Why is my bin folder empty?

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If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
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(3) if the problems occur compiling in serial/in parallel
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(5) the relevant compiler error message
Peace
Posts: 21
Joined: Wed Jan 18, 2023 9:39 am

Why is my bin folder empty?

Post by Peace » Thu Mar 16, 2023 12:32 pm

I downloaded yambo 5.0.1 then inside the file I ran the 2 commands : ` ./configure ` then ` make all ` . But my ./bin directory is always empty .
Can you please help me to resolve this issue?
I attached the log and config files
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Salma NAIMI
PhD student
Mohamed 5 university-Rabat

User avatar
Davide Sangalli
Posts: 610
Joined: Tue May 29, 2012 4:49 pm
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Re: Why is my bin folder empty?

Post by Davide Sangalli » Thu Mar 16, 2023 11:53 pm

Dear Salma,
if you check the file log/config_netcdf-c-4.7.4.log you will see the following error:

Code: Select all

checking for library containing deflate... no
configure: error: Can't find or link to the z library. Turn off netCDF-4 and      DAP clients with --disable-netcdf-4 --disable-dap, or see config.log for errors.
One solution would be to install the libz on your machine and then re-run both ./configure and make all

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

Peace
Posts: 21
Joined: Wed Jan 18, 2023 9:39 am

Re: Why is my bin folder empty?

Post by Peace » Tue Apr 04, 2023 11:59 am

Dear Davide

I installed from the zlib.net website, zlib source code, version 1.2.13, zipfile format (1594K, SHA-256 hash d233fca7cf68db4c16dc5287af61f3cd01ab62495224c66639ca3da537701e42).

By following the steps in the link bellow:
https://www.youtube.com/watch?v=6as-wCwEYno

However my bin/ folder is always empty. I checked the file log/config_netcdf-c-4.7.4.log again and the same error always occur.

Kind regards,
Salma NAIMI
PhD student
Mohamed 5 university-Rabat

User avatar
Davide Sangalli
Posts: 610
Joined: Tue May 29, 2012 4:49 pm
Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
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Re: Why is my bin folder empty?

Post by Davide Sangalli » Tue Apr 04, 2023 12:56 pm

When you run the configure, what do you see at this step:

Code: Select all

checking for library containing deflate...
Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

Peace
Posts: 21
Joined: Wed Jan 18, 2023 9:39 am

Re: Why is my bin folder empty?

Post by Peace » Tue Apr 04, 2023 2:26 pm

When I ran the command ./configure, the only places where deflate is used are :

Code: Select all

 checking for deflate in -lz ... yes
checking for deflate in -lsz... no 
You'll find bellow a copy of what's generated in my terminal when I run the command ./configure

Code: Select all

(base) salma@salma-Precision-3640-Tower:~/Desktop/yambo$ ./configure
checking for vim... no
checking for vi... vi
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for struct mallinfo.arena... yes
checking for git... yes
checking for malloc.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking whether lstat correctly handles trailing slash... yes
checking whether stat accepts an empty string... no
checking whether make sets $(MAKE)... yes
checking for the size of a pointer... 8 bytes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for GNU make... make
checking for ar... ar
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking if the current OS is supported... yes
configure: WIDESETUP: using build_os="linux"
configure: WIDESETUP: using F90SUFFIX=".f90"
configure: WIDESETUP: using AR="ar"
configure: WIDESETUP: using AR_FLAGS="-r"
checking for Fortran flag to compile .f90 files... none
checking for gfortran kind and version... gfortran GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 unknown
checking for specific gfortran flags... -O3 -g -mtune=native
checking for specific Open-MP flags... -fopenmp
checking for specific gcc flags... -O2
checking for specific unoptimized flags... -O0 -g -mtune=native
checking for specific NETCDF flags... -DgFortran
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran...  -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking for external C routine (test) naming scheme... test_
checking for Fortran flag needed to accept free-form source... none
checking fortran 90 modules inclusion flag... -I
configure: testing C-preprocessor gcc -E -P
checking if C precompiler works on C source... yes
configure: testing FC-preprocessor gfortran -E -P -cpp
checking if FC precompiler works on FC source... yes
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking if Fortran 77 compiler gfortran works... yes
checking for mpipgifort... no
checking for mpiifort... no
checking for mpifort... mpifort
checking for a working mpif.h... yes
checking for mpifort... no
checking for mpifort... mpifort
checking for mpipgicc... no
checking for mpiicc... no
checking for mpicc... mpicc
checking for a working mpi.h... yes
checking for MPI version... Open MPI v4.0.3, package: Debian OpenMPI, ident: 4.0.3, repo rev: v4.0.3, Mar 03, 2020
checking for /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/mpif.h... no
checking for /usr/lib/x86_64-linux-gnu/openmpi/include/mpif.h... yes
checking how to get verbose linking output from mpifort... -v
checking for Fortran 77 libraries of mpifort...  -L/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lquadmath -lpthread
checking for caxpy... no
checking for ATL_xerbla in -latlas... no
checking for caxpy in -lblas... yes
checking for daxpy in -ldaxpy... no
checking for caxpy in -lcxml... no
checking for caxpy in -ldxml... no
checking for caxpy in -lscs... no
checking for caxpy in -lcomplib.sgimath... no
checking for caxpy in -lblas... (cached) yes
checking for caxpy in -lessl... no
checking for caxpy in -lblas... (cached) yes
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking for cheev... no
checking for cheev in -llapack... yes
checking for dlaran_ in -llapack... no
checking for FFT... checking for FFT... Internal FFTW3
checking for dlopen in -ldl... yes
checking for deflate in -lz ... yes
checking for deflate in -lsz... no
checking for dlopen in -ldl... (cached) yes
checking for curl_version in -lcurl... no
checking for cos in -lm... yes
checking for HDF5 using h5pfc/h5fc system compilers... no
checking for HDF5 using automatic library list... no
checking for internal HDF5 library... already compiled
checking for internal NETCDF library... to be compiled
checking for YAML library... no
checking for FUTILE library... no
checking for internal IOTK library... already compiled
checking for ETSF_IO Library... no
checking for libxc... Compatible external LibXC not found/specified. Internal to be compiled.
checking for CUDA support... no
checking for NVTX support... configure: creating ./config.status
config.status: creating config/setup
config.status: creating config/mk/global/defs.mk
config.status: creating config/report
config.status: creating config/msg_ydb
config.status: creating src/wf_and_fft/sgfft.F
config.status: creating src/tools/.objects
config.status: creating config/mk/local/defs.mk
config.status: creating config/mk/defs.mk
config.status: creating sbin/compilation/helper.inc.sh
config.status: creating include/branch.inc
config.status: creating include/driver/editor.h
config.status: creating lib/archive/git.list
config.status: creating include/headers/common/have_malloc.h
config.status: include/headers/common/have_malloc.h is unchanged
#
# [VER] 5.1
#
# Legend: [E]=external library [C]=internal lib to be compiled [I]=internal lib already compiled [X]=used [-]=not used
# 
# - GENERAL CONFIGURATIONS -
# 
# [SYS] linux@x86_64
# [SRC] /home/salma/Desktop/yambo
# [BRN] 5.1
# [CMP] /home/salma/Desktop/yambo
# [TGT] /home/salma/Desktop/yambo
# [BIN] /home/salma/Desktop/yambo/bin
# [LIB] /home/salma/Desktop/yambo/lib/external
#
# [EDITOR] vi
# [ MAKE ] make
#
# [-] Double precision
# [X] Keep object files
# [X] Run-Time timing profile 
# [-] Run-Time memory profile 
#
# - SCRIPTS -
#
# [-] YDB: Yambo DataBase
# [-] YAMBOpy: Yambo Python scripts
# 
# - PARALLEL/CUDA SUPPORT -
#
# [-] CUDA
# [E] MPI
# [-] OpenMP
# 
# - I/O -
#
# [-]: Parallel I/O  
# [I]: HDF5 
# [C]: NETCDF Large Files Support enabled, Version 4
# [-]: Parallel NETCDF 
# [-]: Parallel HDF5  
# 
# - LIBRARIES - 
#
# [-] FUTILE  :  
#                  
# [-] YAML    :  
#                  
# [I] IOTK    : /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/lib/libiotk.a (QE hdf5-support)
#                 -I/home/salma/Desktop/yambo/lib/external/gfortran/mpifort/include/
# [-] ETSF_IO :  
#                  
# [C] NETCDF  : /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/lib/libnetcdff.a /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/lib/libnetcdf.a 
#                 -I/home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/include -I/home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/include 
# [I] HDF5    : /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/lib/libhdf5_hl_fortran.a /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/lib/libhdf5_fortran.a /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/lib/libhdf5_hl.a /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/lib/libhdf5.a -lz -lm -ldl
#                 -I/home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/include
#
# > MATH: (Internal FFTW3) 
#
# [I] FFT       : /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/lib/libfftw3.a
#                 -I/home/salma/Desktop/yambo/lib/external/gfortran/mpifort/include/
# [E] BLAS      : -lblas
# [E] LAPACK    : -llapack
# [-] SCALAPACK :  
# [-] BLACS     : 
# [-] PETSC     :  
#                  
# [-] SLEPC     :  
#                  
#
# > OTHERs
#
# [C] LibXC     : /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/lib/libxcf90.a /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/lib/libxcf03.a  /home/salma/Desktop/yambo/lib/external/gfortran/mpifort/lib/libxc.a
#                 -I/home/salma/Desktop/yambo/lib/external/gfortran/mpifort/include
# [E] MPI       : -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi 
#                 -I/usr/lib/x86_64-linux-gnu/openmpi/include 
#
# - COMPILERS -
#
# FC kind = gfortran GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
# MPI kind= Open MPI v4.0.3, package: Debian OpenMPI, ident: 4.0.3, repo rev: v4.0.3, Mar 03, 2020
#
# [ CPP ] gcc -E -P -D_HDF5_LIB -D_HDF5_IO -D_MPI -D_FFTW       -D_TIMING     -D_P2Y_QEXSD_HDF5
# [ FPP ] gfortran -E -P -cpp -D_HDF5_LIB -D_HDF5_IO -D_MPI -D_FFTW       -D_TIMING    
# [ CC  ] mpicc -O2 -D_C_US -D_FORTRAN_US
# [ FC  ] mpifort -O3 -g -mtune=native    
# [ FCUF] -O0 -g -mtune=native 
# [ F77 ] mpifort -O3 -g -mtune=native 
# [ F77U] -O0 -g -mtune=native 
# [Cmain] 
#
Salma NAIMI
PhD student
Mohamed 5 university-Rabat

User avatar
Davide Sangalli
Posts: 610
Joined: Tue May 29, 2012 4:49 pm
Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
Contact:

Re: Why is my bin folder empty?

Post by Davide Sangalli » Tue Apr 04, 2023 2:59 pm

Run

Code: Select all

make distclean
before re-running the configure and make.

Best,
D
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

Peace
Posts: 21
Joined: Wed Jan 18, 2023 9:39 am

Re: Why is my bin folder empty?

Post by Peace » Tue Apr 04, 2023 3:13 pm

I ran "make distclean" then "./configure" then "make all" , but unfortunatly my bin is always empty.

In a similar post someone suggested that after installing zlib, to use the two commands bellow then resume the ''make all''

Code: Select all

make clean netcdf
make clean netcdff
So I ran the 2 commands above then ''make all'' , but the bin/ folder is always empty. You'll find bellow what I get in the terminal after typing the command "make all"

Code: Select all

(base) salma@salma-Precision-3640-Tower:~/Desktop/yambo$ make all
	[yambo] Compilation Precision check
	           to compile in SINGLE
	[netcdf-c-4.7.4] configuration
	[netcdf-c-4.7.4]  compilation
	[netcdf-c-4.7.4] installation
chmod: cannot access '/home/salma/Desktop/yambo/lib/external/gfortran/mpifort/v4/serial/lib*/*netcdf*a': No such file or directory
	[libxc-5.1.5] configuration
	[libxc-5.1.5]  compilation
	[libxc-5.1.5] installation
chmod: cannot access '/home/salma/Desktop/yambo/lib/external/gfortran/mpifort/lib*/*xc*a': No such file or directory
	[lib/qe_pseudo] qe_pseudo (checking work to be done)
	[lib/qe_pseudo] libqe_pseudo.a (lib)
	[lib/slatec] slatec (checking work to be done)
	[lib/slatec] libslatec.a (lib)
	[lib/math77] math77 (checking work to be done)
	[lib/math77] libmath77.a (lib)
	[lib/local] local (checking work to be done)
	[lib/local] liblocal.a (lib)
	[lib/yambo/driver/src/interface] interface (checking work to be done)
	[lib/yambo/driver/src/main] main (checking work to be done)
	[lib/yambo/driver/src/options] options (checking work to be done)
	[lib/yambo/driver/src/interface] get_running_tool
	[lib/yambo/driver/src/interface] get_running_project
	[lib/yambo/driver/src/interface] get_runlevel
	[lib/yambo/driver/src/interface] get_libraries
	[lib/yambo/driver/src/interface] get_version
	[lib/yambo/driver/src/interface] mod_C_driver
	[lib/yambo/driver/src/interface] C_driver_transfer
	[lib/yambo/driver/src/interface] libyambo_Ydriver_interface.a (lib)
	[lib/yambo/driver/src/main] launcher
	[lib/yambo/driver/src/main] command_line
	[lib/yambo/driver/src/main] input_file
	[lib/yambo/driver/src/main] load_environments
	[lib/yambo/driver/src/main] options_maker
	[lib/yambo/driver/src/main] title
	[lib/yambo/driver/src/main] tool_init
	[lib/yambo/driver/src/main] usage
	[lib/yambo/driver/src/main] use_me
	[lib/yambo/driver/src/main] libyambo_Ydriver_main.a (lib)
	[lib/yambo/driver/src/options] options_help
	[lib/yambo/driver/src/options] libyambo_Ydriver_options.a (lib)
	[src/driver] driver (checking work to be done)
	[src/tools] tools (checking work to be done)
	[src/modules] modules (checking work to be done)
	[src/memory] memory (checking work to be done)
	[src/matrices] matrices (checking work to be done)
	[src/linear_algebra] linear_algebra (checking work to be done)
	[src/parallel] parallel (checking work to be done)
	[src/parser] parser (checking work to be done)
	[src/communicate] communicate (checking work to be done)
	[src/common] common (checking work to be done)
	[src/timing] timing (checking work to be done)
	[src/Yio] Yio (checking work to be done)
	[src/io] io (checking work to be done)
	[src/xc_functionals] xc_functionals (checking work to be done)
	[src/interface] interface (checking work to be done)
	[src/stop_and_restart] stop_and_restart (checking work to be done)
	[src/wf_and_fft] wf_and_fft (checking work to be done)
	[src/bz_ops] bz_ops (checking work to be done)
	[src/coulomb] coulomb (checking work to be done)
	[src/interpolate] interpolate (checking work to be done)
	[src/qp_control] qp_control (checking work to be done)
	[src/setup] setup (checking work to be done)
	[src/tddft] tddft (checking work to be done)
	[src/dipoles] dipoles (checking work to be done)
	[src/pol_function] pol_function (checking work to be done)
	[src/qp] qp (checking work to be done)
	[src/acfdt] acfdt (checking work to be done)
	[src/bse] bse (checking work to be done)
	[src/driver] options_control
	[src/driver] options_interfaces
	[src/driver] options_projects
	[src/driver] options_yambo
	[src/driver] options_ypp
	[src/driver] libdriver.a (lib)
	[src/tools] ct_cptimer
	[src/tools] c_printing
	[src/tools] io
	[src/tools] stack
	[src/tools] memstat
	[src/tools] libtools.a (lib)
make[2]: *** [/home/salma/Desktop/yambo/config/mk/local/rules.mk:9: mod_pars.o] Error 1
Fatal Error: Cannot open module file ‘netcdf.mod’ for reading at (1): No such file or directory
	[driver] yambo (checking work to be done)
yambo linking failed. Check log/compile_yambo.log
Fatal Error: Cannot open module file ‘netcdf.mod’ for reading at (1): No such file or directory
make[1]: *** [config/mk/global/actions/compile_yambo.mk:42: yambo] Error 1
yambo build failed
Salma NAIMI
PhD student
Mohamed 5 university-Rabat

User avatar
Davide Sangalli
Posts: 610
Joined: Tue May 29, 2012 4:49 pm
Location: Via Salaria Km 29.3, CP 10, 00016, Monterotondo Stazione, Italy
Contact:

Re: Why is my bin folder empty?

Post by Davide Sangalli » Tue Apr 04, 2023 3:35 pm

Ok. The

Code: Select all

log/*netcdf*.log
must still contain an error message. But it should be different now.

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

Peace
Posts: 21
Joined: Wed Jan 18, 2023 9:39 am

Re: Why is my bin folder empty?

Post by Peace » Tue Apr 04, 2023 4:27 pm

Dear Davide,

Yes, you're right. Thank you for assisting me. I attached the new log/ folder
You do not have the required permissions to view the files attached to this post.
Salma NAIMI
PhD student
Mohamed 5 university-Rabat

Peace
Posts: 21
Joined: Wed Jan 18, 2023 9:39 am

Re: Why is my bin folder empty?

Post by Peace » Wed Apr 05, 2023 12:12 pm

Dear Davide,
I still can't find a way to compile Yambo successfully, especially that I'm beginner to the code. I need your help please!
I want to mention also that I'm using Quantum ESPRESSO 7.0 and UBUNTU 20.04.6 in case those information were useful
Salma NAIMI
PhD student
Mohamed 5 university-Rabat

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