{devel,bio}[GCC/11.3.0,foss/2022a] CTPL v0.0.2, Xmipp v3.22.07-Helios w/ Python 3.10.4

easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb

@@ -0,0 +1,30 @@
+easyblock = 'CmdCp'
+
+name = 'CTPL'
+version = '0.0.2'
+
+homepage = 'https://github.com/vit-vit/CTPL.git'
+
+description = "Modern and efficient C++ Thread Pool Library"
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+github_account = 'vit-vit'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(namelower)s_v.%(version)s.tar.gz']
+checksums = ['8c1cec7c570d6d84be1d29283af5039ea27c3e69703bd446d396424bf619816e']
+
+dependencies = [
+    ('Boost', '1.79.0'),
+]
+
+cmds_map = [('.*', "echo Nothing to build")]
+
+files_to_copy = [(['ctpl.h', 'ctpl_stl.h'], 'include/CTPL'), 'LICENSE', 'example.cpp']
+
+sanity_check_paths = {
+    'files': ['include/CTPL/%s' % x for x in ['ctpl.h', 'ctpl_stl.h']],
+    'dirs': []
+}
+
+moduleclass = 'devel'

easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb

@@ -0,0 +1,37 @@
+easyblock = 'PythonBundle'
+
+name = 'SCons'
+version = '4.4.0'
+
+homepage = 'https://www.scons.org/'
+description = "SCons is a software construction tool."
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [('Python', '3.10.4')]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    (name, version, {
+        'modulename': False,
+        'patches': ['SCons-4.4.0_install_man_pages_correctly.patch'],
+        'checksums': [
+            {'SCons-4.4.0.tar.gz': '7703c4e9d2200b4854a31800c1dbd4587e1fa86e75f58795c740bcfa7eca7eaa'},
+            {'SCons-4.4.0_install_man_pages_correctly.patch':
+             '9d216c2ea8e152ae1531593b17adc4042eb88f1d9524d7f3b08ace5137d6d5e7'},
+        ],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/scons', 'bin/sconsign'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'],
+}
+
+sanity_check_commands = ["scons --help"]
+
+moduleclass = 'devel'

easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch

@@ -0,0 +1,15 @@
+Install the man pages in the correct directory.
+
+Åke Sandgren, 2022-10-27
+diff -ru SCons-4.4.0.orig/setup.cfg SCons-4.4.0/setup.cfg
+--- SCons-4.4.0.orig/setup.cfg	2022-07-30 23:16:02.000000000 +0200
++++ SCons-4.4.0/setup.cfg	2022-10-27 11:55:33.457877253 +0200
+@@ -58,7 +58,7 @@
+ SCons.Tool.docbook = *.*
+
+ [options.data_files]
+-. = scons.1
++man/man1 = scons.1
+ 	scons-time.1
+ 	sconsign.1
+

easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb

@@ -0,0 +1,87 @@
+name = 'Xmipp'
+version = '3.22.07-Helios'
+
+homepage = 'https://github.com/I2PC/scipion/wiki'
+description = """Scipion is an image processing framework to obtain 3D
+models of macromolecular complexes using Electron Microscopy (3DEM). It
+integrates several software packages and presents an unified interface
+for both biologists and developers. Scipion allows to execute workflows
+combining different software tools, while taking care of formats and
+conversions. Additionally, all steps are tracked and can be reproduced
+later on. 
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+sources = [
+    {
+        'source_urls': ['https://github.com/I2PC/xmipp/archive/'],
+        'download_filename': 'v%(version)s.tar.gz',
+        'filename': '%(namelower)s-v%(version)s.tar.gz',
+    },
+    {
+        'source_urls': ['https://github.com/I2PC/xmippCore/archive/'],
+        'download_filename': 'v%(version)s.tar.gz',
+        'filename': 'xmippCore-v%(version)s.tar.gz',
+        'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src',
+    },
+    {
+        'source_urls': ['https://github.com/I2PC/xmippViz/archive/'],
+        'download_filename': 'v%(version)s.tar.gz',
+        'filename': 'xmippViz-v%(version)s.tar.gz',
+        'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src',
+    },
+]
+patches = [
+    '%(name)s-%(version)s_fix_scons_Environent_calls.patch',
+    '%(name)s-%(version)s_drop_useless_CXXFLAGS_setting.patch',
+    '%(name)s-%(version)s_correct_order_of_cu_includes.patch',
+    '%(name)s-%(version)s_dont_add_useless_libs.patch',
+    '%(name)s-%(version)s_dont_change_EB_build_flags.patch',
+    ('XmippCore-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippCore'),
+    ('XmippCore-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippCore'),
+    ('XmippViz-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippViz'),
+    ('XmippViz-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippViz'),
+]
+checksums = [
+    {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'},
+    {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'},
+    {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'},
+    {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch':
+     '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'},
+    {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch':
+     '34ed0cb591e1e2788acd3e58696b1f45ce9210836d14ed1c99de1e574e4824e6'},
+    {'Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch':
+     '2b0b2ddf349003be4112f4dca623586a03235214d6e64d232deb26468b52f0e3'},
+    {'Xmipp-3.22.07-Helios_dont_add_useless_libs.patch':
+     '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'},
+    {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch':
+     '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'},
+    {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch':
+     '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'},
+    {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch':
+     'd86b0d3ecc339b81c9aa7a33d2b44b428643aa7e2e686529b4bb6b16d36805c2'},
+    {'XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch':
+     '7724fc3953d9c4c308a5755f54229259425fdbad5a909153bd173292434407b9'},
+    {'XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch':
+     'a8bea23c243174fb27a140a34a064a622cc96f0e7231fd31caf20f90c7ba9555'},
+]
+
+builddependencies = [
+    ('SCons', '4.4.0'),
+    ('CTPL', '0.0.2'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('Java', '11', '', SYSTEM),
+    ('OpenCV', '4.6.0', '-contrib'),
+    ('SQLite', '3.38.3'),
+    ('HDF5', '1.12.2'),
+    ('LibTIFF', '4.3.0'),
+    ('libjpeg-turbo', '2.1.3'),
+    ('LIBSVM', '3.30'),
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch

@@ -0,0 +1,19 @@
+commit baac03018283296f90c08366e0e092c95d25173b
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Tue Oct 18 14:34:34 2022 +0200
+
+    cuda_gpu_multidim_array.cu is just an include file containing templates.
+    Needs to be before cuda_gpu_geo_transformer.cu
+
+diff --git xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp
+index f7e5178c..8ccbefd3 100644
+--- xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp
++++ xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp
+@@ -31,6 +31,6 @@
+  */
+
+ #include "cuda_gpu_bilib.cu"
++#include "cuda_gpu_multidim_array.cu"
+ #include "cuda_gpu_geo_transformer.cu"
+ #include "cuda_gpu_iirconvolve.cu"
+-#include "cuda_gpu_multidim_array.cu"

easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch

@@ -0,0 +1,21 @@
+commit 4c1e2d678c5a33eae2ddb9f0558523d6d697e2b6
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Thu Oct 27 08:04:04 2022 +0200
+
+    Don't add useless libraries to XmippInterfaceCuda and XmippParallelCuda
+
+diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct
+index e70ea2cd..077541e8 100644
+--- xmipp-3.22.07-Helios/src/xmipp/SConstruct
++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct
+@@ -209,9 +209,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte
+     """
+     _libs = list(libs)
+     _libpath = list(libpath)+external_libdirs
+-    if name == "XmippInterfaceCuda":
+-        _libs.append("XmippCuda")
+-    if "Cuda" in name:
++    if name == "XmippCuda":
+         _libs.append("cudart")
+         #_libs.append("cuda")
+         _libs.append("cufft")

easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch

@@ -0,0 +1,41 @@
+commit e53881505ae212fa913fc536e60869e9b8e7f73c
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Thu Oct 27 09:45:11 2022 +0200
+
+    Don't change flags from what EasyBuild has decided to use.
+
+diff --git xmipp-3.22.07-Helios/scripts/config.py xmipp-3.22.07-Helios/scripts/config.py
+index 0f58cbe3..b442a035 100644
+--- xmipp-3.22.07-Helios/scripts/config.py
++++ xmipp-3.22.07-Helios/scripts/config.py
+@@ -293,7 +293,7 @@ class Config:
+                 self.configDict["CCFLAGS"] += " -std=c99"
+         if 'g++' in self.get(Config.KEY_CXX):
+             # optimize for current machine
+-            self.configDict["CXXFLAGS"] += " -mtune=native -march=native -flto"
++            #self.configDict["CXXFLAGS"] += " -mtune=native -march=native -flto"
+             if "-std=c99" not in self.configDict["CXXFLAGS"]:
+                 self.configDict["CXXFLAGS"] += " -std=c++17"
+             if isCIBuild():
+@@ -301,8 +301,8 @@ class Config:
+                 self.configDict["CXXFLAGS"] += " -Werror"
+                 # don't optimize, as it slows down the build
+                 self.configDict["CXXFLAGS"] += " -O0"
+-            else:
+-                self.configDict["CXXFLAGS"] += " -O3"
++            #else:
++            #    self.configDict["CXXFLAGS"] += " -O3"
+             if self.is_true("DEBUG"):
+                 self.configDict["CXXFLAGS"] += " -g"
+
+@@ -315,8 +315,8 @@ class Config:
+         if self.configDict["LIBDIRFLAGS"] == "":
+             # /usr/local/lib or /path/to/virtEnv/lib
+             localLib = "%s/lib" % info['data']
+-            self.configDict["LIBDIRFLAGS"] = "-L%s" % localLib
+-            self.environment.update(LD_LIBRARY_PATH=localLib)
++            #self.configDict["LIBDIRFLAGS"] = "-L%s" % localLib
++            #self.environment.update(LD_LIBRARY_PATH=localLib)
+
+             # extra libs
+             hdf5InLocalLib = findFileInDirList("libhdf5*", localLib)

easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch

@@ -0,0 +1,18 @@
+commit f647cd54c8fa2b0894f347cbf7f13aacc0b8c785
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Tue Oct 18 14:30:08 2022 +0200
+
+    Drop redundant setting of env var CXXFLAGS to what it already is.
+
+diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct
+index c921c3c5..e70ea2cd 100644
+--- xmipp-3.22.07-Helios/src/xmipp/SConstruct
++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct
+@@ -148,7 +148,6 @@ env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS')
+ env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split()
+ cxxFlags = os.environ.get('CXXFLAGS', '')
+ env['CXXFLAGS'] = cxxFlags.split()
+-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code
+ env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split()
+
+

easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch

@@ -0,0 +1,37 @@
+commit 8ff0a1295743fae1eb069fe8242e524f348f5937
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Tue Oct 18 14:28:47 2022 +0200
+
+    Make sure SCons sees the complete environment from EasyBuild.
+
+diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct
+index 22ea72cf..c921c3c5 100644
+--- xmipp-3.22.07-Helios/src/xmipp/SConstruct
++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct
+@@ -236,7 +236,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte
+     # the reason is a compilation error for CUDA, which results in a multiple symbol detection
+     # when the order is different. This has to be fixed in the future by changing the CUDA
+     # build system FIXME David Strelak
+-    env2 = Environment()
++    env2 = Environment(ENV=os.environ)
+     env2['ENV']['PATH'] = env['ENV']['PATH']
+     env2['CXXFLAGS']=list(env['CXXFLAGS']) # list(.) causes a true copy and not just a pointer 
+     env2['LINKFLAGS']=list(env['LINKFLAGS'])
+@@ -425,7 +425,7 @@ def addProgram(env, name, src=None, pattern=None, installDir=None,
+     ldLibraryPathCopy = [env['LIBPATH']]
+     appendUnique(libPathsCopy, external_libdirs) # This order is important, because if we should use Scipion libs, these will be before the system libs
+     appendUnique(libPathsCopy, env.get('LIBPATH', '').split(os.pathsep))
+-    env2 = Environment()
++    env2 = Environment(ENV=os.environ)
+     env2['ENV']['LD_LIBRARY_PATH'] = env['ENV'].get('LD_LIBRARY_PATH', '')
+     env2['ENV']['PATH'] = env['ENV']['PATH']
+
+@@ -486,7 +486,7 @@ def compilerConfig(env):
+
+ def libraryTest(env, name, lang='c'):
+     """Check the existence of a concrete C/C++ library."""
+-    env2 = Environment(LIBS=env.get('LIBS',''))
++    env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS',''))
+     conf = Configure(env2)
+     conf.CheckLib(name, language=lang)
+     env2 = conf.Finish()

easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch

@@ -0,0 +1,28 @@
+commit 901b41d324b351995b9256d7ee6b370276274497
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Tue Oct 18 14:21:03 2022 +0200
+
+    Make sure SCons sees the complete environment from EasyBuild.
+
+diff --git xmippCore-3.22.07-Helios/SConstruct xmippCore-3.22.07-Helios/SConstruct
+index 1c5fec3..40ed01f 100644
+--- xmippCore-3.22.07-Helios/SConstruct
++++ xmippCore-3.22.07-Helios/SConstruct
+@@ -207,7 +207,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte
+     if not sources and env.TargetInBuild(name):
+         Exit('No sources found for Library: %s. Exiting!!!' % name)
+
+-    env2 = Environment()
++    env2 = Environment(ENV=os.environ)
+     env2['ENV']['PATH'] = env['ENV']['PATH']
+     env2['CXX'] = env['CXX']
+
+@@ -363,7 +363,7 @@ def compilerConfig(env):
+
+ def libraryTest(env, name, lang='c'):
+     """Check the existence of a concrete C/C++ library."""
+-    env2 = Environment(LIBS=env.get('LIBS',''))
++    env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS',''))
+     conf = Configure(env2)
+     conf.CheckLib(name, language=lang)
+     env2 = conf.Finish()

easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch

@@ -0,0 +1,24 @@
+commit 36ca78858e442f1df23f5cb6b87c877a864eff44
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Tue Oct 18 14:23:16 2022 +0200
+
+    Only use CXXFLAGS from EasyBuild.
+
+diff --git xmippCore-3.22.07-Helios/SConstruct xmippCore-3.22.07-Helios/SConstruct
+index 40ed01f..277443d 100644
+--- xmippCore-3.22.07-Helios/SConstruct
++++ xmippCore-3.22.07-Helios/SConstruct
+@@ -136,13 +136,7 @@ env['CXX'] = os.environ.get('CXX')
+ env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS')
+ env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split()
+ cxxFlags = os.environ.get('CXXFLAGS', '') 
+-if os.environ.get('DEBUG', '0') == 'True': #FIXME, use 1, true, yes...
+-   cxxFlags += ' -g'
+-else:
+-    if cxxFlags.find("-O")==-1:
+-        cxxFlags += (" -O3" if 'TRAVIS' not in os.environ else " -O0") #don't optimize on Travis, as it slows down the build
+ env['CXXFLAGS'] = cxxFlags.split()
+-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code
+ env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split()
+
+

easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch

@@ -0,0 +1,28 @@
+commit 0e749b55db29360c9804f8c5e07094b7a5bf0597
+Author: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
+Date:   Tue Oct 18 14:25:17 2022 +0200
+
+    Make sure scons sees the complete environment from EasyBuild.
+
+diff --git xmippViz-3.22.07-Helios/SConstruct xmippViz-3.22.07-Helios/SConstruct
+index dc0a809..32c75be 100644
+--- xmippViz-3.22.07-Helios/SConstruct
++++ xmippViz-3.22.07-Helios/SConstruct
+@@ -237,7 +237,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte
+     if not sources and env.TargetInBuild(name):
+         Exit('No sources found for Library: %s. Exiting!!!' % name)
+
+-    env2 = Environment()
++    env2 = Environment(ENV=os.environ)
+     env2['ENV']['PATH'] = env['ENV']['PATH']
+
+     mpiArgs = {}
+@@ -474,7 +474,7 @@ def compilerConfig(env):
+
+ def libraryTest(env, name, lang='c'):
+     """Check the existence of a concrete C/C++ library."""
+-    env2 = Environment(LIBS=env.get('LIBS', ''))
++    env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS', ''))
+     conf = Configure(env2)
+     conf.CheckLib(name, language=lang)
+     env2 = conf.Finish()