CRASH: Zapdos-opt not found #135

LPennings · 2022-06-20T17:31:12Z

LPennings
Jun 20, 2022

Hello,

I am having trouble failing tests after compiling Zapdos. I am getting the error that zapdos-opt cannot be found, even though it is in the directory as it should be. Strangely, I can use zapdos-opt to run the tutorial files and they seem to work (although very slowly). See below.

Sorry if this is a very basic question or easy fix with a path manipulation, I am a total beginner.

(moose) lpennings@L-03-151:~/projects/zapdos$ ./run_tests -j8
test:1d_dc.non_local_potential_bc ............................................................... [HEAVY] SKIP
test:TM10_circular_wg.test_vac_dielectric ....................................................... [HEAVY] SKIP
test:1d_dc.1d_dc: Working Directory: /home/lpennings/projects/zapdos/test/tests/1d_dc
test:1d_dc.1d_dc: Running command: zapdos-opt -i mean_en.i --no-gdb-backtrace
test:1d_dc.1d_dc: /bin/sh: 1: zapdos-opt: not found
test:1d_dc.1d_dc: /bin/sh: 1: zapdos-opt: not found
test:1d_dc.1d_dc:
test:1d_dc.1d_dc:
test:1d_dc.1d_dc: Exit Code: 127
test:1d_dc.1d_dc: ################################################################################
test:1d_dc.1d_dc: Tester failed, reason: CRASH
test:1d_dc.1d_dc:
test:1d_dc.1d_dc .............................................................................. FAILED (CRASH)

Full terminal text:
errors.txt

Answered by cticenhour

Jun 20, 2022

The MOOSE/Zapdos test harness appears to be trying to call zapdos-opt at the test location, which is unexpected behavior. It should be able to find the executable in its ~/projects/zapdos location. I would like to take a closer look at your environment. Could you post the output text of env in your Terminal with the moose environment enabled?

View full answer

cticenhour · 2022-06-20T17:52:29Z

cticenhour
Jun 20, 2022
Maintainer

The MOOSE/Zapdos test harness appears to be trying to call zapdos-opt at the test location, which is unexpected behavior. It should be able to find the executable in its ~/projects/zapdos location. I would like to take a closer look at your environment. Could you post the output text of env in your Terminal with the moose environment enabled?

11 replies

cticenhour Jun 20, 2022
Maintainer

@LPennings I passed your environment along to a second set of eyes, and it appears as though your system PATH might be causing the MOOSE test harness to prioritize looking locally for the executable first. I see :. at the end of your PATH variable, which is not the default. I would start a new Terminal session, activate your MOOSE environment, and then check the value of PATH by performing the following command:

echo $PATH

Ensure that :. is not at the end of the line that is printed to your screen. If it is not, then navigate to Zapdos and try running your tests again.

csdechant Jun 20, 2022
Maintainer

I just installed Ubuntu 20.04.4 through WSL and download Zapdos. For my Windows 10 configuration, all the test pass. @cticenhour for reference, here is the MOOSE env on my Windows.

(moose) csdechant_test@LAPTOP-SFM60ITD:~/projects/zapdos$ env
SHELL=/bin/bash
DEBUG_FFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/csdechant_test/mambaforge3/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
GCC_RANLIB=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ranlib
CONDA_EXE=/home/csdechant_test/mambaforge3/bin/conda
_CE_M=
WSL_DISTRO_NAME=Ubuntu-20.04
build_alias=x86_64-conda-linux-gnu
CMAKE_ARGS=-DCMAKE_AR=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-strip
GPROF=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gprof
CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
HDF5_DIR=/home/csdechant_test/mambaforge3/envs/moose
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
STRINGS=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-strings
CPP=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-cpp
FFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/csdechant_test/mambaforge3/envs/moose/include
NAME=LAPTOP-SFM60ITD
PWD=/home/csdechant_test/projects/zapdos
GSETTINGS_SCHEMA_DIR=/home/csdechant_test/mambaforge3/envs/moose/share/glib-2.0/schemas
LOGNAME=csdechant_test
CONDA_PREFIX=/home/csdechant_test/mambaforge3/envs/moose
MOOSE_NO_CODESIGN=true
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
CXX=mpicxx
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/csdechant_test/mambaforge3/envs/moose/include -std=c++17
CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
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/csdechant_test/mambaforge3/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/csdechant_test/mambaforge3/envs/moose/lib -Wl,-rpath-link,/home/csdechant_test/mambaforge3/envs/moose/lib -L/home/csdechant_test/mambaforge3/envs/moose/lib
HOME=/home/csdechant_test
LANG=C.UTF-8
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/csdechant_test/mambaforge3/envs/moose/include
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:*.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:
CXX_FOR_BUILD=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-c++
ELFEDIT=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-elfedit
CONDA_PROMPT_MODIFIER=(moose)
CMAKE_PREFIX_PATH=/home/csdechant_test/mambaforge3/envs/moose:/home/csdechant_test/mambaforge3/envs/moose/x86_64-conda-linux-gnu/sysroot/usr
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/csdechant_test/mambaforge3/envs/moose/include
LD=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-ld
LIBMESH_DIR=/home/csdechant_test/mambaforge3/envs/moose/libmesh
READELF=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-readelf
GXX=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-g++
PETSC_DIR=/home/csdechant_test/mambaforge3/envs/moose
FC_FOR_BUILD=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gfortran
GCC_AR=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gcc-ar
LESSCLOSE=/usr/bin/lesspipe %s %s
ADDR2LINE=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-addr2line
TERM=xterm-256color
_CE_CONDA=
GCC_NM=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gcc-nm
SIZE=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-size
F77=mpif77
HOST=x86_64-conda-linux-gnu
LESSOPEN=| /usr/bin/lesspipe %s
CC_FOR_BUILD=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-cc
USER=csdechant_test
CONDA_SHLVL=2
AR=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-ar
AS=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-as
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/csdechant_test/mambaforge3/envs/moose/include
F95=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-f95
F90=mpif90
host_alias=x86_64-conda-linux-gnu
SHLVL=1
NM=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-nm
GCC=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gcc
DEBUG_FORTRANFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/csdechant_test/mambaforge3/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
FORTRANFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/csdechant_test/mambaforge3/envs/moose/include
VTKLIB_DIR=/home/csdechant_test/mambaforge3/envs/moose/libmesh-vtk/lib
LD_GOLD=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-ld.gold
CONDA_PYTHON_EXE=/home/csdechant_test/mambaforge3/bin/python
GFORTRAN=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-gfortran
CONDA_DEFAULT_ENV=moose
OBJCOPY=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-objcopy
WSLENV=
MPIHOME=/home/csdechant_test/mambaforge3/envs/moose
FC=mpif90
STRIP=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-strip
XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop
OBJDUMP=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-objdump
PATH=/home/csdechant_test/mambaforge3/envs/moose/bin:/home/csdechant_test/mambaforge3/condabin:/home/csdechant_test/mambaforge3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu20.04LTS_2004.4.5.0_x64__79rhkp1fndgsc:/mnt/c/Program Files/Intel/iCLS Client:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/Program Files/MATLAB/R2021b/bin:/mnt/c/Program Files/MATLAB/R2020b/bin:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program Files/Intel/WiFi/bin:/mnt/c/Program Files/Common Files/Intel/WirelessCommon:/mnt/c/Program Files (x86)/Common Files/Pleora/eBUS SDK:/mnt/c/Program Files/Common Files/Pleora/eBUS SDK:/mnt/c/Program Files/Common Files/Princeton Instruments/Picam/Runtime:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Users/corey/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/corey/AppData/Local/Programs/MiKTeX 2.9/miktex/bin/x64:/snap/bin
VTKINCLUDE_DIR=/home/csdechant_test/mambaforge3/envs/moose/libmesh-vtk/include/vtk-9.1
CC=mpicc
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/csdechant_test/mambaforge3/envs/moose/include
CXXFILT=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-c++filt
C_INCLUDE_PATH=/home/csdechant_test/mambaforge3/envs/moose/include
BUILD=x86_64-conda-linux-gnu
HOSTTYPE=x86_64
CONDA_PREFIX_1=/home/csdechant_test/mambaforge3
RANLIB=/home/csdechant_test/mambaforge3/envs/moose/bin/x86_64-conda-linux-gnu-ranlib
CONDA_BUILD_SYSROOT=/home/csdechant_test/mambaforge3/envs/moose/x86_64-conda-linux-gnu/sysroot
_=/usr/bin/env
OLDPWD=/home/csdechant_test

cticenhour Jun 20, 2022
Maintainer

Thanks @csdechant, that's a good result. I am leaning toward this being a PATH issue at this point.

LPennings Jun 20, 2022
Author

I went into /.bashrc and removed the : at the end of the peacock line. Things are running correctly, at least the first few tests have passed!

I appreciate all the help.

I'll mark this as solved. As an aside, could anyone link me a good resource on what physics equations Zapdos is solving? I couldn't find that in the documentation.

-L

csdechant Jun 20, 2022
Maintainer

@LPennings Documentation is in the doc directory. We recommend Zapdos_Tutorial.pdf found here (https://github.com/shannon-lab/zapdos/blob/devel/doc/tutorial_pdf/Zapdos_Tutorial.pdf) or Lindsay_thesis_coupling_of_plasmas_and_liquids.pdf found here (https://github.com/shannon-lab/zapdos/blob/devel/doc/Lindsay_thesis_coupling_of_plasmas_and_liquids.pdf). If you have any more question, please let us know.

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CRASH: Zapdos-opt not found #135

LPennings Jun 20, 2022

Replies: 1 comment · 11 replies

cticenhour Jun 20, 2022 Maintainer

cticenhour Jun 20, 2022 Maintainer

csdechant Jun 20, 2022 Maintainer

cticenhour Jun 20, 2022 Maintainer

LPennings Jun 20, 2022 Author

csdechant Jun 20, 2022 Maintainer

LPennings
Jun 20, 2022

Replies: 1 comment 11 replies

cticenhour
Jun 20, 2022
Maintainer

cticenhour Jun 20, 2022
Maintainer

csdechant Jun 20, 2022
Maintainer

cticenhour Jun 20, 2022
Maintainer

LPennings Jun 20, 2022
Author

csdechant Jun 20, 2022
Maintainer