[scipion-users] Antw: Antw: Re: Antw: Re: Antw: Re: SCIPION installation error -- xmipp: Something

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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_config. There are some path missing
in PATH, but alternatives are found so I guess this is fine (see output
below).

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 '/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/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/miniconda/envs/scipion3/lib/libtiff.so:
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 `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/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! 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

--------------------------------------------------------------------------------
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/Software/miniconda/envs/scipion3/lib/./libz.so.1
> (0x00007f8f7244d000)
> 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/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 '/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 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
> - 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] 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
> 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>
/home/user/Data/Software/miniconda/envs/scipion3/lib/libtiff.so:
> 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/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 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 already installed.
>
>
> 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...> wrote:
>
> > Hi all,
> >
> > Dmitrys collegue here.
> >
> > 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 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 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
> >
>
>
>
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[scipion-users] Antw: Antw: Re: Antw: Re: Antw: Re: SCIPION installation error -- xmipp: Something

Image processing framework to integrate EM software packages.

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