Compilation issues...

[mbelouso]

Comrades!!!

I was thinking of using SIMPLE for some fun projects over here, and decided to try and compile it on a new workstation. So first some details:

OS: Linux Mint 22.1 (Kernel Version 6.8.0-55)
gfortran 13.3.0
gcc 13.3.0
cmake 3.28.3

cmake output seems OK (see below), but when I run make I get the following compilation error (see below). Thanks guys I would love to get this working on my system again! Speak soon!

[ 57%] No update step for 'nodejs_unix'
[ 58%] No patch step for 'nodejs_unix'
[ 58%] No configure step for 'nodejs_unix'
[ 58%] No build step for 'nodejs_unix'
[ 58%] No install step for 'nodejs_unix'
[ 58%] No test step for 'nodejs_unix'
[ 59%] Completed 'nodejs_unix'
[ 59%] Built target nodejs_unix
[ 59%] Installing GUI multiuser ... 

added 1 package, and audited 3 packages in 399ms

found 0 vulnerabilities
[ 59%] Built target gui_multi_unix
[ 59%] Installing precompiled single-user GUI ... 
[ 59%] Built target gui_single_unix
[ 59%] Building Fortran object bin/CMakeFiles/simple_exec.dir/simple_exec/simple_exec.f90.o
[ 59%] Linking CXX executable simple_exec
/usr/bin/ld: warning: json_value_module.f90.o: requires executable stack (because the .note.GNU-stack section is executable)
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libtiff.a(tif_lerc.o): in function `LERCPostEncode':
(.text+0x67d): undefined reference to `lerc_encodeForVersion'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libtiff.a(tif_lerc.o): in function `LERCPreDecode':
(.text+0x1095): undefined reference to `lerc_getBlobInfo'
/usr/bin/ld: (.text+0x118f): undefined reference to `lerc_decode'
/usr/bin/ld: (.text+0x1507): undefined reference to `lerc_decode'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libwebp.a(picture_csp_enc.c.o): in function `ImportYUVAFromRGBA':
(.text+0xed5): undefined reference to `SharpYuvInit'
/usr/bin/ld: (.text+0xedc): undefined reference to `SharpYuvGetConversionMatrix'
/usr/bin/ld: (.text+0xf30): undefined reference to `SharpYuvConvert'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/CMakeFiles/simple_exec.dir/build.make:119: bin/simple_exec] Error 1
make[1]: *** [CMakeFiles/Makefile2:684: bin/CMakeFiles/simple_exec.dir/all] Error 2
make: *** [Makefile:146: all] Error 2

CMAKE OUTPUT:

-- The Fortran compiler identification is GNU 13.3.0
-- The C compiler identification is GNU 13.3.0
-- The CXX compiler identification is GNU 13.3.0
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /usr/bin/gfortran - skipped
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Checking whether /usr/bin/gfortran supports Fortran 2008
-- Checking whether /usr/bin/gfortran supports Fortran 2008 -- yes
-- Checking whether /usr/bin/gfortran supports Fortran 2008 Unicode 10646
-- Checking whether /usr/bin/gfortran supports Unicode 10646 -- yes
-- Checking whether /usr/bin/gfortran supports Fortran 2008 iso_fortran_env compiler_version and compiler_options
-- Checking whether /usr/bin/gfortran supports ISO_FORTRAN_ENV compiler_version/options -- yes
-- Checking whether /usr/bin/gfortran supports variadic macros
-- Checking whether /usr/bin/gfortran supports Fortran variadic macros -- no
-- CMAKE_Fortran_COMPILER_ID: GNU
-- -march=native -fPIC  -std=f2008 -fall-intrinsics -Wintrinsics-std
-- CMAKE_C_FLAGS_RELEASE_INIT:  -O3 -DNDEBUG (Old version)
-- CMAKE_C_FLAGS_DEBUG_INIT:  -g (Old version)
-- CMAKE_CXX_FLAGS_RELEASE_INIT:  -O3 -DNDEBUG (Old version)
-- CMAKE_CXX_FLAGS_DEBUG_INIT:  -g (Old version)
-- CMAKE_C_FLAGS_RELEASE_INIT:   -O3 -DNDEBUG -std=c11 -DGNU
-- CMAKE_C_FLAGS_DEBUG_INIT:   -g -std=c11 -DGNU
-- CMAKE_CXX_FLAGS_RELEASE_INIT:  -O3 -DNDEBUG -std=c++14 -DGNU
-- CMAKE_CXX_FLAGS_DEBUG_INIT:  -g -std=c++14 -DGNU
-- CMAKE_Fortran_FLAGS_RELEASE_INIT:  -O3 -DNDEBUG -O3 (Old version)
-- CMAKE_Fortran_FLAGS_DEBUG_INIT:  -g  (Old version)
-- CMAKE_Fortran_FLAGS_RELEASE_INIT:  -O3 -DNDEBUG -O3 -cpp  -Wp,C,CC,no-endif-labels -ffree-form  -fimplicit-none  -ffree-line-length-none  -fno-second-underscore -march=native -fPIC  -std=f2008 -fall-intrinsics -Wintrinsics-std -Waliasing -Wampersand  -Wsurprising -Wline-truncation -Wreal-q-constant  -O3 -ffrontend-optimize -fno-stack-protector -fno-lifetime-dse  -DGNU
-- CMAKE_Fortran_FLAGS_DEBUG_INIT:   -g -cpp  -Wp,C,CC,no-endif-labels -ffree-form  -fimplicit-none  -ffree-line-length-none  -fno-second-underscore -march=native -fPIC  -std=f2008 -fall-intrinsics -Wintrinsics-std -Waliasing -Wampersand  -Wsurprising -Wline-truncation -Wreal-q-constant  -Og -g -pedantic -fno-inline -fno-f2c -Og -ggdb -fbacktrace  -Wall -Wcompare-reals -Wtype-limits -Wuninitialized -Wunused-but-set-parameter -Wimplicit-interface -Wno-unused-dummy-argument -Wno-unused-value -Wno-surprising -frange-check -fstack-protector -fstack-check -fbounds-check -fcheck=all -fcheck=array-temps   -DGNU
-- CMAKE_BUILD_TYPE not given, defaulting to RELEASE
-- In ZSetParallelLibrary -- OMP_NUM_PROCS 32
-- Try OpenMP Fortran flag = [-fopenmp]
-- OpenMP testing : -fopenmp
-- Try OpenMP version
--  OpenMP version compilation flag: 0
--  OpenMP version runtime flag: TRUE
--  OpenMP version runtime output: 201511
--  openmp version test output: 201511
--  openmp version test output: 201511
--  openmp version test numerical output: 201511: regex 
-- Setting OpenMP_Fortran_Version to 201511
-- OpenMP Version string cleanup
-- OpenMP Version string = 201511
-- Found OpenMP_Fortran: -fopenmp  
-- Making sure your MPI Fortran compiler enables the USE_MPI flag
-- Making sure your Fortran compiler points to the correct binary
-- FORTRAN ABSPATH /usr/bin/x86_64-linux-gnu-gfortran-13
-- FORTRAN_PARENT_DIR /usr/bin
-- Making sure your C compiler points to the correct binary
-- GCC version: cc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-- Making sure your C++ compiler points to the correct binary
-- G++ version: c++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-- Making sure your preprocessor points to the correct binary
-- C Preprocessor points to /usr/bin/cpp
-- Found Git: /usr/bin/git (found version "2.43.0") 
-- Git version: git4e7a1b3e
-- Git version template : /home/mbelouso/src/SIMPLE/cmake/Modules/GitVersion.h.in
-- Git version template : /home/mbelouso/src/SIMPLE/build/lib/simple/SimpleGitVersion.h
-- Fortran compiler: gfortran
-- Fortran compiler GNU
-- CMAKE_Fortran_FLAGS_RELEASE_INIT:  -O3 -DNDEBUG -O3 -cpp  -Wp,C,CC,no-endif-labels -ffree-form  -fimplicit-none  -ffree-line-length-none  -fno-second-underscore -march=native -fPIC  -std=f2008 -fall-intrinsics -Wintrinsics-std -Waliasing -Wampersand  -Wsurprising -Wline-truncation -Wreal-q-constant  -O3 -ffrontend-optimize -fno-stack-protector -fno-lifetime-dse  -DGNU
-- Build static executables.
-- On glibc-based systems, OpenMP enabled applications cannot be statically linked due to limitations of the underlying pthreads-implementation. It might be possible to get a working solution if -Wl,--whole-archive -lpthread -Wl,--no-whole-archive is added to the command line. However, this is not supported by gcc and thus not recommended.
-- fftw3 found
-- lib: /usr/lib/x86_64-linux-gnu/libfftw3f.a;/usr/lib/x86_64-linux-gnu/libfftw3.a;/usr/lib/x86_64-linux-gnu/libfftw3f_threads.a
-- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.a (found suitable version "4.5.1", minimum required is "4.0.10")  
-- JBIG_LIBRARY: /usr/lib/x86_64-linux-gnu/libjbig.a
-- JPEG_LIBRARY: /usr/lib/x86_64-linux-gnu/libjpeg.a
-- LZMA_LIBRARY: /usr/lib/x86_64-linux-gnu/liblzma.a
-- Z_LIBRARY: /usr/lib/x86_64-linux-gnu/libz.a
-- ZSTD_LIBRARY: /usr/lib/x86_64-linux-gnu/libzstd.a
-- WEBP_LIBRARY: /usr/lib/x86_64-linux-gnu/libwebp.a
-- Deflate_LIBRARY: /usr/lib/x86_64-linux-gnu/libdeflate.a
-- Executing: /usr/bin/gfortran -dumpversion
-- EXTRA_LIBS /usr/lib/x86_64-linux-gnu/libfftw3f.a;/usr/lib/x86_64-linux-gnu/libfftw3.a;/usr/lib/x86_64-linux-gnu/libfftw3f_threads.a;/usr/lib/x86_64-linux-gnu/libtiff.a;/usr/lib/x86_64-linux-gnu/libjbig.a;/usr/lib/x86_64-linux-gnu/libjpeg.a;/usr/lib/x86_64-linux-gnu/liblzma.a;/usr/lib/x86_64-linux-gnu/libz.a;/usr/lib/x86_64-linux-gnu/libzstd.a;/usr/lib/x86_64-linux-gnu/libwebp.a;/usr/lib/x86_64-linux-gnu/libdeflate.a;-lm;SIMPLE3.0.0;/usr/lib/x86_64-linux-gnu/libfftw3f.a;/usr/lib/x86_64-linux-gnu/libfftw3.a;/usr/lib/x86_64-linux-gnu/libfftw3f_threads.a;/usr/lib/x86_64-linux-gnu/libtiff.a;/usr/lib/x86_64-linux-gnu/libjbig.a;/usr/lib/x86_64-linux-gnu/libjpeg.a;/usr/lib/x86_64-linux-gnu/liblzma.a;/usr/lib/x86_64-linux-gnu/libz.a;/usr/lib/x86_64-linux-gnu/libzstd.a;/usr/lib/x86_64-linux-gnu/libwebp.a;/usr/lib/x86_64-linux-gnu/libdeflate.a;-lm
-- Found Perl: /usr/bin/perl (found version "5.38.2") 
CMake Deprecation Warning at gui/CMakeLists.txt:3 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


-- Located pre-built single-user gui binary for linux
-- Set runtime variables. 
-- Test directories tests/test_2D_core_finder;tests/test_3D_core_finder;tests/test_3D_lpbasic;tests/test_3D_opt_filt;tests/test_AFM;tests/test_AFM_IO;tests/test_angres;tests/test_ansi_colors;tests/test_atom_posmatch;tests/test_bfactor;tests/test_binimage;tests/test_binoris;tests/test_bounds_from_mask3D;tests/test_cavg_kpca;tests/test_cc_gradient;tests/test_class_sample;tests/test_clustering;tests/test_common_lines;tests/test_core_atoms;tests/test_correlation;tests/test_corrs2weights;tests/test_corrweights;tests/test_crys_score;tests/test_ctf;tests/test_dists_cluster;tests/test_dock_vols;tests/test_eigh;tests/test_eo_diff;tests/test_euler;tests/test_eval_polarftcc;tests/test_extr_frac;tests/test_fast_corrcalc;tests/test_fileio;tests/test_find_boundaries;tests/test_fit_lattice;tests/test_fm;tests/test_fplane_proj;tests/test_ft_expanded;tests/test_gauss2Dfit;tests/test_gencorrs_fft;tests/test_graphene_mask;tests/test_imgfile;tests/test_inside_write;tests/test_install;tests/test_invlinear_vols;tests/test_io;tests/test_io_parallel;tests/test_kpca;tests/test_lbfgsb;tests/test_lbfgsb_cosine;tests/test_lplims;tests/test_lpstages;tests/test_mask;tests/test_masscen_nano;tests/test_maxnloc;tests/test_memuse;tests/test_mrc_validation;tests/test_multinomal;tests/test_nano_detect_atoms;tests/test_nano_mask;tests/test_nanoparticle;tests/test_neigh;tests/test_openmp;tests/test_opt_genetic;tests/test_opt_lp;tests/test_opt_reg;tests/test_order2D_byresol;tests/test_order_corr;tests/test_ori;tests/test_otsu;tests/test_pca_all;tests/test_pca_imgvar;tests/test_pdb2mrc;tests/test_pdb_register;tests/test_phasecorr;tests/test_picker_comp;tests/test_point_cluster;tests/test_polar2cartesian;tests/test_ptcl_center;tests/test_rad_med;tests/test_radial_cc;tests/test_rank_weights;tests/test_replace_substr;tests/test_reshape2cube;tests/test_rotate_ref;tests/test_seg_regression;tests/test_segpicker;tests/test_serialize;tests/test_shift;tests/test_shiftinvariant;tests/test_shiftsrch;tests/test_simd;tests/test_simnano;tests/test_sp_project;tests/test_speed;tests/test_stack;tests/test_stack_io;tests/test_starexport;tests/test_starfile;tests/test_stringmatch;tests/test_sym;tests/test_tseries_neigh;tests/test_uniform_euler;tests/test_uniform_rot;tests/test_units;tests/test_val_map;tests/test_val_per_atom;tests/test_val_rescale_map
-- Configuring done (1.0s)
-- Generating done (0.2s)
-- Build files have been written to: /home/mbelouso/src/SIMPLE/build

[mbelouso]

Sorry I should have said that I cloned the latest repo on the 12/03/2025

[congv]

It looks like a tiff library problem of the GUI. Could you please try to compile without the GUI and see if the compilation works fine? i.e.
cmake .. -DGUI=off -DUSE_LIBTIFF=off
make -j install

[mbelouso]

Yep, definitely compiles fine with:

cmake -DUSE_LIBTIFF=off ..

So its clearly an issue with whatever version of tibtiff I'm using.

ldconfig -v | grep tiff

spits out:

	libtiff.so.6 -> libtiff.so.6.0.1
	libtiffxx.so.6 -> libtiffxx.so.6.0.1

So maybe libtiff6 has some different calls?

[cyrilreboul]

Hi Matt, you're right, we only supported libtiff.so.5.3 so far, some new dependencies have been added since. It's updated and fixed with latest commit. On my machine that has the same tiff/gcc/cmake versions as yours I can now compile fine without deactivating tiff/eer support.
To be clear the linking was missing, you should not have to install anything.