{bio}[GCCcore/12.3.0] AreTomo2 v1.1.2 w/ CUDA 12.1.1

easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.1.2-GCCcore-12.3.0-CUDA-12.1.1.eb

@@ -0,0 +1,56 @@
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/1
+easyblock = 'MakeCp'
+
+name = 'AreTomo2'
+version = '1.1.2'
+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_lib.patch']
+checksums = [
+    {'v1.1.2.tar.gz': '4cbb4d25d28778041d80ef2c598519b17b9a40aa84e1e99daf48ad5a90d946b4'},
+    {'AreTomo2-1.1.2_makefile_lib.patch': '53b3694104c4149d2714e503fb2a7cb9be7cbb0e500ee6991a606faa1c10a314'},
+]
+
+github_account = 'czimaginginstitute'
+
+prebuildopts = 'rm -rf LibSrc/Lib/*.a && '
+build_cmd = 'make clean -f makefile11 && 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/AreTomo2-1.1.2_makefile_lib.patch

@@ -0,0 +1,96 @@
+# Thomas Hoffmann, EBML Heidelberg, structures-it@embl.de, 2024/10
+# Allow to inject cuda compute capabilities and cfalgs.
+# Add targets for libmrcfile.a, libutil.a, and libclean
+diff -ru AreTomo2-1.1.2/LibSrc/Mrcfile/makefile AreTomo2-1.1.2_makefile/LibSrc/Mrcfile/makefile
+--- AreTomo2-1.1.2/LibSrc/Mrcfile/makefile	2024-02-21 05:57:47.000000000 +0100
++++ AreTomo2-1.1.2_makefile/LibSrc/Mrcfile/makefile	2024-10-31 12:55:25.131194106 +0100
+@@ -19,8 +19,8 @@
+ OBJS	= $(patsubst %.cpp, %.o, $(SRCS))
+ OUT	= libmrcfile.a
+
+-CC = g++ -std=c++11
+-CFLAGS	= -m64 -c -g -pthread -IInclude -I$(INCDIR)
++#CC = g++ -std=c++11
++CFLAGS_	= -m64 -c -g -pthread -IInclude -I$(INCDIR) $(CFLAGS)
+
+ all: $(OBJS)
+ 	@ar rcs $(OUT) $(OBJS)
+@@ -33,7 +33,9 @@
+
+ %.o: %.cpp
+ 	@echo Compile $<
+-	@$(CC) $(CFLAGS) $< -o $@
++	@echo $(CC) $(CFLAGS_) $< -o $@
++	@$(CC) $(CFLAGS_) $< -o $@
+
+ clean:
++	@echo rm -f $(OUT) $(OBJS) *.*~ makefile~
+ 	@rm -f $(OUT) $(OBJS) *.*~ makefile~
+diff -ru AreTomo2-1.1.2/LibSrc/Util/makefile AreTomo2-1.1.2_makefile/LibSrc/Util/makefile
+--- AreTomo2-1.1.2/LibSrc/Util/makefile	2024-02-21 05:57:47.000000000 +0100
++++ AreTomo2-1.1.2_makefile/LibSrc/Util/makefile	2024-10-31 12:55:10.603854025 +0100
+@@ -5,8 +5,8 @@
+ #-------------------
+ OUT = libutil.a
+
+-CC = g++ -std=c++11
+-CFLAG = -c -g -pthread -m64
++#CC = g++ -std=c++11
++CFLAG = -c -g -pthread -m64 $(CFLAGS)
+
+ all: $(OBJS)
+ 	@echo create library $(OUT) and move to $(PROJ_DIR)/Lib
+@@ -16,6 +16,7 @@
+ 	@cp $(HDRS) $(PROJ_DIR)/Include/Util
+
+ %.o: %.cpp
++	echo $(CC) $(CFLAG) $< -o $@
+ 	$(CC) $(CFLAG) $< -o $@
+
+ list:
+diff -ru AreTomo2-1.1.2/makefile11 AreTomo2-1.1.2_makefile/makefile11
+--- AreTomo2-1.1.2/makefile11	2024-02-21 05:57:47.000000000 +0100
++++ AreTomo2-1.1.2_makefile/makefile11	2024-10-31 12:52:55.796679029 +0100
+@@ -179,7 +179,24 @@
+
+ compile: $(OBJS)
+
+-exe: $(OBJS)
++libclean:
++	$(MAKE) -C LibSrc/Util clean
++	$(MAKE) -C LibSrc/Mrcfile clean
++
++LibSrc/Lib/libutil.a:
++	$(MAKE) -C LibSrc/Util   
++
++LibSrc/Lib/libmrcfile.a:
++	$(MAKE) -C LibSrc/Mrcfile  
++
++exe: $(OBJS) LibSrc/Lib/libmrcfile.a LibSrc/Lib/libutil.a
++	@echo g++ -g -pthread -m64 $(OBJS) \
++	$(PRJLIB)/libmrcfile.a \
++	$(PRJLIB)/libutil.a \
++	-L$(CUDALIB) -L/usr/lib64 \
++	-lcufft -lcudart -lcuda -lc -lm -lpthread \
++	-o AreTomo2
++ 
+ 	@g++ -g -pthread -m64 $(OBJS) \
+ 	$(PRJLIB)/libmrcfile.a \
+ 	$(PRJLIB)/libutil.a \
+@@ -193,10 +210,12 @@
+ 	@echo $< has been compiled.
+
+ %.o: %.cpp
++	@echo $(CC) $(CFLAG) -I$(PRJINC) -I$(CUDAINC) \
++		$< -o $@
+ 	@$(CC) $(CFLAG) -I$(PRJINC) -I$(CUDAINC) \
+ 		$< -o $@
+ 	@echo $< has been compiled.
+
+-clean:
+-	@rm -f $(OBJS) $(CUCPPS) *.h~ makefile~ AreTomo2
+-	
++clean: libclean
++	@echo rm -f $(OBJS) $(CUCPPS) *.h~ makefile~ AreTomo2 LibSrc/Lib/*.a
++	@rm -f $(OBJS) $(CUCPPS) *.h~ makefile~ AreTomo2 LibSrc/Lib/*.a
+Only in AreTomo2-1.1.2_makefile: .makefile11.swp