Re: [scipion-users] Antw: Antw: Re: Antw: Re: Antw: Antw: Re: Antw: Re: Antw: Re: SCIPION installat

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Hi Christian,

I'm glad to hear that it finally worked out for you!

PS. I think you don't need to export var to run scipion, it was only needed
to compile xmipp.

On Fri, May 21, 2021, 07:48 Christian Tüting <
chr...@bi...> wrote:

> Hi all,
>
> this is just summarizing our issue and the solution. We had some
> problems during installation. The scipion3 core was installed, but xmipp
> failed. There were two different issues. If you observe the same, here
> is our solution:
>
> First Issue: 'libfftw3' not found in the system. Installation using
> conda automatically during installation failed.
> Solution: Installed libtiff systemwide with: yum install libtiff*
>
> Second issue: /usr/bin/ld: warning: libwebp.so.7, needed by
> /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so, not
> found (try using -rpath or -rpath-link)
> The library libwebp.so.7 was not found, even though present in the
> <condapath>/envs/scipion3/lib folder.
> Solution: export the library path of the enviroment to LD_LIBRARY_PATH
> with: export
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/conda/envs/scipion3/lib/
> With this, we were able to compile xmipp.
>
> To add the path not always to the path but only when scipion3 is
> executed, I add a little function instead of a alias to start scipion3
> in ~/.bashrc:
>
> # scipion3
> scipion3() {
>   export
>
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/user/Data/Software/miniconda/envs/scipion3/lib/
>   /home/user/Data/Software/scipion3/scipion3 "$@"
> }
>
> With this function, the envs/lib path is added first and then scipion is
> started with all args given to the function.
>
>
> Thanks @Grigory for all the support.
>
> Best
> Christian
>
>
> >>> Christian Tüting <chr...@bi...>
> 20.05.21 22.48 Uhr >>>
> Hi Jose Miguel,
>
> it looks like adding the scipion3 env library path to LD_LIBRARY_PATH
> did the job. xmipp was compiled and installed successfully and the first
> test were also running fine (preprocess micrographs and particle
> picking). We setting up our workflow with all plugins and test tomorrow
> again. But if no furher error occur, I will anser on this mailing thread
> with a summarizing mail, describing the inital issue and our solution,
> so if other have the same issue, they dont need to go through all mails.
>
> Best
>
> Christian
>
>
> >>> Jose Miguel de la Rosa Trevin <del...@gm...> 20.05.21
> 22.40 Uhr >>>
> Hi Christian,
>
> I have a repository with an alternative Scipion installation script and
> with pre-compiled Xmipp binaries.
> Let me know if you want to give it a try.
>
> Best,
> Jose Miguel
>
>
>
> On Thu, May 20, 2021 at 8:59 PM Christian Tüting <
> chr...@bi...> wrote:
>
> > Ok. We will test this and keep you informed.
> >
> > >>> Grigory Sharov <sha...@gm...> 20.05.21 20.56 Uhr >>>
> > If you were able to successfully build xmipp, you need to check if you
> > can
> > display images in scipion to make sure it works.
> >
> > Best regards,
> > Grigory
> >
> >
> >
>
> --------------------------------------------------------------------------------
> > Grigory Sharov, Ph.D.
> >
> > MRC Laboratory of Molecular Biology,
> > Francis Crick Avenue,
> > Cambridge Biomedical Campus,
> > Cambridge CB2 0QH, UK.
> > tel. +44 (0) 1223 267228 <+44%201223%20267228>
> > e-mail: gs...@mr...
> >
> >
> > On Thu, May 20, 2021 at 7:54 PM Christian Tüting <
> > chr...@bi...> wrote:
> >
> > > I (temporarily) fixed the error with:
> > >
> > > export
> > >
> > >
> >
> >
>
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/user/Data/Software/miniconda/envs/scipion3/lib/
> > >
> > >
> > > xmipp is currently compiling. I am really no expert in server
> > > maintainance, so I am not sure what are the implications of this.
> > Afaik,
> > > this is only a fix for the current shell, so after reboot, this fix
> > > should be gone. So if xmipp needs this library, I guess I have to
> add
> > > this export command to ~/.bashrc, right?
> > >
> > > Best
> > >
> > > Christian
> > >
> > >
> > > >>> Christian Tüting <chr...@bi...>
> > > 20.05.21 20.20 Uhr >>>
> > > Hi,
> > >
> > > I tried yum install libtiff libtiff-devel before, but yum says,
> > "nothing
> > > to do". But, yum install libtiff* helped to install the missing
> > packages
> > > somehow.
> > >
> > > So the error disappers from ./xmipp_c> >
> > > But ./xmipp check_config still fails.
> > >
> > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ./xmipp
> > config
> > > Configuring -----------------------------------------
> > > gcc detected
> > > g++ -c -w  -mtune=native -march=native -std=c++11 -O3
> > > xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I../
> > > -I/home/user/Data/Software/miniconda/envs/scipion3/include
> > > OpenCV not found
> > > rm -v xmipp_test_opencv*
> > > 'mpirun' and 'mpiexec' not found in the PATH
> > > Alternative found at '/usr/lib64/openmpi/bin'.
> > > Please, press [return] to use it or type a path where to locate it:
> > > -> /usr/lib64/openmpi/bin
> > > 'mpicc' not found in the PATH
> > > Alternative found at '/usr/lib64/openmpi/bin'.
> > > Please, press [return] to use it or type a path where to locate it:
> > > -> /usr/lib64/openmpi/bin
> > > 'mpicxx' not found in the PATH
> > > Alternative found at '/usr/lib64/openmpi/bin'.
> > > Please, press [return] to use it or type a path where to locate it:
> > > -> /usr/lib64/openmpi/bin
> > > Java detected at: /home/user/Data/Software/miniconda/envs/scipion3
> > > 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN)
> > > Alternative found at '/usr/local/cuda/bin'.
> > > Please, press [return] to use it or type a path where to locate it:
> > > -> /usr/local/cuda/bin
> > > CUDA-10.1.243 detected.
> > > CUDA-8.0 is recommended.
> > > Using '> > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$
> ./xmipp
> > > check_config
> > > Checking configuration ------------------------------
> > > Checking compiler configuration ...
> > > g++ 4.8.5 detected
> > > g++ -c -w -mtune=native -march=native -std=c++11 -O3
> > xmipp_test_main.cpp
> > > -o xmipp_test_main.o -I../
> > > -I/home/user/Data/Software/miniconda/envs/scipion3/include
> > > -I/home/user/Data/Software/miniconda/envs/scipion3/include/python3.8
> > >
> > >
> >
> >
>
> -I/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/numpy/core/include
> > > g++  -L/home/user/Data/Software/miniconda/envs/scipion3/lib
> > > xmipp_test_main.o -o xmipp_test_main -lfftw3 -lfftw3_threads -lhdf5
> > > -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread
> > > /usr/bin/ld: warning: libwebp.so.7, needed by
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so, not
> > > found (try using -rpath or -rpath-link)
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPPictureImportRGB'
> > > /home/user/Data/Software/>
> > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPPictureFree'
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPIAppend'
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPIDecGetRGB'
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPINewDecoder'
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPPictureImportRGBA'
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPConfigInitInternal'
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPEncoundefined reference to
> > `WebPValidateConfig'
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPPictureInitInternal'
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPFreeDecBuffer'
> > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > undefined reference to `WebPIDelete'
> > > collect2: error: ld returned 1 exit status
> > > Check the LINKERFORPROGRAMS, LINKFLAGS and LIBDIRFLAGS
> > > Cannot compile
> > > Possible solutiolibhdf5-dev libopencv-dev python3-dev python3-numpy
> > > python3-scipy
> > > python3-mpi4py
> > > In Manjaro: sudo pacman -Syu install hdf5 python3-numpy
> python3-scipy
> > > --noconfirm
> > > Please, see
> > > '
> > >
> >
> >
> https://scipion-em.github.io/docs> > for more information about libraries
> dependencies.
> > > Remember to re-run './xmipp config' after installing libraries in
> > order
> > > to take into account the new system configuration.
> > > rm xmipp_test_main*
> > > Check failed! Something wrong with the configuration.
> > >
> > >
> > > It's still looking for libwebp.so.7, but this is present:
> > >
> > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ls -ltr
> > > ../../../../miniconda/envs/scipion3/lib/libwebp.so*
> > > -rwxrwxrwx. 2 user user 598608 Feb  1 16:15
> > > ../../../../miniconda/envs/scipion3/lib/libwebp.so.7.1.1
> > > lrwxrwxrwx. 1 user user
> > > 16 May 20 10:07 ../../../../miniconda/envs/scipion3/lib/libwebp.so.7
> > ->
> > > libwebp.so.7.1.1
> > > lrwxrwxrwx. 1 user user
> > > 16 May 20 10:07 ../../../../miniconda/envs/scipion3/lib/libwebp.so
> ->
> > > libwebp.so.7.1.1
> > >
> > > Best
> > >
> > > Christian
> > >
> > >
> > > >>> Grigory Sharov <sha...@gm...> 20.05.21 19.54 Uhr >>>
> > > Hi Christian,
> > >
> > > I guess xmipp script still cannot recognize libtiff that it has
> > > installed.
> > > I can reproduce your problem on my machine. But I have a system
> > library
> > > installed.
> > >
> > > So, the easiest solution is to install libtiff /  libtiff-devel
> using
> > > your
> > > package manager (yum)
> > >
> > > Best regards,
> > >> > Grigory Sharov, Ph.D.
> > >
> > > MRC Laboratory of Molecular Biology,
> > > Francis Crick Avenue,
> > > Cambridge Biomedical Campus,
> > > Cambridge CB2 0QH, UK.
> > > tel. +44 (0) 1223 267228 <+44%201223%20267228>
> > > e-mail: gs...@mr...
> > >
> > >
> > > On Thu, May 20, 2021 at 6:34 PM Christian Tüting <
> > > chr...@bi...> wrote:
> > >
> > > > Hi,
> > > >
> > > > it fails with similar errors like in the automatic installation:
> > > >
> > > >
> > > > (scipion3) [user@dataanalysisserver1 scipion3]$ ldd
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so
> > > > linux-vdso.so.1 =>  (0x00007ffe872c3000)
> > > > libwebp.so.7 =>
> > > >
> /home/user/Data/Software/miniconda/envs/scipion3/lib/./libwebp.so.7
> > > > (0x00007f8f7253a000)
> > > > libzstd.so.1 =>
> > > >
> /home/user/Data/Software/miniconda/envs/scipion3/lib/./libzstd.so.1
> > > > (0x00007f8f7246e000)
> > > > liblzma.so.5 =>
> > > >
> /home/user/Data/Software/miniconda/envs/scipion3/lib/./liblzma.so.5
> > > > (0x00007f8f723fe000)
> > > > libjpeg.so.9 =>
> > > >
> /home/user/Data/Software/miniconda/envs/scipion3/lib/./libjpeg.so.9
> > > > (0x00007f8f721c2000)
> > > > libz.so.1 =>
> > > > /home/user/Data/Softw> > libm.so.6 => /lib64/libm.so.6
> > (0x00007f8f71ea4000)
> > > > libc.so.6 => /lib64/libc.so.6 (0x00007f8f71ad6000)
> > > > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f8f718ba000)
> > > > librt.so.1 => /lib64/librt.so.1 (0x00007f8f716b2000)
> > > > /lib64/ld-linux-x86-64.so.2 (0x00007f8f72427000)
> > > >
> > > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ./xmipp
> > > config
> > > > Configuring -----------------------------------------
> > > > gcc detected
> > > > 'libtiff' not found in the system
> > > > 'libtiff' dependency not found. Do you want to install it using
> > conda?
> > > > [YES/no] Y
> > > > Trying to install libtiff with conda
> > > > conda activate scipion3 ; conda install libtiff -y -c defaults
> > > > CommandNotFoundError: Your shell has not been properly configured
> to
> > > use
> > > > 'conda activate'.
> > > > To initialize your shell, run
> > > > $ conda init <SHELL_NAME>
> > > > Currently supported shells are:
> > > > - bash
> > > > - fish
> > > > - tcsh
> > > > - x> IMPORTANT: You may need to close and restart your shell after
> > > running
> > > > 'conda init'.
> > > > Collecting package metadata (current_repodata.json): ...working...
> > > done
> > > > Solving environment: ...working... done
> > > > # All requested packages already installed.
> > > > 'libtiff' installed in conda environ 'scipion3'.
> > > > g++ -c -w  -mtune=native -march=native -std=c++11 -O3
> > > > xmipp_test_opencv.cpp -o xmipp_test_opencv.o -I..> 'mpirun' and
> > > 'mpiexec' not found in the PATH
> > > > Alternative found at '/usr/lib64/openmpi/bi> > > 'mpicc' not found
> in the PATH
> > > > Alternative found at '/usr/lib64/openmpi/bin'.
> > > > Please, press [return] to use it or type a path where to locate
> it:
> > > > -> /usr/lib64/openmpi/bin
> > > > 'mpicxx' not found in the PATH
> > > > Alternative found at '/usr/lib64/openmpi/bin'.
> > > > Please, press [return] to use it or type a path where to locate
> it:
> > > > -> /usr/lib64/openmpi/bin
> > > > Java detected at: /home/user/Data/Software/miniconda/envs/scipion3
> > > > 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN)
> > > > Alternative found at '/usr/local/cuda/bin'.
> > > > Please, press [return] to use it or type a path where to locate
> it:
> > > > -> /usr/local/cuda/bin
> > > > CUDA-10.1.243 detected.
> > > > CUDA-8.0 is recommended.
> > > > Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'.
> > > > Configuration completed.....
> > > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ./xmipp
> > > config
> > > > Configuring -----------------------------------------
> > > > gcc detected
> > > > 'libtiff' not found in the system
> > > > 'libtiff' dependency not found. Do you want to install it using
> > conda?
> > > > [YES/no]
> > > > Trying to install libtiff with conda
> > > > conda activate scipi> > > CommandNotFoundError: Your shell has not
> been properly configured
> to
> > > use
> > > > 'conda activate'.
> > > > To initialize your shell, run
> > > > $ conda init <SHELL_NAME>
> > > > Currently supported shells are:
> > > > - bash
> > > > - fish
> > > > - tcsh
> > > > - xonsh
> > > > - zsh
> > > > - powershell
> > > > See 'conda init --help' for more information and options.
> > > > IMPORTANT: You may need to close and restart your shell after
> > running
> > > > 'conda init'.
> > > > Collecting package metadata (current_repodata.json): ...working...
> > > done
> > > > Solving environment: ...working... done
> > > > # All requested packages already installed.
> > > > 'libtiff' installed in conda exmipp_test_opencv.cpp -o
> > > xmipp_test_opencv.o
> > > > -I../
> > > > -I/home/user/Data/Software/miniconda/envs/scipion3/include
> > > > OpenCV not found
> > > > rm -v xmipp_test_opencv*
> > > > 'mpirun' and 'mpiexec' not found in the PATH
> > > > Alternative found at '/usr/lib64/openmpi/bin'.
> > > > Please, press [return] to use it or type a path where to locate
> it:
> > > > -> /usr/lib64/openmpi/bin
> > > > 'mpicc' not found in the PATH
> > > > Alternative found at '/usr/lib64/openmpi/bin'.
> > > > Please, press [return] to use it or type a path where to locate
> it:
> > > > -> /usr/lib64/openmpi/bin
> > > > 'mpicxx' not found in the PATH
> > > > Alternative found at '/usr/lib64/openmpi/bin'.
> > > > Please, press [return> > Java detected at:
> > /home/user/Data/Software/miniconda/envs/scipion3
> > > > 'nvcc' not found in the PATH (either in CUDA_BIN/XMIPP_CUDA_BIN)
> > > > Alternative found at '/usr/local/cuda/bin'.
> > > > Please, press [return] to use it or type a path where to locate
> it:
> > > > -> /usr/local/cuda/bin
> > > > CUDA-10.1.243 detected.
> > > > CUDA-8.0 is recommended.
> > > > Using '/usr/local/cuda-10.1/targets/x86_64-linux/lib'.
> > > > Configuration completed.....
> > > >
> > > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ ./xmipp
> > > > check_config
> > > > Checking configuration ------------------------------
> > > > Checking compiler configuration ...
> > > > g++ 4.8.5 detected
> > > > g++ -c -w -mtune=native -march=native -std=c++11 -O3
> > > xmipp_test_main.cpp
> > > > -o xmipp_test_main.o -I../
> > > > -I/home/user/Data/Software/miniconda/envs/scipion3/include
> > > >
> -I/home/user/Data/Software/miniconda/envs/scipion3/include/python3.8
> > > >
> > > >
> > >
> >
> >
>
> -I/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/numpy/c>
> > > xmipp_test_main.o -o xmipp_test_main -lfftw3 -lfftw3_threads -lhdf5
> > > > -lhdf5_cpp -ltiff -ljpeg -lsqlite3 -lpthread
> > > > /usr/bin/ld: warning: libwebp.so.7, needed by
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so,
> not
> > > > found (try using -rpath or -rpath-link)
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/lib>
> > >> > > undefined reference to `WebPInitDecBufferInternal'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPPictureFree'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPIAppend'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPIDecGetRGB'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPINewDecoder'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPPictureImportRGBA'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPConfigInitInternal'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPEncode'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPValidateConfig'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPPictureInitInternal'
> > > > /home/user/Dat> > > undefined reference to `WebPFreeDecBuffer'
> > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> > > > undefined reference to `WebPIDelete'
> > > > collect2: error: ld returned 1 exit status
> > > > Check the LINKERFORPROGRAMS, LINKFLAGS and LIBDIRFLAGS
> > > > Cannot compile
> > > > Possible solutions
> > > > In Ubuntu: sudo apt-get -y install libsqlite3-dev libfftw3-dev
> > > > libhdf5-dev libopencv-dev python3-dev python3-numpy python3-scipy
> > > > python3-mpi4py
> > > > In Manjaro: sudo pacman -Syu install hdf5 python3-numpy
> > python3-scipy
> > > > --noconfirm
> > > > Please, see
> > > > '
> > > >
> > >
> > >
> >
> >
>
> https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources.html#step-2-dependencies
> > > > '
> > > > for more information about libraries dependencies.
> > > > Remember to re-run './xmipp config' after installing libraries in
> > > order
> > > > to take into account the new system configuration.
> > > > rm xmipp_test_main*
> > > > Check failed! Trying to install libtiff with conda
> > > > conda activate scipion3 ; conda install libtiff -y -c defaults
> > > > CommandNotFoundError: Your shell has not been properly configured
> to
> > > use
> > > > 'conda activate'.
> > > >
> > > > Because I can run it manually without errors:
> > > >
> > > > (scipion3) [user@dataanalysisserver1 xmippSrc-v3.20.07]$ conda
> > > activate
> > > > scipion3 ; conda install libtiff -y -c defaults
> > > > Collecting package metadata (current_repodata.json): done
> > > > Solving environment: done
> > > > # All requested packages alre> > And also, thanks already in
> advance.
> > I really appreciate your help.
> > > >
> > > > Best Christian
> > > >
> > > >
> > > >
> > > > >>> Grigory Sharov <sha...@gm...> 20.05.21 18.12 Uhr
> >>>
> > > > Hi,
> > > >
> > > > Let's try manual installation:
> > > >
> > > > conda activate scipion3
> > > > > ldd
> > /home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so
> > > ->
> > > > > check output for errors
> > > > > export SCIPION_HOME="/home/user/Data/Software/scipion3/"
> > > > > cd
> /home/user/Data/Software/scipion3/software/em/xmippSrc-v3.20.07
> > > > > ./xmipp config -> check if all is correct in xmipp.conf
> > > > > ./xmipp check_config -> check for errors
> > > > > ./xmipp compileAndInstall N=4 && ln -srfn build
> > > > > /home/user/Data/Software/scipion3/software/em/xmipp && cd - &&
> > touch
> > > > > installation_finished && rm bindings_linked 2> /dev/null
> > > >
> > > >
> > > > You can post output errors from these commands here.
> > > >
> > > > Best regards,
> > > > Grigory
> > > >
> > > >
> > > >
> > >
> > >
> >
> >
>
> --------------------------------------------------------------------------------
> > > > Grigory Sharov, Ph.D.
> > > >
> > > > MRC Laboratory of Molecular Biology,
> > > > Francis Crick Avenue,
> > > > Cambridge Biomedical Campus,
> > > > Cambridge CB2 0QH, UK.
> > > > tel. +44 (0) 1223 267228 <+44%201223%20267228>
> > > > e-mail: gsharov@mrc-lmb.>
> > chr...@bi...>
> > > > > yes we have the library in the scipion3 env:
> > > > >
> > > > >
> > > > > [user@dataanalysisserver1 lib]$ ls -d $PWD/libwebp.so.7
> > > > >
> > > > >
> > > > > /home/user/Data/Software> > [92m conda activate scipion3 ; conda
> > > install fftw -y -c defaults[0m
> > > > > CommandNotFoundError: Your shell has not been properly
> configured
> > to
> > > > use
> > > > > 'conda activate'.
> > > > >
> > > > > When I am coping this command, it runs without any issue.
> > > > >
> > > > >
> > > > > Thanks for your help.
> > > > >
> > > > > best
> > > > > Christian
> > > > >
> > > > >
> > > > >
> > > > > >>> Grigory Sharov <sha...@gm...> 20.05.21 16.39 Uhr
> > >>>
> > > > > Hi,
> > > > >
> > > > > do you have libwebp.so.7 in
> > > > > /home/user/Data/Software/miniconda/envs/scipion3/lib/ ?
> > > > >
> > > > > Best regards,
> > > > > Grigory
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > >
> > >
> >
> >
>
> --------------------------------------------------------------------------------
> > > > > Grigory Sharov, Ph.D.
> > > > >
> > > > > MRC Laboratory of Molecular Biology,
> > > > > Francis Cri> > > > e-mail: gs...@mr...
> > > > >
> > > > >
> > > > > On Thu, May 20, 2021 at 3:00 PM Dmitry Semchonok
> > > <Sem...@gm...>
> > > > > wrote:
> > > > >
> > > > > > Dear colleagues,
> > > > > >
> > > > > > We reinstalled the centos 7 on our server as well as
> miniconda.
> > > > > >
> > > > > >
> > > > > >
> > > > > > The core was installed correctly but during xmipp installation
> > > some
> > > > error
> > > > > > appeared. Please have a look on the file attached.
> > > > > >
> > > > > >
> > > > > >
> > > > > > Could you please advice how to proceed?
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > Thank you in  advance.
> > > > > >
> > > > > >
> > > > > > Sincerely,
> > > > > > Dmitry and
> > > Christian_______________________________________________
> > > > > > scipion-users mailing list
> > > > > > sci...@li...
> > > > > > https://lists.sourceforge.net/lists/listinfo/scipion-users
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > scipion-users mailing list
> > > > > sci...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/scipion-users
> > > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > scipion-users mailing list
> > > > sci...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/scipion-users
> > > >
> > >
> > >
> > >
> > > _______________________________________________
> > > scipion-users mailing list
> > > sci...@li...
> > > https://lists.sourceforge.net/lists/listinfo/scipion-users
> > >
> > >
> > > _______________________________________________
> > > scipion-users mailing list
> > > sci...@li...
> > > https://lists.sourceforge.net/lists/listinfo/sci
> >
> >
> > _______________________________________________
> > scipion-users mailing list
> > sci...@li...
> > https://lists.sourceforge.net/lists/listinfo/scipion-users
> >
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> _______________________________________________
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>

Re: [scipion-users] Antw: Antw: Re: Antw: Re: Antw: Antw: Re: Antw: Re: Antw: Re: SCIPION installat

Image processing framework to integrate EM software packages.

Re: [scipion-users] Antw: Antw: Re: Antw: Re: Antw: Antw: Re: Antw: Re: Antw: Re: SCIPION installation error -- xmipp: Something went wrong (SEE ERRORS ABOVE) when running: