「minicondaにCMakeの検索パスを持ってかれる」の版間の差分

2019年5月15日 (水) 05:25時点における版 (ソースを閲覧) Kttn (トーク | 投稿記録) (→‎とりあえずの対処) ←古い編集		2019年5月15日 (水) 05:32時点における版 (ソースを閲覧) Kttn (トーク | 投稿記録) 新しい編集→
行167:		行167:
	=== CMakeのパラメータ ===		=== CMakeのパラメータ ===
−	一応、CMakeCache.txtの内容を以下に貼り付けておく。MediaWikiのせいで一部の記号が変に化けてるけど対処策がわからないのでとりあえず放っておく。	+	一応、CMakeCache.txtの内容は[[File:CMakeCache-190515.txt|こちら]]。
−		+
−	# This is the CMakeCache file.	+
−	# For build in directory: /home/kttn/softwares/relion/build	+
−	# It was generated by CMake: /usr/bin/cmake	+
−	# You can edit this file to change values found and used by cmake.	+
−	# If you do not want to change any of the values, simply exit the editor.	+
−	# If you do want to change a value, simply edit, save, and exit the editor.	+
−	# The syntax for the file is as follows:	+
−	# KEY:TYPE=VALUE	+
−	# KEY is the name of a variable in the cache.	+
−	# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.	+
−	# VALUE is the current value for the KEY.	+
−		+
−	########################	+
−	# EXTERNAL cache entries	+
−	########################	+
−		+
−	//Enable Accelerated CPU version	+
−	ALTCPU:BOOL=OFF	+
−		+
−	//BUILD_SHARED_LIBS	+
−	BUILD_SHARED_LIBS:BOOL=ON	+
−		+
−	//Path to a program.	+
−	CMAKE_AR:FILEPATH=/usr/bin/ar	+
−		+
−	//Choose the type of build, options are: None(CMAKE_CXX_FLAGS or	+
−	// CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.	+
−	CMAKE_BUILD_TYPE:STRING=	+
−		+
−	//Enable/Disable color output during build.	+
−	CMAKE_COLOR_MAKEFILE:BOOL=ON	+
−		+
−	//CXX compiler	+
−	CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/c++	+
−		+
−	//Flags used by the compiler during all build types.	+
−	CMAKE_CXX_FLAGS:STRING=	+
−		+
−	CMAKE_CXX_FLAGS_BENCHMARKING:STRING='-O3 -DNDEBUG  '	+
−		+
−	//Flags used by the compiler during debug builds.	+
−	CMAKE_CXX_FLAGS_DEBUG:STRING=-g	+
−		+
−	//Flags used by the compiler during release builds for minimum	+
−	// size.	+
−	CMAKE_CXX_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG	+
−		+
−	CMAKE_CXX_FLAGS_PROFILING:STRING='-O3 -DNDEBUG  '	+
−		+
−	//Flags used by the compiler during release builds.	+
−	CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG	+
−		+
−	//Flags used by the compiler during release builds with debug info.	+
−	CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG	+
−		+
−	//C compiler	+
−	CMAKE_C_COMPILER:FILEPATH=/usr/bin/cc	+
−		+
−	//Flags used by the compiler during all build types.	+
−	CMAKE_C_FLAGS:STRING=	+
−		+
−	CMAKE_C_FLAGS_BENCHMARKING:STRING='-O3 -DNDEBUG '	+
−		+
−	//Flags used by the compiler during debug builds.	+
−	CMAKE_C_FLAGS_DEBUG:STRING=-g	+
−		+
−	//Flags used by the compiler during release builds for minimum	+
−	// size.	+
−	CMAKE_C_FLAGS_MINSIZEREL:STRING=-Os -DNDEBUG	+
−		+
−	CMAKE_C_FLAGS_PROFILING:STRING='-O3 -DNDEBUG '	+
−		+
−	//Flags used by the compiler during release builds.	+
−	CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG	+
−		+
−	//Flags used by the compiler during release builds with debug info.	+
−	CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=-O2 -g -DNDEBUG	+
−		+
−	//Flags used by the linker.	+
−	CMAKE_EXE_LINKER_FLAGS:STRING=	+
−		+
−	CMAKE_EXE_LINKER_FLAGS_BENCHMARKING:STRING=' '	+
−		+
−	//Flags used by the linker during debug builds.	+
−	CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING=	+
−		+
−	//Flags used by the linker during release minsize builds.	+
−	CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING=	+
−		+
−	CMAKE_EXE_LINKER_FLAGS_PROFILING:STRING=' '	+
−		+
−	//Flags used by the linker during release builds.	+
−	CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=	+
−		+
−	//Flags used by the linker during Release with Debug Info builds.	+
−	CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING=	+
−		+
−	//Enable/Disable output of compile commands during generation.	+
−	CMAKE_EXPORT_COMPILE_COMMANDS:BOOL=OFF	+
−		+
−	//Install path prefix, prepended onto install directories.	+
−	CMAKE_INSTALL_PREFIX:PATH=/home/kttn/softwares/relion/install	+
−		+
−	//Path to a program.	+
−	CMAKE_LINKER:FILEPATH=/usr/bin/ld	+
−		+
−	//Path to a program.	+
−	CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/make	+
−		+
−	//Flags used by the linker during the creation of modules.	+
−	CMAKE_MODULE_LINKER_FLAGS:STRING=	+
−		+
−	//Flags used by the linker during debug builds.	+
−	CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING=	+
−		+
−	//Flags used by the linker during release minsize builds.	+
−	CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING=	+
−		+
−	//Flags used by the linker during release builds.	+
−	CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING=	+
−		+
−	//Flags used by the linker during Release with Debug Info builds.	+
−	CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING=	+
−		+
−	//Path to a program.	+
−	CMAKE_NM:FILEPATH=/usr/bin/nm	+
−		+
−	//Path to a program.	+
−	CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy	+
−		+
−	//Path to a program.	+
−	CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump	+
−		+
−	//Value Computed by CMake	+
−	CMAKE_PROJECT_NAME:STATIC=Relion	+
−		+
−	//Path to a program.	+
−	CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib	+
−		+
−	//Flags used by the linker during the creation of dll's.	+
−	CMAKE_SHARED_LINKER_FLAGS:STRING=	+
−		+
−	//Flags used by the linker during debug builds.	+
−	CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING=	+
−		+
−	//Flags used by the linker during release minsize builds.	+
−	CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING=	+
−		+
−	//Flags used by the linker during release builds.	+
−	CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING=	+
−		+
−	//Flags used by the linker during Release with Debug Info builds.	+
−	CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING=	+
−		+
−	//If set, runtime paths are not added when installing shared libraries,	+
−	// but are added when building.	+
−	CMAKE_SKIP_INSTALL_RPATH:BOOL=OFF	+
−		+
−	//If set, runtime paths are not added when using shared libraries.	+
−	CMAKE_SKIP_RPATH:BOOL=OFF	+
−		+
−	//Flags used by the linker during the creation of static libraries.	+
−	CMAKE_STATIC_LINKER_FLAGS:STRING=	+
−		+
−	//Flags used by the linker during debug builds.	+
−	CMAKE_STATIC_LINKER_FLAGS_DEBUG:STRING=	+
−		+
−	//Flags used by the linker during release minsize builds.	+
−	CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL:STRING=	+
−		+
−	//Flags used by the linker during release builds.	+
−	CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING=	+
−		+
−	//Flags used by the linker during Release with Debug Info builds.	+
−	CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=	+
−		+
−	//Path to a program.	+
−	CMAKE_STRIP:FILEPATH=/usr/bin/strip	+
−		+
−	//If this value is on, makefiles will be generated without the	+
−	// .SILENT directive, and all commands will be echoed to the console	+
−	// during the make.  This is useful for debugging only. With Visual	+
−	// Studio IDE projects all commands are done without /nologo.	+
−	CMAKE_VERBOSE_MAKEFILE:BOOL=OFF	+
−		+
−	//Enable CUDA GPU acceleration	+
−	CUDA:BOOL=ON	+
−		+
−	//Compile device code in 64 bit mode	+
−	CUDA_64_BIT_DEVICE_CODE:BOOL=ON	+
−		+
−	//Attach the build rule to the CUDA source file.  Enable only when	+
−	// the CUDA source file is added to at most one target.	+
−	CUDA_ATTACH_VS_BUILD_RULE_TO_CUDA_FILE:BOOL=ON	+
−		+
−	//Generate and parse .cubin files in Device mode.	+
−	CUDA_BUILD_CUBIN:BOOL=OFF	+
−		+
−	//Build in Emulation mode	+
−	CUDA_BUILD_EMULATION:BOOL=OFF	+
−		+
−	//"cudart" library	+
−	CUDA_CUDART_LIBRARY:FILEPATH=/usr/local/cuda-10.1/lib64/libcudart.so	+
−		+
−	//"cuda" library (older versions only).	+
−	CUDA_CUDA_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libcuda.so	+
−		+
−	//Directory to put all the output files.  If blank it will default	+
−	// to the CMAKE_CURRENT_BINARY_DIR	+
−	CUDA_GENERATED_OUTPUT_DIR:PATH=	+
−		+
−	//Generated file extension	+
−	CUDA_HOST_COMPILATION_CPP:BOOL=ON	+
−		+
−	//Host side compiler used by NVCC	+
−	CUDA_HOST_COMPILER:FILEPATH=/usr/bin/cc	+
−		+
−	//Path to a program.	+
−	CUDA_NVCC_EXECUTABLE:FILEPATH=/usr/local/cuda-10.1/bin/nvcc	+
−		+
−	//Semi-colon delimit multiple arguments.	+
−	CUDA_NVCC_FLAGS:STRING=	+
−		+
−	CUDA_NVCC_FLAGS_BENCHMARKING:STRING='-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread '	+
−		+
−	CUDA_NVCC_FLAGS_DEBUG:STRING=-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread	+
−		+
−	//Semi-colon delimit multiple arguments.	+
−	CUDA_NVCC_FLAGS_MINSIZEREL:STRING=	+
−		+
−	CUDA_NVCC_FLAGS_PROFILING:STRING=-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread -lineinfo	+
−		+
−	CUDA_NVCC_FLAGS_RELEASE:STRING=-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread --disable-warnings	+
−		+
−	CUDA_NVCC_FLAGS_RELWITHDEBINFO:STRING=-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread	+
−		+
−	//Propage C/CXX_FLAGS and friends to the host compiler via -Xcompile	+
−	CUDA_PROPAGATE_HOST_FLAGS:BOOL=ON	+
−		+
−	//Path to a file.	+
−	CUDA_SDK_ROOT_DIR:PATH=CUDA_SDK_ROOT_DIR-NOTFOUND	+
−		+
−	//Compile CUDA objects with separable compilation enabled.  Requires	+
−	// CUDA 5.0+	+
−	CUDA_SEPARABLE_COMPILATION:BOOL=OFF	+
−		+
−	//Specify the name of the class of CPU architecture for which the	+
−	// input files must be compiled.	+
−	CUDA_TARGET_CPU_ARCH:STRING=	+
−		+
−	//Path to a file.	+
−	CUDA_TOOLKIT_INCLUDE:PATH=/usr/local/cuda-10.1/include	+
−		+
−	//Toolkit location.	+
−	CUDA_TOOLKIT_ROOT_DIR:PATH=/usr/local/cuda-10.1	+
−		+
−	//Toolkit target location.	+
−	CUDA_TOOLKIT_TARGET_DIR:PATH=/usr/local/cuda-10.1	+
−		+
−	//Use the static version of the CUDA runtime library if available	+
−	CUDA_USE_STATIC_CUDA_RUNTIME:BOOL=ON	+
−		+
−	//Print out the commands run while compiling the CUDA source file.	+
−	//  With the Makefile generator this defaults to VERBOSE variable	+
−	// specified on the command line, but can be forced on with this	+
−	// option.	+
−	CUDA_VERBOSE_BUILD:BOOL=OFF	+
−		+
−	//Version of CUDA as computed from nvcc.	+
−	CUDA_VERSION:STRING=10.1	+
−		+
−	//"cublas" library	+
−	CUDA_cublas_LIBRARY:FILEPATH=/usr/local/cuda-8.0/lib64/libcublas.so	+
−		+
−	//static CUDA runtime library	+
−	CUDA_cudart_static_LIBRARY:FILEPATH=/usr/local/cuda-10.1/lib64/libcudart_static.a	+
−		+
−	//"cufft" library	+
−	CUDA_cufft_LIBRARY:FILEPATH=/usr/local/cuda-10.1/lib64/libcufft.so	+
−		+
−	//"cupti" library	+
−	CUDA_cupti_LIBRARY:FILEPATH=/usr/local/cuda-10.1/extras/CUPTI/lib64/libcupti.so	+
−		+
−	//"curand" library	+
−	CUDA_curand_LIBRARY:FILEPATH=/usr/local/cuda-10.1/lib64/libcurand.so	+
−		+
−	//"cusolver" library	+
−	CUDA_cusolver_LIBRARY:FILEPATH=/usr/local/cuda-10.1/lib64/libcusolver.so	+
−		+
−	//"cusparse" library	+
−	CUDA_cusparse_LIBRARY:FILEPATH=/usr/local/cuda-10.1/lib64/libcusparse.so	+
−		+
−	//"nppc" library	+
−	CUDA_nppc_LIBRARY:FILEPATH=/usr/local/cuda-10.1/lib64/libnppc.so	+
−		+
−	//"nppi" library	+
−	CUDA_nppi_LIBRARY:FILEPATH=/usr/local/cuda-8.0/lib64/libnppi.so	+
−		+
−	//"npps" library	+
−	CUDA_npps_LIBRARY:FILEPATH=/usr/local/cuda-10.1/lib64/libnpps.so	+
−		+
−	//Path to a library.	+
−	CUDA_rt_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/librt.so	+
−		+
−	//CachedAlloc	+
−	CachedAlloc:BOOL=ON	+
−		+
−	//CudaForceSTL	+
−	CudaForceSTL:BOOL=OFF	+
−		+
−	//CudaTexture	+
−	CudaTexture:BOOL=ON	+
−		+
−	//CustomAllocMemGuards	+
−	CustomAllocMemGuards:BOOL=OFF	+
−		+
−	//Accelerated Code use double-precision	+
−	DoublePrec_ACC:BOOL=OFF	+
−		+
−	//DoublePrec_CPU	+
−	DoublePrec_CPU:BOOL=ON	+
−		+
−	//Path to a file.	+
−	FFTW_INCLUDES:PATH=/usr/include	+
−		+
−	//Path to a file.	+
−	FFTW_PATH:PATH=/usr/include	+
−		+
−	//The directory containing FLTKConfig.cmake.  This is either the	+
−	// root of the build tree, or PREFIX/lib/fltk for an installation.	+
−	FLTK_DIR:PATH=/usr/lib/fltk	+
−		+
−	//Path to a library.	+
−	FLTK_MATH_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libm.so	+
−		+
−	//FORCE_OWN_FFTW	+
−	FORCE_OWN_FFTW:BOOL=ON	+
−		+
−	//FORCE_OWN_FLTK	+
−	FORCE_OWN_FLTK:BOOL=OFF	+
−		+
−	//FORCE_OWN_TBB	+
−	FORCE_OWN_TBB:BOOL=OFF	+
−		+
−	//GUI	+
−	GUI:BOOL=ON	+
−		+
−	//Use MKL rather than FFTW for FFT	+
−	MKLFFT:BOOL=OFF	+
−		+
−	//Executable for running MPI programs.	+
−	MPIEXEC:FILEPATH=/usr/bin/mpiexec	+
−		+
−	//Maximum number of processors available to run MPI applications.	+
−	MPIEXEC_MAX_NUMPROCS:STRING=2	+
−		+
−	//Flag used by MPI to specify the number of processes for MPIEXEC;	+
−	// the next option will be the number of processes.	+
−	MPIEXEC_NUMPROC_FLAG:STRING=-np	+
−		+
−	//These flags will come after all flags given to MPIEXEC.	+
−	MPIEXEC_POSTFLAGS:STRING=	+
−		+
−	//These flags will be directly before the executable that is being	+
−	// run by MPIEXEC.	+
−	MPIEXEC_PREFLAGS:STRING=	+
−		+
−	//Path to a program.	+
−	MPI_CXX_COMPILER:FILEPATH=/usr/bin/mpicxx	+
−		+
−	//MPI CXX compilation flags	+
−	MPI_CXX_COMPILE_FLAGS:STRING=	+
−		+
−	//MPI CXX include path	+
−	MPI_CXX_INCLUDE_PATH:STRING=/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include;/usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi	+
−		+
−	//MPI CXX libraries to link against	+
−	MPI_CXX_LIBRARIES:STRING=/usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so	+
−		+
−	//MPI CXX linking flags	+
−	MPI_CXX_LINK_FLAGS:STRING= -Wl,-rpath  -Wl,/usr/lib/openmpi/lib  -Wl,--enable-new-dtags	+
−		+
−	//Path to a program.	+
−	MPI_C_COMPILER:FILEPATH=/usr/bin/mpicc	+
−		+
−	//MPI C compilation flags	+
−	MPI_C_COMPILE_FLAGS:STRING=	+
−		+
−	//MPI C include path	+
−	MPI_C_INCLUDE_PATH:STRING=/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include;/usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi	+
−		+
−	//MPI C libraries to link against	+
−	MPI_C_LIBRARIES:STRING=/usr/lib/openmpi/lib/libmpi.so	+
−		+
−	//MPI C linking flags	+
−	MPI_C_LINK_FLAGS:STRING= -Wl,-rpath  -Wl,/usr/lib/openmpi/lib  -Wl,--enable-new-dtags	+
−		+
−	//Extra MPI libraries to link against	+
−	MPI_EXTRA_LIBRARY:STRING=/usr/lib/openmpi/lib/libmpi.so	+
−		+
−	//MPI library to link against	+
−	MPI_LIBRARY:FILEPATH=/usr/lib/openmpi/lib/libmpi_cxx.so	+
−		+
−	//Path to a library.	+
−	OWN_FFTW_DOUBLE:FILEPATH=/home/kttn/softwares/relion/external/fftw/lib/libfftw3.so	+
−		+
−	//Path to a file.	+
−	OWN_FFTW_INCLUDES:PATH=/home/kttn/softwares/relion/external/fftw/include	+
−		+
−	//Path to a library.	+
−	OWN_FFTW_SINGLE:FILEPATH=/home/kttn/softwares/relion/external/fftw/lib/libfftw3f.so	+
−		+
−	//C++ compiler flags for OpenMP parallization	+
−	OpenMP_CXX_FLAGS:STRING=-fopenmp	+
−		+
−	//C compiler flags for OpenMP parallization	+
−	OpenMP_C_FLAGS:STRING=-fopenmp	+
−		+
−	RELION_FLAGS_BENCHMARKING:STRING=	+
−		+
−	RELION_FLAGS_DEBUG:STRING=-O0	+
−		+
−	RELION_FLAGS_PROFILING:STRING=	+
−		+
−	RELION_FLAGS_RELEASE:STRING=	+
−		+
−	RELION_NVCC_FLAGS:STRING=-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread	+
−		+
−	RELION_NVCC_FLAGS_BENCHMARKING:STRING='-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread '	+
−		+
−	RELION_NVCC_FLAGS_DEBUG:STRING=-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread	+
−		+
−	RELION_NVCC_FLAGS_PROFILING:STRING=-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread -lineinfo	+
−		+
−	RELION_NVCC_FLAGS_RELEASE:STRING=-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread --disable-warnings	+
−		+
−	RELION_NVCC_FLAGS_RELWITHDEBINFO:STRING=-arch=sm_35  -D__INTEL_COMPILER --default-stream per-thread	+
−		+
−	//Value Computed by CMake	+
−	Relion_BINARY_DIR:STATIC=/home/kttn/softwares/relion/build	+
−		+
−	//Value Computed by CMake	+
−	Relion_SOURCE_DIR:STATIC=/home/kttn/softwares/relion	+
−		+
−	//Path to a file.	+
−	TIFF_INCLUDE_DIR:PATH=/usr/include/x86_64-linux-gnu	+
−		+
−	//Path to a library.	+
−	TIFF_LIBRARY_DEBUG:FILEPATH=TIFF_LIBRARY_DEBUG-NOTFOUND	+
−		+
−	//Path to a library.	+
−	TIFF_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64-linux-gnu/libtiff.so.5	+
−		+
−	//Path to a file.	+
−	X11_ICE_INCLUDE_PATH:PATH=/usr/include	+
−		+
−	//Path to a library.	+
−	X11_ICE_LIB:FILEPATH=/usr/lib/x86_64-linux-gnu/libICE.so	+
−		+
−	//Path to a file.	+
−	X11_INCLUDES:PATH=X11_INCLUDES-NOTFOUND	+
−		+
−	//Path to a file.	+
−	X11_SM_INCLUDE_PATH:PATH=/usr/include	+
−		+
−	//Path to a library.	+
−	X11_SM_LIB:FILEPATH=/usr/lib/x86_64-linux-gnu/libSM.so	+
−		+
−	//Path to a file.	+
−	X11_X11_INCLUDE_PATH:PATH=/usr/include	+
−		+
−	//Path to a library.	+
−	X11_X11_LIB:FILEPATH=/usr/lib/x86_64-linux-gnu/libX11.so	+
−		+
−	//Path to a file.	+
−	X11_XRes_INCLUDE_PATH:PATH=X11_XRes_INCLUDE_PATH-NOTFOUND	+
−		+
−	//Path to a library.	+
−	X11_XRes_LIB:FILEPATH=X11_XRes_LIB-NOTFOUND	+
−		+
−	//Path to a file.	+
−	X11_XShm_INCLUDE_PATH:PATH=/usr/include	+
−		+
−	//Path to a file.	+
−	X11_XSync_INCLUDE_PATH:PATH=/usr/include	+
−		+
−	//Path to a file.	+
−	X11_XTest_INCLUDE_PATH:PATH=X11_XTest_INCLUDE_PATH-NOTFOUND	+
−		+
−	//Path to a library.	+
−	X11_XTest_LIB:FILEPATH=X11_XTest_LIB-NOTFOUND	+
−		+
−	//Path to a file.	+
−	X11_Xaccessrules_INCLUDE_PATH:PATH=X11_Xaccessrules_INCLUDE_PATH-NOTFOUND	+
−		+
−	//Path to a file.	+
−	X11_Xaccessstr_INCLUDE_PATH:PATH=/usr/include	+
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---

2019年5月15日 (水) 05:32時点における版

現象

• EMAN2をminicondaでソースからビルドした環境でRELIONをビルドしようとしたら、以下のようにminicondaにCMakeの検索パス？を持ってかれる現象が発生し、RELIONをビルドできない状況に陥った。
• 事象が発生したままに書き留めているので整理できていないが、以下に対処ログ残す。

# relionのルートディレクトリに移動 (cmakeとかsrcとかあるディレクトリ)

$ rm -r build/ install/

$ sudo apt install libtiff5-dev

$ mkdir build/ install/

$ cd build && cmake -DCMAKE_INSTALL_PREFIX=../install ..

(出力の一部抜粋）

CMake Warning at src/apps/CMakeLists.txt:165 (add_executable):
 Cannot generate a safe runtime search path for target tiltpair_plot because
 files in some directories may conflict with libraries in implicit
 directories:

   runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
     /home/kttn/miniconda2/lib
   runtime library [libfftw3f.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
     /home/kttn/miniconda2/lib
   runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
     /home/kttn/miniconda2/lib

 Some of these libraries may not be found correctly.

対処法調査

$ which cmake
/home/kttn/miniconda2/bin/cmake

EMAN2インストールするときに入れたminiconda2のbin/に、condaで入れたcmakeが入ってて、それ使ってるのが問題か

cmakeを/usr/bin/cmakeに置き換えて再ビルド

$ /usr/bin/cmake -DCMAKE_INSTALL_PREFIX=../install ..

(出力の一部抜粋)

CMake Warning at src/apps/CMakeLists.txt:165 (add_executable):
 Cannot generate a safe runtime search path for target maingui because files
 in some directories may conflict with libraries in implicit directories:

   runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
     /home/kttn/miniconda2/lib
   runtime library [libfftw3f.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
     /home/kttn/miniconda2/lib
   runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
     /home/kttn/miniconda2/lib

 Some of these libraries may not be found correctly.

んぁー cmakeわからん

relion.gitのreadmeに" If you installed libtiff in a non-standard location, specify the location by -DTIFF_INCLUDE_DIR=/path/to/include -DTIFF_LIBRARY=/path/to/libtiff.so.5."なる記述があったので、これを使ってみる

• includeとlibはどこですか
  • https://packages.ubuntu.com/xenial/amd64/libtiff5-dev/filelist
  • /usr/include/x86_64-linux-gnu と /usr/lib/x86_64-linux-gnu/ でした

$ cmake -DCMAKE_INSTALL_PREFIX=../install -DTIFF_INCLUDE_DIR=/usr/include/x86_64-linux-gnu -DTIFF_LIBRARY=/usr/lib/x86_64-linux-gnu/libtiff.so.5 ..

(出力の一部抜粋）

CMake Error at /home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/cmTC_3d3bbTargets.cmake:16 (add_library):
 Target "MPI::MPI_C" links to item " -Wl,-rpath,/home/kttn/miniconda2/lib
 -Wl,-rpath -Wl,/home/kttn/miniconda2/lib -Wl,--enable-new-dtags" which has
 leading or trailing whitespace.  This is now an error according to policy
 CMP0004.
Call Stack (most recent call first):
 /home/kttn/softwares/relion/build/CMakeFiles/CMakeTmp/CMakeLists.txt:12 (include)

libtiffは解消されたけど他のライブラリが相変わらずminicondaに持ってかれている

$ conda remove cmake
$ cmake -DCMAKE_INSTALL_PREFIX=../install ..

(一部抜粋)

CMake Warning at src/apps/CMakeLists.txt:165 (add_executable):
 Cannot generate a safe runtime search path for target tiltpair_plot because
 files in some directories may conflict with libraries in implicit
 directories:

   runtime library [libtiff.so.5] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
     /home/kttn/miniconda2/lib
   runtime library [libfftw3f.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
     /home/kttn/miniconda2/lib
   runtime library [libfftw3.so.3] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
     /home/kttn/miniconda2/lib

 Some of these libraries may not be found correctly.

minicondaの呪縛からどうやって逃れたらいいの？

• 色々試す
  • miniconda2をPATHから削除してcmakeする
    • (結果)相変わらずminiconda2に持ってかれたまま

CMakeはインクルードとライブラリを検索するとき、どの設定ファイルまたは環境変数を呼んでどこを探しに行っているのか、それを変更するにはどうしたら良いのかがわからないと対処できない。

とりあえずの対処

CMake GUIでインクルードパスとライブラリパスを頑張って手打ちする。 CMakeはv3.5.1を使用。

FFTWがー

CMake GUIにせっせとパスを打ち込んだが、なぜかFFTW_INCLUDESとFFTW_PATHだけ、わざわざ/usr/includeと入力しても、Configureしたら勝手に/home/kttn/miniconda2/includeに書き換わってしまう。どういう理屈でそうなってんだか全くわからん。

それぞれincludeの中身を比較してみる

$ ls /usr/include/*fftw*
/usr/include/fftw.h     /usr/include/fftw3.h     /usr/include/fftw_mpi.h      /usr/include/rfftw_mpi.h
/usr/include/fftw3.f    /usr/include/fftw3l.f03  /usr/include/fftw_threads.h  /usr/include/rfftw_threads.h
/usr/include/fftw3.f03  /usr/include/fftw3q.f03  /usr/include/rfftw.h

$ ls /home/kttn/miniconda2/include/*fftw*
/home/kttn/miniconda2/include/fftw3-mpi.f03  /home/kttn/miniconda2/include/fftw3.h
/home/kttn/miniconda2/include/fftw3-mpi.h    /home/kttn/miniconda2/include/fftw3l-mpi.f03
/home/kttn/miniconda2/include/fftw3.f        /home/kttn/miniconda2/include/fftw3l.f03
/home/kttn/miniconda2/include/fftw3.f03      /home/kttn/miniconda2/include/fftw3q.f03

/usr/includeの方、fftw3_mpiのファイルが少ない。ファイルが見つからないから/usr/includeがスルーされた？aptで関係しそうなパッケージを入れてみる。

$ sudo apt install libfftw3-mpi-dev

$ ls /usr/include/*fftw*
/usr/include/fftw.h         /usr/include/fftw3.h         /usr/include/fftw_threads.h
/usr/include/fftw3-mpi.f03  /usr/include/fftw3l-mpi.f03  /usr/include/rfftw.h
/usr/include/fftw3-mpi.h    /usr/include/fftw3l.f03      /usr/include/rfftw_mpi.h
/usr/include/fftw3.f        /usr/include/fftw3q.f03      /usr/include/rfftw_threads.h
/usr/include/fftw3.f03      /usr/include/fftw_mpi.h

上記の上で再度configureしてもダメ。

今度はOWN_FFTW_INCLUDESにチェックを入れて試してみる。すると、

--------------------------------------------------------
------ REQUIRED FFTW LIBRARIES WHERE NOT FOUND. --------
-------------- FFTW WILL BE DOWNLOADED AND -------------
--------------- BUILT DURING COMPILE-TIME. -------------
--------------------------------------------------------
---- A WORKING INTERNET CONNECTION WILL BE REQUIRED. ---
--------------------------------------------------------

と出力された。なんで見つけてくれないのかよくわかっていないが、これでRELIONが勝手にFFTWをダウンロードしてコンパイルしてくれると思うので、進めてみる。

$ make -j 12

めっちゃエラー出た。

TIFFという字にまみれているのでlibtiffのリンクが失敗している様。

TIFFがー

CMake GUIに戻るとなぜかTIFF_INCLUDE_DIRとTIFF_LIBRARY_RELEASEが/usr/lib/openmpi/lib/libmpi_cxx.soになっていた。もはやTIFFですらない。自分で打ち間違えたのか？

それぞれ/usr/include/x86_64-linux-gnu と /usr/lib/x86_64-linux-gnu/libtiff.so.5 にして、再ビルド。

$ make -j 12
$ make install

やっと通った。

CMakeのパラメータ

一応、CMakeCache.txtの内容はこちら。