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Compilation failed when downloading fltk source files #835

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BertrandSim opened this issue Dec 9, 2021 · 5 comments
Closed

Compilation failed when downloading fltk source files #835

BertrandSim opened this issue Dec 9, 2021 · 5 comments

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@BertrandSim
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During the installation of Relion 3.1.3, the program tries to download the fltk source files from
ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz
but failed.

Here are the commands I used

mkdir build
cd build
cmake ..
make -j 8

As I did not have FLTK installed, FLTK would be downloaded and compiled during runtime.

Here is the tail part of the output for the installation. No errors were shown prior to this.

...
Scanning dependencies of target prepare_subtomo
[ 80%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o
[ 81%] Linking CXX executable ../../bin/relion_reconstruct
[ 82%] Linking CXX executable ../../bin/relion_demodulate
[ 82%] Built target reconstruct
Scanning dependencies of target preprocess
[ 82%] Built target demodulate
[ 82%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o
Scanning dependencies of target reconstruct_mpi
[ 82%] Linking CXX executable ../../bin/relion_motion_refine_mpi
[ 82%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o
[ 82%] Built target motion_refine_mpi
Scanning dependencies of target refine_mpi
[ 83%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o
[ 83%] Linking CXX executable ../../bin/relion_particle_subtract_mpi
[ 84%] Linking CXX executable ../../bin/relion_preprocess
[ 85%] Linking CXX executable ../../bin/relion_plot_delocalisation
[ 85%] Built target preprocess
Scanning dependencies of target run_ctffind
[ 85%] Built target particle_subtract_mpi
Scanning dependencies of target run_motioncorr
[ 85%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o
[ 86%] Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o
[ 86%] Built target plot_delocalisation
Scanning dependencies of target estimate_gain
[ 87%] Building CXX object src/apps/CMakeFiles/estimate_gain.dir/estimate_gain.cpp.o
[ 88%] Linking CXX executable ../../bin/relion_run_ctffind
[ 88%] Built target run_ctffind
Scanning dependencies of target run_motioncorr_mpi
[ 88%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o
[ 88%] Linking CXX executable ../../bin/relion_reposition
[ 88%] Built target reposition
[ 88%] Linking CXX executable ../../bin/relion_run_motioncorr
Scanning dependencies of target stack_create
[ 88%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o
[ 89%] Linking CXX executable ../../bin/relion_reconstruct_mpi
[ 89%] Built target run_motioncorr
Scanning dependencies of target scheduler
[ 89%] Building CXX object src/apps/CMakeFiles/scheduler.dir/scheduler.cpp.o
[ 89%] Built target reconstruct_mpi
Scanning dependencies of target star_handler
[ 90%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o
[ 90%] Linking CXX executable ../../bin/relion_refine_mpi
[ 90%] Built target refine_mpi
Scanning dependencies of target tiltpair_plot
[ 90%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o
[ 91%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi
[ 91%] Built target run_motioncorr_mpi
[ 91%] Linking CXX executable ../../bin/relion_estimate_gain
[ 91%] Built target estimate_gain
[ 92%] Linking CXX executable ../../bin/relion_scheduler
[ 92%] Built target scheduler
[ 93%] Linking CXX executable ../../bin/relion_tiltpair_plot
[ 93%] Built target tiltpair_plot
[ 93%] Linking CXX executable ../../bin/relion_stack_create
[ 93%] Built target stack_create
[ 94%] Linking CXX executable ../../bin/relion_prepare_subtomo
[ 94%] Built target prepare_subtomo
[ 94%] Linking CXX executable ../../bin/relion_star_handler
[ 94%] Built target star_handler
-- Retrying...
-- Using src='ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz'
-- Retry after 5 seconds (attempt #2) ...
-- Using src='ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz'
-- Retry after 5 seconds (attempt #3) ...
-- Using src='ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz'
-- Retry after 15 seconds (attempt #4) ...
-- Using src='ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz'
-- Retry after 60 seconds (attempt #5) ...
-- Using src='ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz'
CMake Error at /home/sslb/cryoem/relion/build/OWN_FLTK-prefix/src/OWN_FLTK-stamp/download-OWN_FLTK.cmake:159 (message):
  Each download failed!

    error: downloading 'ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz' failed
         status_code: 28
         status_string: "Timeout was reached"
         log:
         --- LOG BEGIN ---
           Trying 131.111.85.35:21...

  TCP_NODELAY set

  Connected to ftp.mrc-lmb.cam.ac.uk (131.111.85.35) port 21 (#0)

  220 Welcome to LMB Anonymous FTP service

  USER anonymous

  230 Login successful.

  PWD

  257 "/"

  Entry path is '/'

  CWD pub

  ftp_perform ends with SECONDARY: 0

  250 Directory successfully changed.

  CWD scheres

  250 Directory successfully changed.

  EPSV

  Connect data stream passively

  229 Entering Extended Passive Mode (|||33930|).

    Trying 131.111.85.35:33930...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 33930

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Failed EPSV attempt.  Disabling EPSV

  PASV

  227 Entering Passive Mode (131,111,85,35,82,168).

  Skip 131.111.85.35 for data connection, re-use ftp.mrc-lmb.cam.ac.uk
  instead

    Trying 131.111.85.35:21160...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 21160

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Closing connection 0

  

         --- LOG END ---
         error: downloading 'ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz' failed
         status_code: 28
         status_string: "Timeout was reached"
         log:
         --- LOG BEGIN ---
           Trying 131.111.85.35:21...

  TCP_NODELAY set

  Connected to ftp.mrc-lmb.cam.ac.uk (131.111.85.35) port 21 (#0)

  220 Welcome to LMB Anonymous FTP service

  USER anonymous

  230 Login successful.

  PWD

  257 "/"

  Entry path is '/'

  CWD pub

  ftp_perform ends with SECONDARY: 0

  250 Directory successfully changed.

  CWD scheres

  250 Directory successfully changed.

  EPSV

  Connect data stream passively

  229 Entering Extended Passive Mode (|||18493|).

    Trying 131.111.85.35:18493...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 18493

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Failed EPSV attempt.  Disabling EPSV

  PASV

  227 Entering Passive Mode (131,111,85,35,103,105).

  Skip 131.111.85.35 for data connection, re-use ftp.mrc-lmb.cam.ac.uk
  instead

    Trying 131.111.85.35:26473...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 26473

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Closing connection 0

  

         --- LOG END ---
         error: downloading 'ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz' failed
         status_code: 28
         status_string: "Timeout was reached"
         log:
         --- LOG BEGIN ---
           Trying 131.111.85.35:21...

  TCP_NODELAY set

  Connected to ftp.mrc-lmb.cam.ac.uk (131.111.85.35) port 21 (#0)

  220 Welcome to LMB Anonymous FTP service

  USER anonymous

  230 Login successful.

  PWD

  257 "/"

  Entry path is '/'

  CWD pub

  ftp_perform ends with SECONDARY: 0

  250 Directory successfully changed.

  CWD scheres

  250 Directory successfully changed.

  EPSV

  Connect data stream passively

  229 Entering Extended Passive Mode (|||14324|).

    Trying 131.111.85.35:14324...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 14324

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Failed EPSV attempt.  Disabling EPSV

  PASV

  227 Entering Passive Mode (131,111,85,35,125,122).

  Skip 131.111.85.35 for data connection, re-use ftp.mrc-lmb.cam.ac.uk
  instead

    Trying 131.111.85.35:32122...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 32122

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Closing connection 0

  

         --- LOG END ---
         error: downloading 'ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz' failed
         status_code: 28
         status_string: "Timeout was reached"
         log:
         --- LOG BEGIN ---
           Trying 131.111.85.35:21...

  TCP_NODELAY set

  Connected to ftp.mrc-lmb.cam.ac.uk (131.111.85.35) port 21 (#0)

  220 Welcome to LMB Anonymous FTP service

  USER anonymous

  230 Login successful.

  PWD

  257 "/"

  Entry path is '/'

  CWD pub

  ftp_perform ends with SECONDARY: 0

  250 Directory successfully changed.

  CWD scheres

  250 Directory successfully changed.

  EPSV

  Connect data stream passively

  229 Entering Extended Passive Mode (|||9467|).

    Trying 131.111.85.35:9467...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 9467

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Failed EPSV attempt.  Disabling EPSV

  PASV

  227 Entering Passive Mode (131,111,85,35,142,76).

  Skip 131.111.85.35 for data connection, re-use ftp.mrc-lmb.cam.ac.uk
  instead

    Trying 131.111.85.35:36428...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 36428

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Closing connection 0

  

         --- LOG END ---
         error: downloading 'ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz' failed
         status_code: 28
         status_string: "Timeout was reached"
         log:
         --- LOG BEGIN ---
           Trying 131.111.85.35:21...

  TCP_NODELAY set

  Connected to ftp.mrc-lmb.cam.ac.uk (131.111.85.35) port 21 (#0)

  220 Welcome to LMB Anonymous FTP service

  USER anonymous

  230 Login successful.

  PWD

  257 "/"

  Entry path is '/'

  CWD pub

  ftp_perform ends with SECONDARY: 0

  250 Directory successfully changed.

  CWD scheres

  250 Directory successfully changed.

  EPSV

  Connect data stream passively

  229 Entering Extended Passive Mode (|||13876|).

    Trying 131.111.85.35:13876...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 13876

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Failed EPSV attempt.  Disabling EPSV

  PASV

  227 Entering Passive Mode (131,111,85,35,226,24).

  Skip 131.111.85.35 for data connection, re-use ftp.mrc-lmb.cam.ac.uk
  instead

    Trying 131.111.85.35:57880...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 57880

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Closing connection 0

  

         --- LOG END ---
         error: downloading 'ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz' failed
         status_code: 28
         status_string: "Timeout was reached"
         log:
         --- LOG BEGIN ---
           Trying 131.111.85.35:21...

  TCP_NODELAY set

  Connected to ftp.mrc-lmb.cam.ac.uk (131.111.85.35) port 21 (#0)

  220 Welcome to LMB Anonymous FTP service

  USER anonymous

  230 Login successful.

  PWD

  257 "/"

  Entry path is '/'

  CWD pub

  ftp_perform ends with SECONDARY: 0

  250 Directory successfully changed.

  CWD scheres

  250 Directory successfully changed.

  EPSV

  Connect data stream passively

  229 Entering Extended Passive Mode (|||46855|).

    Trying 131.111.85.35:46855...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 46855

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Failed EPSV attempt.  Disabling EPSV

  PASV

  227 Entering Passive Mode (131,111,85,35,49,26).

  Skip 131.111.85.35 for data connection, re-use ftp.mrc-lmb.cam.ac.uk
  instead

    Trying 131.111.85.35:12570...

  TCP_NODELAY set

  Connecting to 131.111.85.35 (131.111.85.35) port 12570

  connect to 131.111.85.35 port 21 failed: Connection timed out

  Failed to connect to ftp.mrc-lmb.cam.ac.uk port 21: Connection timed out

  Closing connection 0

  

         --- LOG END ---
         
    


make[2]: *** [CMakeFiles/OWN_FLTK.dir/build.make:91: OWN_FLTK-prefix/src/OWN_FLTK-stamp/OWN_FLTK-download] Error 1
make[1]: *** [CMakeFiles/Makefile2:243: CMakeFiles/OWN_FLTK.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

Environment:

  • OS: [Linux Mint Cinammon]
  • RELION version [3.1.3 (current master branch)]

build output

-- 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....
-- MPI_INCLUDE_PATH : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/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
-- 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
-- Could NOT find FLTK (missing: FLTK_LIBRARIES FLTK_INCLUDE_DIR FLTK_FLUID_EXECUTABLE) 
-- No FLTK installation was found
-- --------------------------------------------------------
-- -------- NO EXISTING FLTK LIBRARIES WHERE FOUND. -------
-- -------------- FLTK WILL BE DOWNLOADED AND -------------
-- --------------- BUILT DURING COMPILE-TIME. -------------
-- --------------------------------------------------------
-- ---- A WORKING INTERNET CONNECTION WILL BE REQUIRED. ---
-- --------------------------------------------------------
-- no previous fltk found, the following paths are set for libs/headers TO BE built
-- FLTK_INCLUDE_DIR: /home/sslb/cryoem/relion/external/fltk/include
-- FLTK_LIBRARIES:   /home/sslb/cryoem/relion/external/fltk/lib/libfltk.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
BUILD_SHARED_LIBS = OFF
-- Building static libs (larger build size and binaries)
Running apps/CMakeLists.txt...
-- CMAKE_BINARY_DIR:/home/sslb/cryoem/relion/build
-- Git commit ID: 72bbf0c06cea68f8992328703ee5ae5f3d1fc9b7
-- Found OpenMP_C: -fopenmp  
-- Found OpenMP_CXX: -fopenmp  
-- Found OpenMP: TRUE   
-- Configuring done
-- Generating done
-- Build files have been written to: /home/sslb/cryoem/relion/build
@biochem-fan
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The FTP server is working fine. If you still cannot get the file, it is your network problem, not ours. If you can download the file from other network (e.g. your home), you can put the file in the external/fltk and let the build script use it instead.

@aceerez
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aceerez commented Feb 28, 2022

I have the same Error. do you have a guide on how to override this?

@biochem-fan
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It is explained above. Did you try that?

@aceerez
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aceerez commented Feb 28, 2022

How do I download it? I try to connect to your server with remote FTP to 131.111.85.35 port 21 but I don't see the "fltk-1.3.5-source.tar.gz" file.

@biochem-fan
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Try wget.

@biochem-fan biochem-fan mentioned this issue Jun 24, 2024
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@biochem-fan @BertrandSim @aceerez