Segfault (4.4.14) | The Grigorieff Lab

Forums

Firstly, thank you all for your work on ctffind.

The Error:

I'm trying to use ctffind with relion to determine the ctf of micrographs taken with a Leo912 scope. I'm experience segfault errors at multiple points.

1) If I run from inside Relion, I receive this output:

TIFFReadDirectoryCheckOrder: Warning, Invalid TIFF directory; tags are not sorted in ascending order.
TIFFReadDirectory: Warning, Unknown field with tag 33560 (0x8318) encountered.
TIFFFetchNormalTag: Warning, ASCII value for tag "Artist" does not end in null byte.
Segmentation fault (core dumped)

However, once Relion gets through all of those, I arrive at:

WARNING: skipping, since cannot get CTF values for Movies/CCMV-WH-40-8.tif
WARNING: skipping, since cannot get CTF values for Movies/CCMV-WH-40-9.tif
WARNING: skipping, since cannot get CTF values for Movies/CMMV-NB-40-12.tif
Did not find any of the expected EPS files to generate a PDF file
+ Will make an empty PDF-file in CtfFind/job003/logfile.pdf

Presumably because there's no output from ctffind.

2) If I run tif2mrc manually on a .tif image from the detector, I still get these errors:

However, the .mrc file does in fact generate, and Chimera can open it, and it looks right. So I don't think it's actually a problem with .mrc generation.

If I then take that .mrc file, and run ctffind manually, here is how it goes:

** Welcome to Ctffind **

            Version : 4.1.14
           Compiled : Jul 29 2020
               Mode : Interactive

Input image file name [ccmv.mrc]                   :
Output diagnostic image file name [ccmv_out.mrc]   :
Pixel size [2.6238]                                :
Acceleration voltage [100]                         :
Spherical aberration [2]                           :
Amplitude contrast [0.07]                          :
Size of amplitude spectrum to compute [512]        :
Minimum resolution [30.0]                          :
Maximum resolution [5.0]                           :
Minimum defocus [5000.0]                           :
Maximum defocus [50000.0]                          :
Defocus search step [500]                          :
Do you know what astigmatism is present? [no]      :
Slower, more exhaustive search? [yes]              : no
Use a restraint on astigmatism? [no]               :
Find additional phase shift? [no]                  :
Do you want to set expert options? [yes]           : no
File name: ccmv.mrc
File type: MRC
Dimensions: X = 2044 Y = 2044 Z = 1
Number of slices: 1
Working on micrograph 1 of 1
OpenMP is not available - will not use parallel threads.

DFMID1 DFMID2 ANGAST CC
6639.17 6639.17 32.50 -0.82105
Segmentation fault (core dumped)

It's also able to write this .txt file:

# Output from CTFFind version 4.1.14, run on 2020-07-29 12:52:05
# Input file: ccmv.mrc ; Number of micrographs: 1
# Pixel size: 2.624 Angstroms ; acceleration voltage: 100.0 keV ; spherical aberration: 2.00 mm ; amplitude contrast: 0.07
# Box size: 512 pixels ; min. res.: 30.0 Angstroms ; max. res.: 5.0 Angstroms ; min. def.: 5000.0 um; max. def. 50000.0 um
# Columns: #1 - micrograph number; #2 - defocus 1 [Angstroms]; #3 - defocus 2; #4 - azimuth of astigmatism; #5 - additional phase shift [radians]; #6 - cross correlation; #7 - spacing (in Angstroms) up to which CTF rings were fit successfully

System

The system I'm running is OpenSUSE Tumbleweed. I'm using gcc-10 and gcc-c++-10. I built ctffind from source with debug mode disabled and MKL enabled.

My configure output:

configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for icc... no
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 style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for icpc... no
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking whether gcc and cc understand -c and -o together... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/x86_64-suse-linux/bin/ld
checking if the linker (/usr/x86_64-suse-linux/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/x86_64-suse-linux/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -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 for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/x86_64-suse-linux/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/x86_64-suse-linux/bin/ld -m elf_x86_64
checking if the linker (/usr/x86_64-suse-linux/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/x86_64-suse-linux/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
configure: static_link = false
checking wxWidgets version... 3.0.4
checking fftw3.h usability... yes
checking fftw3.h presence... yes
checking for fftw3.h... yes
checking for fftwf_malloc in -lmkl_intel_lp64... no
checking for fftwf_malloc in -lfftw3f... yes
configure: Using FFTW for Fourier transforms
checking for TIFFOpen in -lwxtiff-3.0... no
checking for library containing inflate... -lz
checking for library containing jpeg_read_header... -ljpeg
checking for library containing TIFFOpen... -ltiff
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: executing depfiles commands
config.status: executing libtool commands