Hi,
> After importing movies which
> takes less then 1 s when I try to display even only
> one micrograph I don't see relion_display process in the system and the
> bar:
Displaying raw movies does not make sense and will take huge memory!
You should first perform motion correction.
Best regards,
Takanori Nakane
> Dear Takanori,
>
> We have recently collected data sets at EMBL in Heidelberg (.tif), but I
> have also tried a tutorial data set (.tiff). After importing movies which
> takes less then 1 s when I try to display even only
> one micrograph I don't see relion_display process in the system and the
> bar:
>
> Reading in all images...
> 000/??? sec ~~(,_,">
> [oo]
>
> doesn't change at all.
>
> Best,
> --
> Marcin Jaciuk, PhD
> **********************************
> Max Planck Research Group
> Malopolska Centre of Biotechnology
> Jagiellonian University
> 7a, Gronostajowa str
> 30-387 Krakow, Poland
> Office: +48 12 664 6332
> Laboratory: +48 12 664 6322
>
> -----Original Message-----
> From: Takanori Nakane <[log in to unmask]>
> To: Marcin Jaciuk <[log in to unmask]>
> Cc: [log in to unmask]
> Subject: Re: [ccpem] tif/tiff files processing
> Date: Fri, 26 Jul 2019 12:52:34 +0100
>
> Hi,
>
>> seems to not work with tif/tiff files
>
> Please explain more. What happens when you try to process TIFF movies?
> Where did your movies come from?
>
>> -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version
>> "4.0.9")
>> TIFF FOUND
>
> This sounds OK. Version 4.0.9 supports BigTIFF so it should be able
> to process any TIFF movies from SerialEM.
>
> Best regards,
>
> Takanori Nakane
>
>> Dear All,
>>
>> Our relion3 compilation seems to not work with tif/tiff files. Below is
>> the sum up of cmake-configuration:
>>
>> -- The C compiler identification is GNU 7.4.0
>> -- The CXX compiler identification is GNU 7.4.0
>> -- 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'
>> -- Using provided CUDA_ARCH=75
>> -- CUDA enabled - Building CUDA-accelerated version of RELION
>> -- Setting cpu precision to double
>> -- Setting accelerated code precision to single
>> -- Looking for pthread.h
>> -- Looking for pthread.h - found
>> -- Looking for pthread_create
>> -- Looking for pthread_create - not found
>> -- Looking for pthread_create in pthreads
>> -- Looking for pthread_create in pthreads - not found
>> -- Looking for pthread_create in pthread
>> -- Looking for pthread_create in pthread - found
>> -- Found Threads: TRUE
>> -- Found CUDA: /usr/local/cuda (found version "10.0")
>> -- Using cuda wrapper to compile....
>> -- Cuda version is >= 7.5 and single-precision build, enable double
>> usage
>> warning.
>> -- 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")
>> BUILD_SHARED_LIBS = OFF
>> -- Building static libs (larger build size and binaries)
>> Running apps/CMakeLists.txt...
>> -- CMAKE_BINARY_DIR:/home/mjaciuk/git/relion/build
>> TIFF FOUND
>> -- Found OpenMP_C: -fopenmp (found version "4.5")
>> -- Found OpenMP_CXX: -fopenmp (found version "4.5")
>> -- Found OpenMP: TRUE (found version "4.5")
>> OPENMP FOUND
>> -- Configuring done
>> -- Generating done
>>
>> Can you help us with solving this problem?
>>
>> Best regards,
>> --
>> Marcin Jaciuk, PhD
>> **********************************
>> Max Planck Research Group
>> Malopolska Centre of Biotechnology
>> Jagiellonian University
>> 7a, Gronostajowa str
>> 30-387 Krakow, Poland
>> Office: +48 12 664 6332
>> Laboratory: +48 12 664 6322
>>
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>>
>
>
>
>
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