((double)w0)/log(dScale));
-
- while (i < maxLev)
- {
- double tgtSigma_l0 = sigma * pow(dScale, i);
-
- double dSigma = sqrt(tgtSigma_l0 * tgtSigma_l0 - currL0Var) / currScale;
- currL0Var += currScale * currScale * dSigma * dSigma;
-
- int wNext = (int)(w / currScale + 0.5);
- double dScaleAct = wLast / wNext;
- wLast = wNext;
-
- currScale *= dScaleAct;
-
- Image<T> filt, next;
- FilterHelper::separableGaussianXY(curr, filt, dSigma, 3*dSigma, true);
- ResamplingHelper::subsample2D_cubic(filt, dScaleAct, next);
-
- levels.push_back(next);
- scales.push_back(currScale);
- curr = next;
-
- i++;
- }
-}
-
-template<typename T>
-std::vector<Image<T>> GaussianPyramid<T>::getUpsampled()
-{
- std::vector<Image<T>> out(levels.size());
-
- out[0] = levels[0];
-
- for (int i = 1; i < levels.size(); i++)
- {
- ResamplingHelper::upsample2D_cubic(levels[i], scales[i], out[i], true);
- }
-
- return out;
-}
-
-template<typename T>
-Image<T> GaussianPyramid<T>::getUpsampledLevel(int i)
-{
- Image<T> out;
- ResamplingHelper::upsample2D_cubic(levels[i], scales[i], out, true);
- return out;
-}
-
-template<typename T>
-Image<T> GaussianPyramid<T>::getInterpolated(double sig)
-{
- Image<T> out(levels[0].data.xdim, levels[0].data.ydim);
-
- if (sig <= 0) return levels[0];
- else if (sig < sigma)
- {
- // s = j*sigma/(double)(initial+1)
- // <=>
- // j = (initial+1)*s/sigma
-
- double l = (initial+1)*sig/sigma;
- int l0 = (int)l;
- double f = l - l0;
-
- Image<T> img0 = levels[l0];
- Image<T> img1 = levels[l0+1];
-
- ImageOp::linearCombination(img0, img1, 1.0 - f, f, out);
- }
- else
- {
- double lambda = PI * sigma / cutoff;
- double l = log(sig/sigma) / log(lambda) + 1.0 + initial;
-
- int l0 = (int)l;
- double f = l - l0;
-
- if (l0 >= levels.size()-1) return levels[levels.size()-1];
-
-
- Image<T> img0 = getUpsampledLevel(l0);
- Image<T> img1 = getUpsampledLevel(l0+1);
-
- ImageOp::linearCombination(img0, img1, 1.0 - f, f, out);
- }
-
- return out;
-}
-
-template <typename T>
-void GaussianPyramid<T>::test(const Image<T>& img)
-{
- int lev = 4;
- int mp = 20;
- double k = 2.5;
- double sg = 1.0;
-
- GaussianPyramid<T> gp(img, 1.0, 2.5, lev);
-
- std::vector<Image<T>> test(lev*mp), baseline(lev*mp);
-
- double lambda = PI*sg/k;
-
- for (int i = 0; i < lev; i++)
- for (int j = 0; j < mp; j++)
- {
- double t = (mp*i + j)/(double)(mp);
- double sig = t < 1.0? sg * t : sg * pow(lambda,t-1);
-
- test[mp*i + j] = gp.getInterpolated(sig);
- FilterHelper::separableGaussianXY(img, baseline[mp*i + j], sig, 3*sig, true);
- }
-
- VtkHelper::write(test, "debug/pyr_interpolated.vtk");
- VtkHelper::write(baseline, "debug/pyr_baseline.vtk");
-}
-
-
-template<typename T>
-void GaussianPyramid<T>::interpolationTest(const Image<T> &img)
-{
- const double ds = 0.25;
-
- for (double s0 = 0.0; s0 < 2.0; s0 += ds)
- {
- double s1 = s0 + ds;
-
- Image<T> img0, img1, imgP, imgT;
-
- FilterHelper::separableGaussianXY(img, img0, s0, 6, true);
- FilterHelper::separableGaussianXY(img, img1, s1, 6, true);
-
- imgT.data.resize(img.data);
-
- std::stringstream stss0;
- stss0 << s0;
- std::stringstream stss1;
- stss1 << s1;
-
- std::ofstream ofs("debug/interp_"+stss0.str()+"-"+stss1.str()+".dat");
-
- for (double p = s0; p <= s1; p += ds/50.0)
- {
- FilterHelper::separableGaussianXY(img, imgP, p, 6, true);
-
- double c_min = 1e20;
- double t_opt = 0.0;
-
- for (double t = 0.0; t < 1.0; t += 0.005)
- {
- ImageOp::linearCombination(img0, img1, 1.0 - t, t, imgT);
-
- double c = FilterHelper::L2distance(imgT, imgP);
-
- if (c < c_min)
- {
- c_min = c;
- t_opt = t;
- }
- }
-
- ofs << p << " " << s0 + t_opt*(s1 - s0) << "\n";
- std::cout << p << " between " << s0 << " and " << s1 << ": t = " << t_opt << "\n";
- }
-
- std::cout << "\n";
- }
-}
-
-#endif
View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/bb13c18652e75e37d8a8510a82eb90c4680b203d...5984c17623398d4b826e33537bca0e060a086147
--
View it on GitLab: https://salsa.debian.org/med-team/relion/-/compare/bb13c18652e75e37d8a8510a82eb90c4680b203d...5984c17623398d4b826e33537bca0e060a086147
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