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hael / SIMPLE

A new repository (with deleted history) in preparation for release 3.0 of SIMPLE
GNU General Public License v3.0
22 stars 8 forks source link

simple_multiuser GUI can't start on Cento7 #8

Open qiyubio opened 3 years ago

qiyubio commented 3 years ago

Hi, I installed simple on our cluster, and simple_test_install finished with no error. I edited the /home/test/SIMPLE/gui_data/users.htpasswd with user and passwd. But simple_multiuser GUI can't start and complain about "No argument given", is there something missing? 

simple_multiuser
/snapshot
/snapshot/multi_user
Application data location  /home/test/SIMPLE/gui_data
Found Slurm submission environment
No argument given

My env:

SIMPLE_QSYS=slurm
SIMPLE_EMAIL=test@gmail
SIMPLE_PATH=/home/test/SIMPLE

Also the tutorial file is truncated:

tar zxvf tutorial_betagalactosidase.tgz
./gain.mrc
./movies/
./movies/20170629_00025_frameImage.tif
./movies/20170629_00048_frameImage.tif
./movies/20170629_00027_frameImage.tif
./movies/20170629_00035_frameImage.tif

gzip: stdin: invalid compressed data--format violated
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now
cosmopolitanadmin commented 3 years ago

I apologise. There was an error in the readme and the multiuser server needs to be started with the command : simple_multiuser start

I'll look into the truncation issue asap

qiyubio commented 3 years ago

Is there more information about how are simple and simple_multiuser compiled? I have difficulties to run both, is there instruction of any dependency of them?

simple
fuse: failed to exec fusermount: No such file or directory

Cannot mount AppImage, please check your FUSE setup.
You might still be able to extract the contents of this AppImage
if you run it with the --appimage-extract option.
See https://github.com/AppImage/AppImageKit/wiki/FUSE
for more information
open dir error: No such file or directory
simple_multiuser start
/snapshot
/snapshot/multi_user
pkg/prelude/bootstrap.js:1248
      throw error;
      ^

Error: Cannot find module '~/SIMPLE/gui_data/server/src/httpServer'
1) If you want to compile the package/file into executable, please pay attention to compilation warnings and specify a literal in 'require' call. 2) If you don't want to compile the package/file into executable and want to 'require' it from filesystem (likely plugin), specify an absolute path in 'require' call using process.cwd() or process.execPath.
    at Function.Module._resolveFilename (module.js:546:15)
    at Function.Module._resolveFilename (pkg/prelude/bootstrap.js:1350:46)
    at Function.Module._load (module.js:473:25)
    at Module.require (module.js:595:17)
    at Module.require (pkg/prelude/bootstrap.js:1229:31)
    at require (internal/module.js:11:18)
    at Object.<anonymous> (/snapshot/multi_user/simple_multiuser.js:0:0)
    at Module._compile (pkg/prelude/bootstrap.js:1324:22)
    at Object.Module._extensions..js (module.js:662:10)
    at Module.load (module.js:564:32)
ls ~/SIMPLE/gui_data/server/src/httpServer*
/home/test/SIMPLE/gui_data/server/src/httpServer.js
donghuachensu commented 2 years ago

My installation was successful. However, I could not even see the command 'simple' or 'simple_multiuser' (in bin directory I can see the command simple_exec and others simpletest*). Did I make any silly mistake?

hael commented 2 years ago

There is a file add2bashrc.txt generated in the build folder that you can append to your .bashrc. After that you should be able to execute simple or simple-multiuser. Let me know if this works for you

On Fri, Nov 5, 2021 at 4:49 PM donghuachensu @.***> wrote:

My installation was successful. However, I could not even see the command 'simple' or 'simple_multiuser' (in bin directory I can see the command simple_exec and others simpletest*). Did I make any silly mistake?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/hael/SIMPLE/issues/8#issuecomment-962211535, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJENUXAKCT5TPJOY4N7KZ3UKRGPZANCNFSM427W3JYA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

donghuachensu commented 2 years ago

Thanks for your quick reply. Indeed I added that to the end of my .bashrc. As I said, I can run simple_exec. I also run simple_test_install without any problem. However, I could NOT find the commands simple and simple_multiuser in the bin folder of SIMPLE-3.0.1

cosmopolitanadmin commented 2 years ago

Please could you confirm the version of CMake that you're using and the commands that you are using to build SIMPLE? I'm trying to reproduce what you observe.

It would also be useful to know if there are any lines in the output from the make step that relate to the gui.

From: donghuachensu @.> Sent: 05 November 2021 22:13 To: hael/SIMPLE @.> Cc: Joseph Caesar @.>; Comment @.> Subject: Re: [hael/SIMPLE] simple_multiuser GUI can't start on Cento7 (#8)

Thanks for your quick reply. Indeed I added that to the end of my .bashrc. As I said, I can run simple_exec. I also run simple_test_install without any problem. However, I could NOT find the commands simple and simple_multiuser in the bin folder of SIMPLE-3.0.1

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/hael/SIMPLE/issues/8#issuecomment-962252095, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABPQCUULVGQ52USBG7KHD5TUKRQKLANCNFSM427W3JYA. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

donghuachensu commented 2 years ago

Sorry for my late reply. Here is the info you asked:

cmake --version cmake version 3.7.2

cmake -DCMAKE_INSTALL_PREFIX=/data/SIMPLE-3.0.1 .. -- Checking whether /data/openmpi/bin/mpif90 supports Fortran 2008 -- Checking whether /data/openmpi/bin/mpif90 supports Fortran 2008 -- yes -- Checking whether /data/openmpi/bin/mpif90 supports Fortran 2008 Unicode 10646 -- Checking whether /data/openmpi/bin/mpif90 supports Unicode 10646 -- yes -- Checking whether /data/openmpi/bin/mpif90 supports Fortran 2008 iso_fortran_env compiler_version and compiler_options -- Checking whether /data/openmpi/bin/mpif90 supports ISO_FORTRAN_ENV compiler_version/options -- yes -- Checking whether /data/openmpi/bin/mpif90 supports variadic macros -- Checking whether /data/openmpi/bin/mpif90 supports Fortran variadic macros -- no -- CMAKE_Fortran_COMPILER_ID: GNU -- CMAKE_C_FLAGS_RELEASE_INIT: -O3 -DNDEBUG -std=c11 -DGNU -O3 -DNDEBUG (Old version) -- CMAKE_C_FLAGS_DEBUG_INIT: -g -std=c11 -DGNU -g (Old version) -- CMAKE_CXX_FLAGS_RELEASE_INIT: -O3 -DNDEBUG -std=c++14 -DGNU -O3 -DNDEBUG (Old version) -- CMAKE_CXX_FLAGS_DEBUG_INIT: -g -std=c++14 -DGNU -g (Old version) -- CMAKE_C_FLAGS_RELEASE_INIT: -O3 -DNDEBUG -std=c11 -DGNU -O3 -DNDEBUG -std=c11 -DGNU -- CMAKE_C_FLAGS_DEBUG_INIT: -g -std=c11 -DGNU -g -std=c11 -DGNU -- CMAKE_CXX_FLAGS_RELEASE_INIT: -O3 -DNDEBUG -std=c++14 -DGNU -O3 -DNDEBUG -std=c++14 -DGNU -- CMAKE_CXX_FLAGS_DEBUG_INIT: -g -std=c++14 -DGNU -g -std=c++14 -DGNU -- 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 -O3 -DNDEBUG -O3 (Old version) -- 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 -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 -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 -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 -- In ZSetParallelLibrary -- OMP_NUM_PROCS 64 -- 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 -- Making sure your MPI Fortran compiler enables the USE_MPI flag -- Making sure your Fortran compiler points to the correct binary -- FORTRAN ABSPATH /data/openmpi/bin/opal_wrapper -- FORTRAN_PARENT_DIR /data/openmpi/bin -- Making sure your C compiler points to the correct binary -- GCC version: cc (GCC) 8.5.0 20210514 (Red Hat 8.5.0-3) Copyright (C) 2018 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++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-3) Copyright (C) 2018 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 -- Git version: -3.0.0 -- Git version template : /data/SIMPLE-3.0.1/cmake/Modules/GitVersion.h.in -- Git version template : /data/SIMPLE-3.0.1/lib/simple/SimpleGitVersion.h -- Fortran compiler: mpif90 -- 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 -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: /lib64/libfftw3f.a;/lib64/libfftw3.a;/lib64/libfftw3f_threads.a -- JBIG_LIBRARY: /usr/lib64/libjbig2dec.so.0 -- JPEG_LIBRARY: /usr/lib64/libjpeg.so -- LZMA_LIBRARY: /usr/lib64/liblzma.so.5 -- Z_LIBRARY: /usr/lib64/libz.so -- Executing: /data/openmpi/bin/mpif90 -dumpversion -- SIMPLE CUDA LIBRARY /data/SIMPLE-3.0.1/src/cuda/CUDA.F90;/data/SIMPLE-3.0.1/src/cuda/cublas_fortran_iso.f90;/data/SIMPLE-3.0.1/src/cuda/cuda_h.F90;/data/SIMPLE-3.0.1/src/cuda/cuda_runtime_h.F90;/data/SIMPLE-3.0.1/src/cuda/cuda_unknowns.F90;/data/SIMPLE-3.0.1/src/cuda/simple_cuda.f90;/data/SIMPLE-3.0.1/src/cuda/simple_cuda_kernels.f90;/data/SIMPLE-3.0.1/src/cuda/simple_cuda_timer.f90 -- EXTRA_LIBS /lib64/libfftw3f.a;/lib64/libfftw3.a;/lib64/libfftw3f_threads.a;/usr/lib64/libtiff.so;/usr/lib64/libjbig2dec.so.0;/usr/lib64/libjpeg.so;/usr/lib64/liblzma.so.5;/usr/lib64/libz.so;-lm;SIMPLE3.0.0;/lib64/libfftw3f.a;/lib64/libfftw3.a;/lib64/libfftw3f_threads.a;/usr/lib64/libtiff.so;/usr/lib64/libjbig2dec.so.0;/usr/lib64/libjpeg.so;/usr/lib64/liblzma.so.5;/usr/lib64/libz.so;-lm -- Found Perl: /usr/bin/perl (found version "5.26.3") -- Located pre-built gui binary for linux -- Set runtime variables -- Test directories tests/test_angres;tests/test_ansi_colors;tests/test_bal_part_prob;tests/test_binoris;tests/test_cartcorr_sanity;tests/test_chiara_HT;tests/test_chiara_NLmean;tests/test_chiara_binarize_cavgs;tests/test_chiara_cc;tests/test_chiara_cc_score;tests/test_chiara_ctf;tests/test_chiara_micctf;tests/test_chiara_ppca;tests/test_chiara_try;tests/test_corrs2weights;tests/test_corrweights;tests/test_extr_frac;tests/test_fileio;tests/test_ft_expanded;tests/test_gencorrs_fft;tests/test_graphene_mask;tests/test_imgfile;tests/test_inside_write;tests/test_install;tests/test_laplace_solver;tests/test_list_files;tests/test_maxnloc;tests/test_multinomal;tests/test_nano_mask;tests/test_order_corr;tests/test_parse;tests/test_phasecorr;tests/test_phaseplate_correct_fsc;tests/test_rank_weights;tests/test_replace_substr;tests/test_serialize;tests/test_shiftsrch;tests/test_simd;tests/test_simnano;tests/test_sp_project;tests/test_speed;tests/test_srch;tests/test_starfile;tests/test_sym;tests/test_tseries_neigh;tests/test_tvfilter;tests/test_ui;tests/test_units -- Configuring done -- Generating done -- Build files have been written to: /data/SIMPLE-3.0.1/build

make -j install Scanning dependencies of target simple_modules Scanning dependencies of target simple_args Scanning dependencies of target gui_unix Creating simple_module [ 0%] Installing precompiled GUI ... [ 0%] Built target simple_args [ 0%] Built target simple_modules Scanning dependencies of target SIMPLE3.0.0 [ 0%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/defs/simple_defs_fname.f90.o [ 0%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/json_kinds.f90.o [ 0%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/defs/simple_ansi_ctrls.f90.o [ 0%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/defs/simple_defs_atoms.f90.o [ 1%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/defs/simple_fftw3.f90.o [ 1%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/defs/simple_defs_conv.f90.o [ 1%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/simple_r8lib.f90.o [ 2%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/fsys/fox_m_fsys_abort_flush.F90.o [ 3%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/fsys/fox_m_fsys_string.F90.o [ 3%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/fsys/fox_m_fsys_realtypes.f90.o [ 3%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/fileio/simple_tifflib.f90.o [ 3%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/fsys/fox_m_fsys_array_str.F90.o [ 4%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/utils/fox_m_utils_mtprng.F90.o [ 4%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/wkml/m_wkml_color_def.F90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/fsys/fox_m_fsys_format.F90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/fsys/fox_m_fsys_parse_input.F90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/utils/fox_m_utils_uuid.F90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/json_parameters.f90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/fsys/fox_m_fsys_count_parse_input.F90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/simple_qr_solve.f90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/common/m_common_charset.F90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/defs/simple_defs.f90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/common/m_common_content_model.F90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/common/m_common_error.F90.o [ 5%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/fsys/fox_m_fsys_string_list.F90.o [ 6%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/json_string_utilities.f90.o [ 6%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/fileio/simple_error.f90.o [ 7%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/simple_testfuns.f90.o [ 7%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/simple_timer_omp.f90.o [ 7%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/main/simple_starfile_wrapper.f90.o [ 7%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/main/simple_ori_light.f90.o [ 7%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/ops/simple_winfuns.f90.o [ 8%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/common/m_common_notations.F90.o [ 8%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/dom/m_dom_error.f90.o [ 8%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/common/m_common_io.F90.o [ 9%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/xml/common/m_common_elstack.F90.o [ 10%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/simple_strings.f90.o [ 10%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/simple_math.f90.o [ 10%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/json_value_module.f90.o [ 13%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/fileio/simple_syslib.f90.o [ 13%] Building Fortran object lib/CMakeFiles/SIMPLE3.0.0.dir/utils/simple_hash.f90.o [ 13%] Building 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bin/CMakeFiles/simple_test_tvfilter.dir/tests/test_tvfilter/simple_test_tvfilter.f90.o [ 86%] Building Fortran object bin/CMakeFiles/simple_test_srch.dir/tests/test_srch/simple_volpft_srch_tester.f90.o [ 86%] Building Fortran object bin/CMakeFiles/simple_test_ansi_colors.dir/tests/test_ansi_colors/simple_test_ansi_colors.f90.o [ 79%] Building Fortran object bin/CMakeFiles/simple_test_extr_frac.dir/tests/test_extr_frac/simple_test_extr_frac.f90.o [ 79%] Building Fortran object bin/CMakeFiles/simple_test_cartcorr_sanity.dir/tests/test_cartcorr_sanity/simple_test_cartcorr_sanity.f90.o [ 79%] Building Fortran object bin/CMakeFiles/simple_test_maxnloc.dir/tests/test_maxnloc/simple_test_maxnloc.f90.o [ 88%] Linking CXX executable simple_test_laplace_solver [ 88%] Linking CXX executable simple_test_ui [ 88%] Linking CXX executable simple_test_replace_substr [ 88%] Linking CXX executable simple_test_simd [ 88%] Linking CXX executable simple_test_extr_frac [ 88%] Linking CXX executable simple_test_corrs2weights [ 88%] Linking CXX executable simple_test_multinomal [ 90%] Linking CXX executable simple_test_angres [ 90%] Linking CXX executable simple_test_tseries_neigh [ 91%] Linking CXX executable simple_test_graphene_mask [ 91%] Linking CXX executable simple_test_ansi_colors [ 91%] Linking CXX executable simple_test_order_corr [ 91%] Linking CXX executable simple_test_maxnloc [ 91%] Linking CXX executable simple_test_phaseplate_correct_fsc [ 92%] Linking CXX executable simple_test_starfile [ 92%] Linking CXX executable simple_test_rank_weights [ 92%] Linking CXX executable simple_test_inside_write [ 92%] Linking CXX executable simple_test_list_files [ 92%] Linking CXX executable simple_test_corrweights [ 92%] Linking CXX executable simple_test_phasecorr [ 92%] Linking CXX executable simple_test_tvfilter [ 92%] Linking CXX executable simple_test_bal_part_prob [ 93%] Linking CXX executable simple_test_parse [ 93%] Linking CXX executable simple_test_binoris [ 93%] Linking CXX executable simple_test_sym [ 93%] Linking CXX executable simple_test_serialize [ 93%] Linking CXX executable simple_test_install [ 93%] Linking CXX executable simple_test_sp_project [ 93%] Linking CXX executable simple_test_chiara_micctf /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 94%] Linking CXX executable simple_test_nano_mask [ 94%] Linking CXX executable simple_test_cartcorr_sanity [ 94%] Linking CXX executable quant_exec [ 94%] Linking CXX executable simple_test_chiara_cc_score /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 94%] Linking CXX executable simple_test_imgfile [ 94%] Linking CXX executable simple_test_chiara_ppca [ 94%] Linking CXX executable simple_test_fileio [ 94%] Built target simple_test_replace_substr [ 94%] Built target simple_test_corrweights /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 94%] Built target simple_test_extr_frac [ 94%] Built target simple_test_laplace_solver /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_corrs2weights [ 95%] Built target simple_test_list_files /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_simd [ 95%] Building Fortran object bin/CMakeFiles/simple_test_speed.dir/tests/test_speed/simple_test_speed.f90.o [ 95%] Built target simple_test_ansi_colors /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_graphene_mask [ 95%] Built target simple_test_tseries_neigh [ 95%] Built target simple_test_phaseplate_correct_fsc [ 95%] Built target simple_test_starfile /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_multinomal [ 95%] Built target simple_test_rank_weights [ 95%] Linking CXX executable simple_test_chiara_NLmean /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_maxnloc /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_order_corr /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_bal_part_prob [ 95%] Built target simple_test_ui [ 95%] Built target simple_test_parse [ 95%] Linking CXX executable simple_test_units /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_angres /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_binoris /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_sym [ 95%] Built target simple_test_chiara_cc_score [ 95%] Building Fortran object bin/CMakeFiles/simple_test_ft_expanded.dir/tests/test_ft_expanded/simple_test_ft_expanded.f90.o [ 95%] Linking CXX executable simple_test_chiara_HT /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Linking CXX executable simple_test_speed /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 95%] Built target simple_test_phasecorr [ 95%] Built target simple_test_tvfilter [ 95%] Built target simple_test_inside_write /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 97%] Linking CXX executable simple_test_chiara_cc [ 97%] Built target simple_test_serialize [ 97%] Linking CXX executable simple_test_ft_expanded [ 97%] Linking CXX executable simple_test_simnano [ 97%] Linking CXX executable simple_test_chiara_binarize_cavgs [ 97%] Building Fortran object bin/CMakeFiles/simple_test_srch.dir/tests/test_srch/simple_test_srch.f90.o [ 98%] Linking CXX executable simple_test_chiara_try [ 98%] Linking CXX executable single_exec /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 98%] Built target simple_test_install [ 98%] Built target simple_test_chiara_micctf /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 98%] Built target simple_test_imgfile [ 98%] Built target simple_test_sp_project [ 98%] Built target simple_test_fileio [ 98%] Linking CXX executable simple_test_srch /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [ 99%] Linking CXX executable simple_test_chiara_ctf [ 99%] Linking CXX executable simple_private_exec [100%] Built target simple_test_cartcorr_sanity [100%] Built target simple_test_chiara_ppca [100%] Linking CXX executable simple_test_gencorrs_fft [100%] Linking CXX executable simple_test_shiftsrch [100%] Built target simple_test_nano_mask [100%] Built target simple_test_units /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target simple_test_chiara_NLmean [100%] Built target simple_test_chiara_HT /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target simple_test_chiara_cc [100%] Built target simple_test_ft_expanded [100%] Linking CXX executable simple_exec /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target quant_exec [100%] Built target simple_test_chiara_try /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target simple_test_chiara_binarize_cavgs /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target simple_test_chiara_ctf /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target simple_test_simnano [100%] Built target simple_test_speed /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target simple_test_gencorrs_fft /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target simple_test_shiftsrch [100%] Built target simple_test_srch /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target simple_private_exec [100%] Built target single_exec /usr/bin/ld: warning: libgfortran.so.3, needed by /data/openmpi/lib/libmpi_usempi.so, may conflict with libgfortran.so.5 [100%] Built target simple_exec Install the project... -- Install configuration: "RELEASE" -- Installing: /data/SIMPLE-3.0.1/add2.bashrc -- Installing: /data/SIMPLE-3.0.1/add2.tcshrc -- Installing: /data/SIMPLE-3.0.1/lib/libSIMPLE3.0.0.a -- Installing: /data/SIMPLE-3.0.1/lib/simple/simple_varlist.txt -- Up-to-date: /data/SIMPLE-3.0.1/simple_distr_config.env -- Installing: /data/SIMPLE-3.0.1/bin/simple_exec -- Installing: /data/SIMPLE-3.0.1/bin/single_exec -- Installing: /data/SIMPLE-3.0.1/bin/simple_private_exec -- Installing: /data/SIMPLE-3.0.1/bin/quant_exec -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_angres -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_ansi_colors -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_bal_part_prob -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_binoris -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_cartcorr_sanity -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_chiara_HT -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_chiara_NLmean -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_chiara_binarize_cavgs -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_chiara_cc -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_chiara_cc_score -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_chiara_ctf -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_chiara_micctf -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_chiara_ppca -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_chiara_try -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_corrs2weights -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_corrweights -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_extr_frac -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_fileio -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_ft_expanded -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_gencorrs_fft -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_graphene_mask -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_imgfile -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_inside_write -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_install -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_laplace_solver -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_list_files -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_maxnloc -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_multinomal -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_nano_mask -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_order_corr -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_parse -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_phasecorr -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_phaseplate_correct_fsc -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_rank_weights -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_replace_substr -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_serialize -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_shiftsrch -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_simd -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_simnano -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_sp_project -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_speed -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_srch -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_starfile -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_sym -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_tseries_neigh -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_tvfilter -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_ui -- Installing: /data/SIMPLE-3.0.1/bin/simple_test_units

Installation complete.

Please ensure the following variables are set properly in add2.rc file:
SIMPLE_EMAIL SIMPLE_QSYS SIMPLE_PATH
To use SIMPLE, append the relevant add2. to your HOME shell rc file:
bash$ cat add2.bashrc >> ~/.bashrc
tcsh$ cat add2.tcshrc >> ~/.tcshrc

For minimal installation to work correctly add: /data/SIMPLE-3.0.1/bin and /data/SIMPLE-3.0.1/scripts to your PATH environment variable.

hael commented 2 years ago

Thanks or the info. Would you be able to clone the development branch of SIMPLE and see how that works out for you (clone https://github.com/hael/SIMPLE.git) rather than using the 3.0.1 release. Joe just pushed quite major changes to the GUI that may impact on your issues. Let me know how you go.

donghuachensu commented 2 years ago

I tried: git clone https://github.com/hael/SIMPLE.git Then did the rest, and still the same problem.

In fact I found there are simple and simple_multiuser in bin folder under build, but not in bin folder of SIMPLE.

cosmopolitanadmin commented 2 years ago

Please can you try a fresh clone of the repository and build again. Found an issue with the handling of the install prefix which has been addressed

donghuachensu commented 2 years ago

Now the installation seems to be fine since I can see commands simple and simple_multiuser in bin folder of SIMPLE. Thank you!