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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
440 stars 194 forks source link

relion3.1.1 installation problem #782

Closed XSAWxsaw closed 3 years ago

XSAWxsaw commented 3 years ago

I've installed and used relion3.0 before, recently when I wanted to upgrade it to 3.1.1 it failed.

Environment:

Firstly I delete the directory where relion3.0 installed and the links, then I completely followed the tutorial to install the new version. I have FLTK 1.3.4, FFTW 3.3.7-1 and TIFF 4.0.9 installed. The commands I used are as follows:

git clone https://github.com/3dem/relion.git
cd relion
git checkout master
mkdir build
cd build
cmake ..
make -j 12
make install

The whole installation finished without failure, but when I typed relion, the error occurs: 

./relion: symbol lookup error: ./relion: undefined symbol: _ZN10Fl_Browser8textsizeEi

The cmake output is:

-- The C compiler identification is GNU 7.5.0
-- The CXX compiler identification is GNU 7.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- BUILD TYPE set to the default type:  'Release'
-- Setting fallback CUDA_ARCH=35
-- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2
-- CUDA enabled - Building CUDA-accelerated version of RELION
-- Setting cpu precision to double
-- Setting accelerated code precision to single
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) 
-- Using non-cuda compilation....
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") 
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- MPI_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include
-- MPI_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-- MPI_CXX_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include
-- MPI_CXX_LIBRARIES : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-- CMAKE_C_COMPILER : /usr/bin/cc
-- CMAKE_CXX_COMPILER : /usr/bin/c++
-- MPI_C_COMPILER : /usr/bin/mpicc
-- MPI_CXX_COMPILER : /usr/bin/mpicxx
-- CMAKE_CXX_COMPILER_ID : GNU
-- CMAKE_C_COMPILER : /usr/bin/mpicc
-- CMAKE_CXX_COMPILER : /usr/bin/mpicxx
-- MPI_C_COMPILER : /usr/bin/mpicc
-- MPI_CXX_COMPILER : /usr/bin/mpicxx
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so
-- Found FLTK: fltk_images;fltk_forms;fltk  
-- X11 and FLTK were found
-- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so;/usr/lib/x86_64-linux-gnu/libm.so
-- Found FFTW
-- FFTW_PATH: /usr/include
-- FFTW_INCLUDES: /usr/include
-- FFTW_LIBRARIES: /usr/lib/x86_64-linux-gnu/libfftw3f.so;/usr/lib/x86_64-linux-gnu/libfftw3.so
-- Looking for sincos
-- Looking for sincos - found
-- Looking for __sincos
-- Looking for __sincos - not found
-- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.0.9") 
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") 
-- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found version "1.6.34") 
BUILD_SHARED_LIBS = OFF
-- Building static libs (larger build size and binaries)
Running apps/CMakeLists.txt...
-- CMAKE_BINARY_DIR:/home/yao/install/relion/build
-- Git commit ID: dcab7933398a8b728e56a08ea1bb2539a5ba71d4
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Configuring done
-- Generating done
-- Build files have been written to: /home/yao/install/relion/build

Then I suggested that this might be ralated to FLTK version, so I run cmake with -DFORCE_OWN_FLTK=ON, then errors occur while make:

[ 48%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o
[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o
[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o
[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o
[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o
[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o
[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o
[ 52%] Linking CXX static library ../../lib/librelion_lib.a
[ 52%] Built target relion_lib
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2

Could anyone gives a suggestion? Thans a lot.

biochem-fan commented 3 years ago

The README file says:

If FLTK related errors are reported, please add -DFORCE_OWN_FLTK=ON to cmake.

Please retry after deleting the whole directroy.

XSAWxsaw commented 3 years ago

I've retried after deleting the whole directroy, but the 'make' process failed when 'Build target relion_lib'

[ 48%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyev2.c.o
[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevc3.c.o
[ 49%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevd3.c.o
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevh3.c.o
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevj3.c.o
[ 50%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevq3.c.o
[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsyevv3.c.o
[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/dsytrd3.c.o
[ 51%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/d3x3/slvsec3.c.o
[ 52%] Building C object src/apps/CMakeFiles/relion_lib.dir/__/jaz/lbfgs/lbfgs.c.o
[ 52%] Linking CXX static library ../../lib/librelion_lib.a
[ 52%] Built target relion_lib
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
XSAWxsaw commented 3 years ago

The complete output is: 

Scanning dependencies of target copy_scripts
Scanning dependencies of target OWN_FLTK
Scanning dependencies of target relion_lib
[  1%] Creating directories for 'OWN_FLTK'
[  1%] Built target copy_scripts
[  1%] Performing download step (download, verify and extract) for 'OWN_FLTK'
-- Downloading...
   dst='/home/yao/install/relion/external/fltk/fltk-1.3.5-source.tar.gz'
   timeout='none'
-- Using src='ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz'
[  2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o
[  2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o
[  2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o
[  2%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o
/home/yao/install/relion/src/CPlot2D.cpp: In member function ‘void CPlot2D::ComputeLabelTickSpacing(double, double, double*, double*, double*, int, std::__cxx11::string)’:
/home/yao/install/relion/src/CPlot2D.cpp:716:6: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
 void CPlot2D::ComputeLabelTickSpacing(double dataMin, double dataMax, double *plotMin, double *plotMax, double *tickSpacing, int numTicks, std::string axis)
      ^~~~~~~
/home/yao/install/relion/src/CPlot2D.cpp:716:6: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/ostream:38,
                 from /usr/include/c++/7/iostream:39,
                 from /home/yao/install/relion/src/CPlot2D.cpp:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 5 and 14 bytes into a destination of size 10
       __bos (__s), __fmt, __va_arg_pack ());
                                           ^
/home/yao/install/relion/src/CPlot2D.cpp:716:6: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
 void CPlot2D::ComputeLabelTickSpacing(double dataMin, double dataMax, double *plotMin, double *plotMax, double *tickSpacing, int numTicks, std::string axis)
      ^~~~~~~
/home/yao/install/relion/src/CPlot2D.cpp:716:6: note: directive argument in the range [0, 2147483647]
In file included from /usr/include/stdio.h:862:0,
                 from /usr/include/c++/7/cstdio:42,
                 from /usr/include/c++/7/ext/string_conversions.h:43,
                 from /usr/include/c++/7/bits/basic_string.h:6361,
                 from /usr/include/c++/7/string:52,
                 from /usr/include/c++/7/bits/locale_classes.h:40,
                 from /usr/include/c++/7/bits/ios_base.h:41,
                 from /usr/include/c++/7/ios:42,
                 from /usr/include/c++/7/ostream:38,
                 from /usr/include/c++/7/iostream:39,
                 from /home/yao/install/relion/src/CPlot2D.cpp:21:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 5 and 14 bytes into a destination of size 10
       __bos (__s), __fmt, __va_arg_pack ());
                                           ^
[  3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o
[  3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o
[  3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o
[  4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o
[  4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o
-- [download 0% complete]
[  4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o
-- [download 1% complete]
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[  5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o
[  5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o
-- [download 3% complete]
[  5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o
-- [download 4% complete]
[  6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o
-- [download 5% complete]
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[  6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o
[  7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o
-- [download 12% complete]
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[  7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/funcs.cpp.o
-- [download 17% complete]
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[  7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o
[  8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o
-- [download 21% complete]
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[  8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o
-- [download 63% complete]
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[  8%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o
-- [download 73% complete]
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[  9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o
-- verifying file...
       file='/home/yao/install/relion/external/fltk/fltk-1.3.5-source.tar.gz'
-- Downloading... done
-- extracting...
     src='/home/yao/install/relion/external/fltk/fltk-1.3.5-source.tar.gz'
     dst='/home/yao/install/relion/external/fltk/fltk'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 10%] No patch step for 'OWN_FLTK'
[ 10%] No update step for 'OWN_FLTK'
[ 10%] Performing configure step for 'OWN_FLTK'
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking if the compiler supports -fvisibility... yes
checking if the compiler supports -fvisibility-inlines-hidden... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for nroff... /usr/bin/nroff
checking for doxygen... no
checking for ranlib... ranlib
checking for ar... /usr/bin/ar
checking for windres... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking whether byte ordering is bigendian... no
checking whether the compiler recognizes bool as a built-in type... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/stdtypes.h usability... no
checking sys/stdtypes.h presence... no
checking for sys/stdtypes.h... no
checking whether we have the POSIX compatible scandir() prototype... yes
checking for vsnprintf... yes
checking for snprintf... yes
checking for strings.h... (cached) yes
checking for strcasecmp... yes
checking for strlcat... no
checking for strlcpy... no
checking locale.h usability... [ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o
yes
checking locale.h presence... yes
checking for locale.h... yes
checking for localeconv... yes
checking for library containing pow... -lm
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for long long int... yes
checking for library containing dlsym... -ldl
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking alsa/asoundlib.h usability... no
checking alsa/asoundlib.h presence... no
checking for alsa/asoundlib.h... no
checking for jpeg_CreateCompress in -ljpeg... yes
checking jpeglib.h usability... yes
checking jpeglib.h presence... yes
checking for jpeglib.h... yes
checking for gzgets in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for png_read_info in -lpng... yes
checking png.h usability... yes
checking png.h presence... yes
checking for png.h... yes
checking libpng/png.h usability... yes
checking libpng/png.h presence... yes
checking for libpng/png.h... yes
checking for png_get_valid in -lpng... yes
checking for png_set_tRNS_to_alpha in -lpng... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking for pthread_create using -lpthreads... no
checking for pthread_create using -lpthread... yes
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... no
checking for library containing dlopen... none required
checking GL/gl.h usability... yes
checking GL/gl.h presence... yes
checking for GL/gl.h... yes
checking for glXMakeCurrent in -lGL... yes
checking for glXGetProcAddressARB in -lGL... yes
checking GL/glu.h usability... [ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o
yes
checking GL/glu.h presence... yes
checking for GL/glu.h... yes
checking for XineramaIsActive in -lXinerama... no
checking for pkg-config... /usr/bin/pkg-config
Package xft was not found in the pkg-config search path.
Perhaps you should add the directory containing `xft.pc'
to the PKG_CONFIG_PATH environment variable
No package 'xft' found
Package freetype2 was not found in the pkg-config search path.
Perhaps you should add the directory containing `freetype2.pc'
to the PKG_CONFIG_PATH environment variable
No package 'freetype2' found
checking for freetype-config... no
configure: please install pkg-config or use 'configure --disable-xft'.
configure: error: Aborting.
CMakeFiles/OWN_FLTK.dir/build.make:108: recipe for target 'OWN_FLTK-prefix/src/OWN_FLTK-stamp/OWN_FLTK-configure' failed
make[2]: *** [OWN_FLTK-prefix/src/OWN_FLTK-stamp/OWN_FLTK-configure] Error 1
CMakeFiles/Makefile2:104: recipe for target 'CMakeFiles/OWN_FLTK.dir/all' failed
make[1]: *** [CMakeFiles/OWN_FLTK.dir/all] Error 2
make[1]: *** 正在等待未完成的任务....
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o
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Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
XSAWxsaw commented 3 years ago

The README file says:

If FLTK related errors are reported, please add -DFORCE_OWN_FLTK=ON to cmake.

Please retry after deleting the whole directroy.

Could you help with this? Thanks a lot.

biochem-fan commented 3 years ago

See the error message carefully:

No package 'freetype2' found
checking for freetype-config... no
configure: please install pkg-config or use 'configure --disable-xft'.
configure: error: Aborting.

FTLK needs xft. In Ubuntu, this can be done by sudo apt-get install xft-dev.

XSAWxsaw commented 3 years ago

See the error message carefully:

No package 'freetype2' found
checking for freetype-config... no
configure: please install pkg-config or use 'configure --disable-xft'.
configure: error: Aborting.

FTLK needs xft. In Ubuntu, this can be done by sudo apt-get install xft-dev.

Thanks !! I've installed it successfully.