Error during build ld: library not found for -lvtkParallelMPI-9.2

[Bigdogcat]

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Issue or question about MOOSE

Hi there,

I'm getting this error when build:

ld: warning: directory not found for option '-L/Users/sunqingpei/miniconda3/envs/moose/lib/gcc/x86_64-apple-darwin13.4.0/9.5.0'
ld: library not found for -lvtkParallelMPI-9.2
clang-16: error: linker command failed with exit code 1 (use -v to see invocation)

Does it mean I need to install some additional packages?

(Optional) code in question / simulation log / errors

No response

Encountering Errors? Please include diagnostic output

System Arch: Darwin Kernel Version 19.6.0: Thu Oct 29 22:56:45 PDT 2020; root:xnu-6153.141.2.2~1/RELEASE_X86_64

MOOSE Package Version: Custom Build

CPU Count: 8

Memory Free: 1591.36 MB

Variable `which $CC` check:
/Users/sunqingpei/miniconda3/envs/moose/bin/mpicc

$CC --version:
clang version 16.0.6
Target: x86_64-apple-darwin13.4.0
Thread model: posix
InstalledDir: /Users/sunqingpei/miniconda3/envs/moose/bin

MPICC:
which mpicc:
	/Users/sunqingpei/miniconda3/envs/moose/bin/mpicc
mpicc -show:
	x86_64-apple-darwin13.4.0-clang -I/Users/sunqingpei/miniconda3/envs/moose/include -I/Users/sunqingpei/miniconda3/envs/moose/include -L/Users/sunqingpei/miniconda3/envs/moose/lib -Wl,-rpath,/Users/sunqingpei/miniconda3/envs/moose/lib -I/Users/sunqingpei/miniconda3/envs/moose/include -L/Users/sunqingpei/miniconda3/envs/moose/lib -lmpi -lpmpi

COMPILER x86_64-apple-darwin13.4.0-clang:
clang version 16.0.6
Target: x86_64-apple-darwin13.4.0
Thread model: posix
InstalledDir: /Users/sunqingpei/miniconda3/envs/moose/bin

Python:
	/Users/sunqingpei/miniconda3/envs/moose/bin/python
	Python 3.11.8

MODULES NOT AVAILABLE

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=/Users/sunqingpei/miniconda3/envs/moose --with-make-np=12 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --with-x=0 --with-ssl=0 --with-mpi-dir=/Users/sunqingpei/miniconda3/envs/moose AR=x86_64-apple-darwin13.4.0-ar RANLIB=x86_64-apple-darwin13.4.0-ranlib CFLAGS="-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /Users/sunqingpei/miniconda3/envs/moose/include -fdebug-prefix-map=/opt/civet0/build/conda/conda-bld/moose-petsc_1721108638565/work=/usr/local/src/conda/moose-petsc-3.20.3 -fdebug-prefix-map=/Users/sunqingpei/miniconda3/envs/moose=/usr/local/src/conda-prefix" CXXFLAGS="-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/sunqingpei/miniconda3/envs/moose/include " CPPFLAGS="-D_FORTIFY_SOURCE=2 -isystem /Users/sunqingpei/miniconda3/envs/moose/include -mmacosx-version-min=10.15" FFLAGS="-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/sunqingpei/miniconda3/envs/moose/include -fdebug-prefix-map=/opt/civet0/build/conda/conda-bld/moose-petsc_1721108638565/work=/usr/local/src/conda/moose-petsc-3.20.3 -fdebug-prefix-map=/Users/sunqingpei/miniconda3/envs/moose=/usr/local/src/conda-prefix" FCFLAGS="-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/sunqingpei/miniconda3/envs/moose/include -fdebug-prefix-map=/opt/civet0/build/conda/conda-bld/moose-petsc_1721108638565/work=/usr/local/src/conda/moose-petsc-3.20.3 -fdebug-prefix-map=/Users/sunqingpei/miniconda3/envs/moose=/usr/local/src/conda-prefix" LDFLAGS="-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/sunqingpei/miniconda3/envs/moose/lib -L/Users/sunqingpei/miniconda3/envs/moose/lib" --prefix=/Users/sunqingpei/miniconda3/envs/moose/petsc";

PETSc linked libraries:
/Users/sunqingpei/miniconda3/envs/moose/petsc/lib/libpetsc.dylib:
	@rpath/../petsc/lib/libpetsc.3.20.dylib (compatibility version 3.20.0, current version 3.20.3)
	@rpath/libHYPRE-2.29.0.dylib (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1281.0.0)
	@rpath/../petsc/lib/libstrumpack.7.1.dylib (compatibility version 7.1.0, current version 7.1.4)
	@rpath/../petsc/lib/libscalapack.2.2.dylib (compatibility version 2.2.0, current version 2.2.1)
	@rpath/../petsc/lib/libsuperlu_dist.8.dylib (compatibility version 8.0.0, current version 8.1.2)
	@rpath/../petsc/lib/libparmetis.dylib (compatibility version 0.0.0, current version 0.0.0)
	@rpath/../petsc/lib/libmetis.dylib (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libhdf5.310.dylib (compatibility version 314.0.0, current version 314.0.0)
	@rpath/libmpifort.12.dylib (compatibility version 17.0.0, current version 17.1.0)
	@rpath/libmpi.12.dylib (compatibility version 17.0.0, current version 17.1.0)
	@rpath/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	@rpath/libc++.1.dylib (compatibility version 1.0.0, current version 1.0.0)
	@rpath/libomp.dylib (compatibility version 5.0.0, current version 5.0.0)

ENVIRONMENT:
AS=x86_64-apple-darwin13.4.0-as
LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/sunqingpei/miniconda3/envs/moose/lib -L/Users/sunqingpei/miniconda3/envs/moose/lib
AR=x86_64-apple-darwin13.4.0-ar
PROJ_LIB=/Applications/GMT-6.3.0.app/Contents/Resources/share/proj
MOOSE_NO_CODESIGN=true
ac_cv_func_malloc_0_nonnull=yes
HDF5_DIR=/Users/sunqingpei/miniconda3/envs/moose
VTKINCLUDE_DIR=/Users/sunqingpei/miniconda3/envs/moose/libmesh-vtk/include/vtk-9.3
TERM_PROGRAM=Apple_Terminal
PROJ_DATA=/Users/sunqingpei/miniconda3/envs/moose/share/proj
ac_cv_func_realloc_0_nonnull=yes
OBJC=x86_64-apple-darwin13.4.0-clang
HOST=x86_64-apple-darwin13.4.0
SHELL=/bin/zsh
TERM=xterm-256color
NM=x86_64-apple-darwin13.4.0-nm
CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem /Users/sunqingpei/miniconda3/envs/moose/include
TMPDIR=/var/folders/z7/035vhs_d6rqgw16tbcjgw6w80000gn/T/
PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
MAGICK_CONFIGURE_PATH=/Applications/GMT-6.3.0.app/Contents/Resources/lib/GraphicsMagick/config
CONDA_SHLVL=2
LIPO=x86_64-apple-darwin13.4.0-lipo
GS_LIB=/Applications/GMT-6.3.0.app/Contents/Resources/share/ghostscript/Resource/Init
CONDA_PROMPT_MODIFIER=(moose) 
TERM_PROGRAM_VERSION=433
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
SIZE=x86_64-apple-darwin13.4.0-size
NMEDIT=x86_64-apple-darwin13.4.0-nmedit
SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
TERM_SESSION_ID=16948A38-05C3-4945-B361-1D2910CA846D
CXX_FOR_BUILD=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-clang++
INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
SEGEDIT=x86_64-apple-darwin13.4.0-segedit
GFORTRAN=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-gfortran
VTK_VERSION=9.3
SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
GMTHOME=/Applications/GMT-6.3.0.app/Contents/Resources
USER=sunqingpei
Eigen3_DIR=/Users/sunqingpei/miniconda3/envs/moose/libmesh/include/Eigen
CLANGXX=x86_64-apple-darwin13.4.0-clang++
LIBTOOL=x86_64-apple-darwin13.4.0-libtool
CONDA_BACKUP_HOST=sundeMBP
CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
FC_FOR_BUILD=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-gfortran
CONDA_EXE=/Users/sunqingpei/miniconda3/bin/conda
WASP_DIR=/Users/sunqingpei/miniconda3/envs/moose/wasp
OTOOL=x86_64-apple-darwin13.4.0-otool
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.NrbK8CnUmR/Listeners
DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/sunqingpei/miniconda3/envs/moose/include -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /Users/sunqingpei/miniconda3/envs/moose/include -std=c++17
STRINGS=x86_64-apple-darwin13.4.0-strings
CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
_CE_CONDA=
CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
CONDA_PREFIX_1=/Users/sunqingpei/miniconda3
PATH=/Applications/GMT-6.3.0.app/Contents/Resources/bin:/Users/sunqingpei/projects/moose/python/peacock:/Users/sunqingpei/miniconda3/envs/moose/bin:/Users/sunqingpei/miniconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/Users/sunqingpei/miniconda3/envs/moose/wasp/bin
PROJ_NETWORK=ON
GSETTINGS_SCHEMA_DIR=/Users/sunqingpei/miniconda3/envs/moose/share/glib-2.0/schemas
MESON_ARGS=--buildtype release
XML_CATALOG_FILES=file:///Users/sunqingpei/miniconda3/envs/moose/etc/xml/catalog file:///etc/xml/catalog
LaunchInstanceID=634297F8-EC47-4359-8B18-3F916B2DB7F4
C_INCLUDE_PATH=/Users/sunqingpei/miniconda3/envs/moose/include
DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem /Users/sunqingpei/miniconda3/envs/moose/include
BUILD=x86_64-apple-darwin13.4.0
LD=x86_64-apple-darwin13.4.0-ld
CONDA_PREFIX=/Users/sunqingpei/miniconda3/envs/moose
F90=mpif90
PWD=/Users/sunqingpei
LIBMESH_DIR=/Users/sunqingpei/miniconda3/envs/moose/libmesh
STRIP=x86_64-apple-darwin13.4.0-strip
CMAKE_ARGS=-DCMAKE_AR=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
F95=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-gfortran
LANG=zh_HK.UTF-8
DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/sunqingpei/miniconda3/envs/moose/include -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
XPC_FLAGS=0x0
F77=mpif77
REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
CXX=mpicxx
CC_FOR_BUILD=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-clang
CLANG=x86_64-apple-darwin13.4.0-clang
_CE_M=
XPC_SERVICE_NAME=0
FI_PROVIDER=tcp
SHLVL=2
HOME=/Users/sunqingpei
FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/sunqingpei/miniconda3/envs/moose/include
CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /Users/sunqingpei/miniconda3/envs/moose/include
MPIHOME=/Users/sunqingpei/miniconda3/envs/moose
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
FC=mpif90
VTKLIB_DIR=/Users/sunqingpei/miniconda3/envs/moose/libmesh-vtk/lib
CONDA_PYTHON_EXE=/Users/sunqingpei/miniconda3/bin/python
LOGNAME=sunqingpei
build_alias=x86_64-apple-darwin13.4.0
PKG_CONFIG_PATH=/Users/sunqingpei/miniconda3/envs/moose/petsc/lib/pkgconfig:
CONDA_DEFAULT_ENV=moose
DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem /Users/sunqingpei/miniconda3/envs/moose/include
RANLIB=x86_64-apple-darwin13.4.0-ranlib
CMAKE_PREFIX_PATH=:/Users/sunqingpei/miniconda3/envs/moose
CC=mpicc
SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
host_alias=x86_64-apple-darwin13.4.0
LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath /Users/sunqingpei/miniconda3/envs/moose/lib -L/Users/sunqingpei/miniconda3/envs/moose/lib
PETSC_DIR=/Users/sunqingpei/miniconda3/envs/moose/petsc
SECURITYSESSIONID=186a6
OBJC_FOR_BUILD=/Users/sunqingpei/miniconda3/envs/moose/bin/x86_64-apple-darwin13.4.0-clang
FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/sunqingpei/miniconda3/envs/moose/include
_=/usr/bin/env

[GiudGiud]

Hello

Did you just update your conda packages?

Guillaume

[milljm]

I was attempting to solve this same reported issue here: #28219 (reply in thread)

But it would seem best to continue in this thread, as there is more information about the error.

My guess is we are using an older version of MOOSE with the latest versions of our packages. Or, that RACCON and therefore MOOSE was built using an older version of the conda packages supporting VTK 9.2, and we are now using the latest version of our conda packages which are now at VTK 9.3.

[milljm]

Lets try the uber clean methods one more time, and then build:

cd ~/projects/raccoon
git clean -xfd  # save your work before doing so

git submodule foreach --recursive git clean -xfd
cd moose/test
make -j 6

If we still run into the same error, I'd like you to list your /usr/local/bin directory:

ls /usr/local/bin

I want to see if perhaps we are picking up VTK from some other system included path.

[Bigdogcat]

Thanks so much. It works by using the commands you suggested. There is no error now during compiling. But it seems Peacock does not work after using this command. Could you please give any suggestion?

(moose) sunqingpei@sundeMBP raccoon % conda activate peacock
(peacock) sunqingpei@sundeMBP raccoon % peacock
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
find: /Users/sunqingpei/projects/moose/framework/contrib/wasp/install/lib: No such file or directory
/bin/sh: /Users/sunqingpei/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Building and linking hit...
bash: -std=c++17: command not found
make: *** [/Users/sunqingpei/projects/moose/framework/moose.mk:137: hit] Error 127
Traceback (most recent call last):
File "/Users/sunqingpei/projects/moose/python/pyhit/init.py", line 13, in
import hit
ModuleNotFoundError: No module named 'hit'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/sunqingpei/projects/moose/python/pyhit/init.py", line 18, in
import hit
ModuleNotFoundError: No module named 'hit'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/sunqingpei/projects/moose/python/peacock/peacock", line 36, in
run_peacock()
File "/Users/sunqingpei/projects/moose/python/peacock/peacock", line 28, in run_peacock
sys.exit(main(sys.argv))
File "/Users/sunqingpei/projects/moose/python/peacock/peacock", line 15, in main
from peacock.PeacockApp import PeacockApp
File "/Users/sunqingpei/projects/moose/python/peacock/PeacockApp.py", line 12, in
from . PeacockMainWindow import PeacockMainWindow
File "/Users/sunqingpei/projects/moose/python/peacock/PeacockMainWindow.py", line 19, in
from .Input.InputFileEditorWithMesh import InputFileEditorWithMesh
File "/Users/sunqingpei/projects/moose/python/peacock/Input/InputFileEditorWithMesh.py", line 19, in
from .InputFileEditorPlugin import InputFileEditorPlugin
File "/Users/sunqingpei/projects/moose/python/peacock/Input/InputFileEditorPlugin.py", line 17, in
from .InputFileEditor import InputFileEditor
File "/Users/sunqingpei/projects/moose/python/peacock/Input/InputFileEditor.py", line 19, in
from .InputTree import InputTree
File "/Users/sunqingpei/projects/moose/python/peacock/Input/InputTree.py", line 12, in
from pyhit import hit
File "/Users/sunqingpei/projects/moose/python/pyhit/init.py", line 22, in
import hit
ModuleNotFoundError: No module named 'hit'

[milljm]

The Raccoon instructions are sorely outdated. There is no need to have a second environment solely for Peacock. Please remain in the moose environment when attempting to run Peacock.

Edit:

Please use due diligence when following any instructions on:

• https://hugary1995.github.io/raccoon/getting_started/conda.html
  And use these instead where applicable:
• https://mooseframework.inl.gov/getting_started/installation/conda.html

[Bigdogcat]

Ok. Thanks a lot. I'll have a try.