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simple_multiuser GUI can't start on Cento7 #8

Open
qiyubio opened this issue Apr 15, 2021 · 11 comments
Open

simple_multiuser GUI can't start on Cento7 #8

qiyubio opened this issue Apr 15, 2021 · 11 comments

Comments

@qiyubio
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qiyubio commented Apr 15, 2021

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
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Collaborator

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
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Author

qiyubio commented Apr 23, 2021

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
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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 simple_test_*). Did I make any silly mistake?

@hael
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Owner

hael commented Nov 5, 2021 via email

@donghuachensu
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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
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Collaborator

cosmopolitanadmin commented Nov 9, 2021 via email

@donghuachensu
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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
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In file included from /usr/include/sys/types.h:25,
from /data/SIMPLE-3.0.1/src/fileio/simple_posix.c:19:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]

warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"

^~~~~~~
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[ 94%] Linking CXX executable simple_test_imgfile
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/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
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/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
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/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
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[ 95%] Built target simple_test_multinomal
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[ 95%] Linking CXX executable simple_test_chiara_NLmean
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[ 95%] Built target simple_test_maxnloc
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/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
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/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
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[ 95%] Built target simple_test_binoris
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[ 95%] Built target simple_test_sym
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[ 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
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[ 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
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[ 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
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[ 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
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Owner

hael commented Nov 18, 2021

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
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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
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Collaborator

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

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