{bio}[GCCcore/12.3.0] AreTomo2 v1.0.0 and MotionCor3 v1.0.1 w/CUDA 12.1.1

easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb

@@ -0,0 +1,55 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/1
+easyblock = 'MakeCp'
+
+name = 'AreTomo2'
+version = '1.0.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/czimaginginstitute/AreTomo2'
+
+description = """AreTomo2, a multi-GPU accelerated software package that fully automates motion- 
+corrected marker-free tomographic alignment and reconstruction, now includes    
+robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single  
+package. AreTomo2 is part of our endeavor to build a fully-automated high-      
+throughput processing pipeline that enables real-time reconstruction of         
+tomograms in parallel with tomographic data collection. It strives to be fast   
+and accurate, as well as provides for easy integration into subtomogram         
+processing workflows by generating IMod compatible files containing alignment   
+and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also 
+be used for on-the-fly reconstruction of tomograms and CTF estimation in        
+parallel with tilt series collection, enabling real-time assessment of sample   
+quality and adjustment of collection parameters"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'cstd': 'c++11'}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_makefile.patch']
+checksums = [
+    {'v1.0.0.tar.gz': '5518cd5d7bc13a6dbb6d9310b22c301e73a0c91dc059da403445d79ca0ff8892'},
+    {'AreTomo2-1.0.0_makefile.patch': '8595b2fc55e0b5e1bf7c077c93c09503b4e8f95123c6aaf0a5fbe44dda871c73'},
+]
+
+github_account = 'czimaginginstitute'
+
+build_cmd = 'make exe -f makefile11 CUDAHOME=$CUDA_HOME CUDACC="%(cuda_cc_cmake)s"'
+
+builddependencies = [
+    ('binutils', '2.40')
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+]
+
+files_to_copy = [(['%(name)s'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = ['%(name)s -h']
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0_makefile.patch

@@ -0,0 +1,46 @@
+# Thomas Hoffmann, EBML Heidelberg, structures-it@embl.de, 2023/10
+# allow to inject cuda compute capabilities and cfalgs
+diff -ru AreTomo2-1.0.0/makefile11 AreTomo2-1.0.0_makefile/makefile11
+--- AreTomo2-1.0.0/makefile11	2023-10-26 19:49:07.000000000 +0200
++++ AreTomo2-1.0.0_makefile/makefile11	2023-10-30 19:00:07.212270395 +0100
+@@ -156,18 +156,21 @@
+ 	$(CUCPPS)
+ OBJS = $(patsubst %.cpp, %.o, $(SRCS))
+ #-------------------------------------
+-CC = g++ -std=c++11
+-CFLAG = -c -g -pthread -m64
++#CC = g++ -std=c++11
++CFLAG = -c -g -pthread -m64 $(CFLAGS)
+ NVCC = $(CUDAHOME)/bin/nvcc -std=c++11
+-CUFLAG = -Xptxas -dlcm=ca -O2 \
+-	-gencode arch=compute_80,code=sm_80 \
+-	-gencode arch=compute_75,code=sm_75 \
+-	-gencode arch=compute_70,code=sm_70 \
+-	-gencode arch=compute_61,code=sm_61 \
+-	-gencode arch=compute_60,code=sm_60 \
+-	-gencode arch=compute_53,code=sm_53 \
+-	-gencode arch=compute_52,code=sm_52 \
+-	-gencode arch=compute_86,code=sm_86
++SPACE= ' '
++SEMI= ;
++GENCODES = $(foreach x,$(subst $(SEMI),$(SPACE),$(CUDACC)),-gencode arch=compute_$x,code=sm_$x)
++CUFLAG = -Xptxas -dlcm=ca -O2 $(GENCODES)
++#	-gencode arch=compute_80,code=sm_80 \
++#	-gencode arch=compute_75,code=sm_75 \
++#	-gencode arch=compute_70,code=sm_70 \
++#	-gencode arch=compute_61,code=sm_61 \
++#	-gencode arch=compute_60,code=sm_60 \
++#	-gencode arch=compute_53,code=sm_53 \
++#	-gencode arch=compute_52,code=sm_52 \
++#	-gencode arch=compute_86,code=sm_86
+ #------------------------------------------
+ cuda: $(CUCPPS)
+
+@@ -183,6 +186,7 @@
+ 	-lcufft -lcudart -lcuda -lc -lm -lpthread \
+ 	-o AreTomo2
+ 	@echo AreTomo2 has been generated.
++	@echo used cuda gencodes: $(GENCODES)
+
+ %.o: %.cu
+ 	@$(NVCC) -c $(CUFLAG) -I$(PRJINC) -I$(CUPRJINC) $< -o $@

easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1-GCCcore-12.3.0-CUDA-12.1.1.eb

@@ -0,0 +1,57 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/1
+easyblock = 'MakeCp'
+
+name = 'MotionCor3'
+version = '1.0.1'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://github.com/czimaginginstitute/MotionCor3'
+
+description = """Anisotropic correction of beam induced motion for cryo-electron microscopy and  
+cryo-electron tomography images.
+MotionCor3, an improved implementation of MotionCor2 with addition of CTF       
+(Contrast Transfer Function) estimation, is a multi-GPU accelerated software    
+package that enables single-pixel level correction of anisotropic beam induced  
+sample motion for cryo-electron microscopy and cryo-electron tomography images. 
+The iterative, patch-based motion detection combined with spatial and temporal  
+constraints and dose weighting provides robust and accurate correction. By      
+refining the measurement of early motion, MotionCor3 further improves correction
+on tilted samples. The efficiency achieved by multi-GPU acceleration and        
+parallelization enables correction to keep pace with automated data collection. 
+The recent addition of a very robust GPU-accelerated CTF estimation makes       
+MotionCor3 more versatile in cryoEM and cryoET processing pipeline."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+toolchainopts = {'cstd': 'c++11'}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s_makefile.patch']
+checksums = [
+    {'v1.0.1.tar.gz': '9b1eaa43f67c6ca54c1cea6ad53ee78726a14a87a3c5d91e7820786ebe0786a3'},
+    {'MotionCor3-1.0.1_makefile.patch': 'd047c1f097eead3173a60fd3ae821ee7b285728bf8470f496021580f11875d12'},
+]
+
+github_account = 'czimaginginstitute'
+
+build_cmd = 'make exe -f makefile11 CUDAHOME=$CUDA_HOME CUDACC="%(cuda_cc_cmake)s"'
+
+builddependencies = [
+    ('binutils', '2.40')
+]
+
+dependencies = [
+    ('CUDA', '12.1.1', '', SYSTEM),
+    ('LibTIFF', '4.5.0'),
+]
+
+files_to_copy = [(['%(name)s'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/%(name)s'],
+    'dirs': ['bin'],
+}
+
+sanity_check_commands = ['%(name)s --help']
+
+moduleclass = 'bio'

easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1_makefile.patch

@@ -0,0 +1,54 @@
+# Thomas Hoffmann, EBML Heidelberg, structures-it@embl.de, 2023/10
+# allow to inject cuda compute capabilities and cfalgs
+diff -ru MotionCor3-1.0.1/makefile11 MotionCor3-1.0.1_makefile/makefile11
+--- MotionCor3-1.0.1/makefile11	2023-10-25 23:59:50.000000000 +0200
++++ MotionCor3-1.0.1_makefile/makefile11	2023-10-31 14:24:25.377992618 +0100
+@@ -1,6 +1,6 @@
+ PRJHOME = $(shell pwd)
+ CONDA = $(HOME)/miniconda3
+-CUDAHOME = $(HOME)/nvidia/cuda-12.1
++#CUDAHOME = $(HOME)/nvidia/cuda-12.1
+ CUDAINC = $(CUDAHOME)/include
+ CUDALIB = $(CUDAHOME)/lib64
+ PRJINC = $(PRJHOME)/Include
+@@ -139,18 +139,21 @@
+ 	$(CUCPPS)
+ OBJS = $(patsubst %.cpp, %.o, $(SRCS))
+ #-------------------------------------
+-CC = g++ -std=c++11
+-CFLAG = -c -g -pthread -m64
++#CC = g++ -std=c++11
++CFLAG = -c -g -pthread -m64 $(CFLAGS)
+ NVCC = $(CUDAHOME)/bin/nvcc -std=c++11
+-CUFLAG = -Xptxas -dlcm=ca -O2 \
+-	-gencode arch=compute_86,code=sm_86 \
+-	-gencode arch=compute_80,code=sm_80 \
+-	-gencode arch=compute_75,code=sm_75 \
+-	-gencode arch=compute_70,code=sm_70 \
+-	-gencode arch=compute_52,code=sm_52 \
+-        -gencode arch=compute_53,code=sm_53 \
+-        -gencode arch=compute_60,code=sm_60 \
+-        -gencode arch=compute_61,code=sm_61 
++SPACE= ' '
++SEMI= ;
++GENCODES = $(foreach x,$(subst $(SEMI),$(SPACE),$(CUDACC)),-gencode arch=compute_$x,code=sm_$x)
++CUFLAG = -Xptxas -dlcm=ca -O2 $(GENCODES)
++#	-gencode arch=compute_86,code=sm_86 \
++#	-gencode arch=compute_80,code=sm_80 \
++#	-gencode arch=compute_75,code=sm_75 \
++#	-gencode arch=compute_70,code=sm_70 \
++#	-gencode arch=compute_52,code=sm_52 \
++#        -gencode arch=compute_53,code=sm_53 \
++#        -gencode arch=compute_60,code=sm_60 \
++#        -gencode arch=compute_61,code=sm_61 
+ #------------------------------------------
+ cuda: $(CUCPPS)
+
+@@ -165,6 +168,7 @@
+ 	-lcufft -lcudart -lcuda -lnvToolsExt -ltiff -lc -lm -lpthread \
+ 	-o MotionCor3
+ 	@echo MotionCor3 has been generated.
++	@echo used cuda gencodes: $(GENCODES)
+
+ %.cpp: %.cu
+ 	@echo "-----------------------------------------------"