About the Step 5 in tutorial, I get Fatal error: <string> no such file or directory #26415

Hatomzre · 2023-12-24T06:27:39Z

Hatomzre
Dec 24, 2023

When I try to follow the step 5 in tutorial, I run 'make -j 8' and get "Fatal error: : no such file or directory". I have no idea about this error and how I should fix it. (ps. examples function well)

Answered by neutralchaos18

Mar 24, 2024

Because of your kernel file extension the compiler is attempting to compile moose in c, rather than its natural c++ language. The kernel file should be '.C' (uppercase dot c) and not '.c' (lowercase dot c).

This issue here has a similar cause and effect: #18050

This is what a successful output looks like. Note that it says 'Compiling C++' rather than C, as it does with your attempts.

(moose) neutralchaos@neutralchaos-To-be-filled-by-O-E-M:~/projects/babbler$ make -j 4
Checking if header needs updating: /home/neutralchaos/projects/moose/framework/include/base/MooseRevision.h...
Creating Unity /home/neutralchaos/projects/babbler/build/unity_src/kernels_Unity.C
Compiling C++ (in opt mode) /h…

View full answer

GiudGiud · 2023-12-24T11:29:09Z

GiudGiud
Dec 24, 2023
Collaborator

Hello

could you please run the diagnostics script in mosoe/scripts?

Guillaume

3 replies

Hatomzre Dec 24, 2023
Author

Does the diagnostics script means 'babbler/scripts/install-format-hook.sh' or some files in 'moose/scripts'. Could you give me more details? Thanks.

GiudGiud Dec 24, 2023
Collaborator

the last ls you ran, you can see diagnostics.sh. That s the diagnostic script.

No need to send screenshots btw, you can copy paste console output

Hatomzre Dec 24, 2023
Author

Thanks. The result is:

Sun Dec 24 20:11:47 CST 2023
diagnostics.sh: 83: [: Linux: unexpected operator
/usr/bin/lsb_release
No LSB modules are available.
-e
System Arch: Distributor ID: Ubuntu Description: Ubuntu 22.04.3 LTS Release: 22.04 Codename: jammy
-e
MOOSE Package Version: Custom Build
diagnostics.sh: 64: [: Linux: unexpected operator
-e
CPU Count: 32
diagnostics.sh: 73: [: Linux: unexpected operator
-e
Memory Free: 14903.668 MB
/home/moose/miniforge/envs/moose/bin/mpicc
-e
Variable `which $CC` check:
/home/moose/miniforge/envs/moose/bin/mpicc

$CC --version:
x86_64-conda-linux-gnu-cc (conda-forge gcc 10.4.0-19) 10.4.0
Copyright (C) 2020 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.
/home/moose/miniforge/envs/moose/bin/mpicc
-e
MPICC:
which mpicc:
        /home/moose/miniforge/envs/moose/bin/mpicc
mpicc -show:
        x86_64-conda-linux-gnu-cc -I/home/moose/miniforge/envs/moose/include -I/home/moose/miniforge/envs/moose/include -L/home/moose/miniforge/envs/moose/lib -Wl,-rpath,/home/moose/miniforge/envs/moose/lib -I/home/moose/miniforge/envs/moose/include -L/home/moose/miniforge/envs/moose/lib -Wl,-rpath -Wl,/home/moose/miniforge/envs/moose/lib -Wl,--enable-new-dtags -lmpi

COMPILER x86_64-conda-linux-gnu-cc:
x86_64-conda-linux-gnu-cc (conda-forge gcc 10.4.0-19) 10.4.0
Copyright (C) 2020 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.
/home/moose/miniforge/envs/moose/bin/python
-e
Python:
        /home/moose/miniforge/envs/moose/bin/python
        Python 3.10.8
module: not found
-e
MODULES:
diagnostics.sh: 1: module: not found
-e
PETSc configure:
static const char *petscconfigureoptions = "--with-64-bit-indices --with-cxx-dialect=C++17 --with-debugging=no --with-fortran-bindings=0 --with-mpi=1 --with-openmp=1 --with-shared-libraries=1 --with-sowing=0 --download-fblaslapack=1 --download-hypre=1 --download-metis=1 --download-mumps=1 --download-ptscotch=1 --download-parmetis=1 --download-scalapack=1 --download-slepc=1 --download-strumpack=1 --download-superlu_dist=1 --with-hdf5-dir=${PREFIX} --with-make-np=16 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --with-x=0 --with-ssl=0 --with-mpi-dir=/home/moose/miniforge/envs/moose AR=${PREFIX}/bin/x86_64-conda-linux-gnu-ar RANLIB=${PREFIX}/bin/x86_64-conda-linux-gnu-ranlib CFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include   -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include   -march=nocona -mtune=haswell" CXXFLAGS="-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem ${PREFIX}/include  -march=nocona -mtune=haswell" CPPFLAGS="-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/moose/miniforge/envs/moose/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/moose/miniforge/envs/moose/include" FFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include   -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include   -I/home/moose/miniforge/envs/moose/include" FCFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include   -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include   -I/home/moose/miniforge/envs/moose/include" LDFLAGS="-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/moose/miniforge/envs/moose/lib -Wl,-rpath-link,/home/moose/miniforge/envs/moose/lib -L/home/moose/miniforge/envs/moose/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/moose/miniforge/envs/moose/lib -Wl,-rpath-link,/home/moose/miniforge/envs/moose/lib -L/home/moose/miniforge/envs/moose/lib" --prefix=/home/moose/miniforge/envs/moose";
-e
PETSc linked libraries:
        linux-vdso.so.1 (0x00007ffce9ff3000)
        libHYPRE-2.29.0.so => /home/moose/miniforge/envs/moose/lib/./libHYPRE-2.29.0.so (0x00007f1392f5e000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f1392f54000)
        libstrumpack.so.7.1 => /home/moose/miniforge/envs/moose/lib/./libstrumpack.so.7.1 (0x00007f1391f35000)
        libscalapack.so.2.2 => /home/moose/miniforge/envs/moose/lib/./libscalapack.so.2.2 (0x00007f139183e000)
        libsuperlu_dist.so.8 => /home/moose/miniforge/envs/moose/lib/./libsuperlu_dist.so.8 (0x00007f13916ba000)
        libparmetis.so => /home/moose/miniforge/envs/moose/lib/./libparmetis.so (0x00007f139167a000)
        libmetis.so => /home/moose/miniforge/envs/moose/lib/./libmetis.so (0x00007f139160f000)
        libhdf5.so.200 => /home/moose/miniforge/envs/moose/lib/./libhdf5.so.200 (0x00007f13911dd000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f13910f6000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f13910f1000)
        libmpifort.so.12 => /home/moose/miniforge/envs/moose/lib/./libmpifort.so.12 (0x00007f13910a0000)
        libmpi.so.12 => /home/moose/miniforge/envs/moose/lib/./libmpi.so.12 (0x00007f1390c84000)
        libgfortran.so.5 => /home/moose/miniforge/envs/moose/lib/./libgfortran.so.5 (0x00007f1390ad9000)
        libgcc_s.so.1 => /home/moose/miniforge/envs/moose/lib/./libgcc_s.so.1 (0x00007f1390abe000)
        libstdc++.so.6 => /home/moose/miniforge/envs/moose/lib/./libstdc++.so.6 (0x00007f13908db000)
        libgomp.so.1 => /home/moose/miniforge/envs/moose/lib/./libgomp.so.1 (0x00007f139089f000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f1390677000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f1394e3f000)
        libquadmath.so.0 => /home/moose/miniforge/envs/moose/lib/././libquadmath.so.0 (0x00007f139063c000)
        libzfp.so.0 => /home/moose/miniforge/envs/moose/lib/././libzfp.so.0 (0x00007f13905e8000)
        libmpicxx.so.12 => /home/moose/miniforge/envs/moose/lib/././libmpicxx.so.12 (0x00007f13905c9000)
        libcrypto.so.1.1 => /home/moose/miniforge/envs/moose/lib/././libcrypto.so.1.1 (0x00007f13902f7000)
        libcurl.so.4 => /home/moose/miniforge/envs/moose/lib/././libcurl.so.4 (0x00007f1390254000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f139024d000)
        libz.so.1 => /home/moose/miniforge/envs/moose/lib/././libz.so.1 (0x00007f1390232000)
        libnghttp2.so.14 => /home/moose/miniforge/envs/moose/lib/./././libnghttp2.so.14 (0x00007f1390206000)
        libssh2.so.1 => /home/moose/miniforge/envs/moose/lib/./././libssh2.so.1 (0x00007f13901c2000)
        libssl.so.1.1 => /home/moose/miniforge/envs/moose/lib/./././libssl.so.1.1 (0x00007f1390130000)
        libgssapi_krb5.so.2 => /home/moose/miniforge/envs/moose/lib/./././libgssapi_krb5.so.2 (0x00007f13900dd000)
        libkrb5.so.3 => /home/moose/miniforge/envs/moose/lib/././././libkrb5.so.3 (0x00007f1390006000)
        libk5crypto.so.3 => /home/moose/miniforge/envs/moose/lib/././././libk5crypto.so.3 (0x00007f138ffec000)
        libcom_err.so.3 => /home/moose/miniforge/envs/moose/lib/././././libcom_err.so.3 (0x00007f138ffe6000)
        libkrb5support.so.0 => /home/moose/miniforge/envs/moose/lib/././././libkrb5support.so.0 (0x00007f138ffd7000)
        libkeyutils.so.1 => /home/moose/miniforge/envs/moose/lib/././././libkeyutils.so.1 (0x00007f138ffce000)
        libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f138ffba000)
-e
ENVIRONMENT:
ADDR2LINE=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-addr2line
AR=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-ar
AS=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-as
BUILD=x86_64-conda-linux-gnu
CC=mpicc
CC_FOR_BUILD=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-cc
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include
CMAKE_ARGS=-DCMAKE_AR=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-strip
CMAKE_PREFIX_PATH=/home/moose/miniforge/envs/moose:/home/moose/miniforge/envs/moose/x86_64-conda-linux-gnu/sysroot/usr
CONDA_BUILD_SYSROOT=/home/moose/miniforge/envs/moose/x86_64-conda-linux-gnu/sysroot
CONDA_DEFAULT_ENV=moose
CONDA_EXE=/home/moose/miniforge/bin/conda
CONDA_PREFIX=/home/moose/miniforge/envs/moose
CONDA_PREFIX_1=/home/moose/miniforge
CONDA_PROMPT_MODIFIER=(moose)
CONDA_PYTHON_EXE=/home/moose/miniforge/bin/python
CONDA_SHLVL=2
CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
CPP=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-cpp
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/moose/miniforge/envs/moose/include
CXX=mpicxx
CXXFILT=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-c++filt
CXXFLAGS=-fvisibility-inlines-hidden  -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include -std=c++17
CXX_FOR_BUILD=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-c++
C_INCLUDE_PATH=/home/moose/miniforge/envs/moose/include
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/moose/miniforge/envs/moose/include
DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include
DEBUG_FFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe
DEBUG_FORTRANFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe
DISPLAY=172.23.32.1:0.0
ELFEDIT=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-elfedit
Eigen3_DIR=/home/moose/miniforge/envs/moose/libmesh/include/Eigen
F77=mpif77
F90=mpif90
F95=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-f95
FC=mpif90
FC_FOR_BUILD=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gfortran
FFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include
FORTRANFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/moose/miniforge/envs/moose/include
GCC=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gcc
GCC_AR=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ar
GCC_NM=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gcc-nm
GCC_RANLIB=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ranlib
GFORTRAN=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gfortran
GPROF=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-gprof
GSETTINGS_SCHEMA_DIR=/home/moose/miniforge/envs/moose/share/glib-2.0/schemas
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
GXX=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-g++
HDF5_DIR=/home/moose/miniforge/envs/moose
HOME=/home/moose
HOST=x86_64-conda-linux-gnu
HOSTTYPE=x86_64
LANG=C.UTF-8
LD=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-ld
LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/moose/miniforge/envs/moose/lib -Wl,-rpath-link,/home/moose/miniforge/envs/moose/lib -L/home/moose/miniforge/envs/moose/lib
LD_GOLD=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-ld.gold
LESSCLOSE=/usr/bin/lesspipe %s %s
LESSOPEN=| /usr/bin/lesspipe %s
LIBMESH_DIR=/home/moose/miniforge/envs/moose/libmesh
LOGNAME=moose
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
MESON_ARGS=--buildtype release
MOOSE_NO_CODESIGN=true
MPIHOME=/home/moose/miniforge/envs/moose
NAME=ythuang
NM=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-nm
OBJCOPY=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-objcopy
OBJDUMP=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-objdump
OLDPWD=/home/moose/projects/moose
PATH=/home/moose/miniforge/envs/moose/bin:/home/moose/miniforge/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Program Files (x86)/NVIDIA Corporation/PhysX/Common:/mnt/c/Program Files/NVIDIA Corporation/NVIDIA NvDLISR:/mnt/c/Users/10250/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/10250/AppData/Local/Programs/Microsoft VS Code/bin:/snap/bin:/home/moose/miniforge/envs/moose/wasp/bin
PETSC_DIR=/home/moose/miniforge/envs/moose
PROJ_LIB=/home/moose/miniforge/envs/moose/share/proj
PROJ_NETWORK=ON
PULSE_SERVER=unix:/mnt/wslg/PulseServer
PWD=/home/moose/projects/moose/scripts
RANLIB=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-ranlib
READELF=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-readelf
SHELL=/bin/bash
SHLVL=1
SIZE=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-size
STRINGS=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-strings
STRIP=/home/moose/miniforge/envs/moose/bin/x86_64-conda-linux-gnu-strip
TERM=xterm-256color
USER=moose
VTKINCLUDE_DIR=/home/moose/miniforge/envs/moose/libmesh-vtk/include/vtk-9.2
VTKLIB_DIR=/home/moose/miniforge/envs/moose/libmesh-vtk/lib
WASP_DIR=/home/moose/miniforge/envs/moose/wasp
WAYLAND_DISPLAY=wayland-0
WSL2_GUI_APPS_ENABLED=1
WSLENV=WT_SESSION:WT_PROFILE_ID:
WSL_DISTRO_NAME=Ubuntu
WSL_INTEROP=/run/WSL/334_interop
WT_PROFILE_ID={61c54bbd-c2c6-5271-96e7-009a87ff44bf}
WT_SESSION=ce2167ec-dde4-437d-9ace-5ef4867d50ff
XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop
XDG_RUNTIME_DIR=/run/user/1000/
XML_CATALOG_FILES=file:///home/moose/miniforge/envs/moose/etc/xml/catalog file:///etc/xml/catalog
_=/usr/bin/sh
_CE_CONDA=
_CE_M=
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
build_alias=x86_64-conda-linux-gnu
host_alias=x86_64-conda-linux-gnu

neutralchaos18 · 2024-03-24T10:41:25Z

neutralchaos18
Mar 24, 2024

Because of your kernel file extension the compiler is attempting to compile moose in c, rather than its natural c++ language. The kernel file should be '.C' (uppercase dot c) and not '.c' (lowercase dot c).

This issue here has a similar cause and effect: #18050

This is what a successful output looks like. Note that it says 'Compiling C++' rather than C, as it does with your attempts.

(moose) neutralchaos@neutralchaos-To-be-filled-by-O-E-M:~/projects/babbler$ make -j 4
Checking if header needs updating: /home/neutralchaos/projects/moose/framework/include/base/MooseRevision.h...
Creating Unity /home/neutralchaos/projects/babbler/build/unity_src/kernels_Unity.C
Compiling C++ (in opt mode) /home/neutralchaos/projects/babbler/build/unity_src/kernels_Unity.C...
Linking Library /home/neutralchaos/projects/babbler/lib/libbabbler-opt.la...
Linking Executable /home/neutralchaos/projects/babbler/babbler-opt...
(moose) neutralchaos@neutralchaos-To-be-filled-by-O-E-M:~/projects/babbler$

For what its worth, I was stuck on this issue for a few days as well.

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About the Step 5 in tutorial, I get Fatal error: <string> no such file or directory #26415

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About the Step 5 in tutorial, I get Fatal error: <string> no such file or directory #26415

Hatomzre Dec 24, 2023

Replies: 2 comments · 3 replies

GiudGiud Dec 24, 2023 Collaborator

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GiudGiud Dec 24, 2023 Collaborator

Hatomzre Dec 24, 2023 Author

neutralchaos18 Mar 24, 2024

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Dec 24, 2023

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