Closed CatarinaGarbacz closed 3 years ago
grgbellasvki
commented
3 years ago Hello, It seems something is wrong with the auto-registration of RrhoDB.cpp file. I would be happy to try and reproduce the problem, but before that:
Do you get the same error with other databases, like NASA-9? Is the error you mention reproducible with mppequil with the mutation++ SU2 compiles? "mppequil -T 300 -P 1000 -m 32 air_5"
CatarinaGarbacz
commented
3 years ago thanks for helping!
this happens for any database. which is expected, since the work I am doing is linking Mutation to another code, so there's probably some link missing for the databases in general. which is strange, because it does not complain about mixture file or mechanism file, which suggests the folder Mutationpp/data is being recognized. so I'm a bit confused about this "contradiction"
also, this error is not reproducible with any executable from Mutation++, because the point is that we are running SU2 and not mutation++. simply inside SU2 we have #include
the only way to reproduce the problem is to install SU2 with mutation++ the way I did. If you'd be willing to help, I can explain to you the necessary steps! let me know :)
thanks again
jbscoggi
commented
3 years ago Hey @CatarinaGarbacz, indeed this seems to be some type of linking problem. In fact, as you can see from the error message Provider for type ThermoDB is not registered. Possible providers are:, the ThermoDB type has no providers, meaning that none of the source files that provide ThermoDB loaders have been linked. Perhaps you can provide a verbose log from a clean Meson build to see if M++ is being compiled correctly?
CatarinaGarbacz
commented
3 years ago could you tell me what these files are, the ones which provide ThermoDB loaders?
The thing is, with meson, Mutation++ is not compiled explicitly, at leats not the way I did it - so I do not have that log. Now, my way is obviously wrong and maybe this is exactly the problem, i.e, the lack of an explicit compilation.
It's bit hard to explain all of what I did here, since I also do not master it, I wonder if it would make more sense to set up a meeting and I could show you all this ?
rdbisme
commented
3 years ago Let's try to see if we can solve it here before :). I'd kindly ask if you can provide:
git clone https://link/to/su2/git/repository/su2.gitenv command just before you run the build jobmeson builduname -aThis will help us to understand how to fix that. Don't worry if you do not master it, just try to do your best to provide those information.
jbscoggi
commented
3 years ago Hey @CatarinaGarbacz, it seems @rubendibattista beat me to it, but I think indeed if you could provide that info first, it would be helpful. I am super swamped with work for next week or so, but I will definitely be happy chat with you offline if it is not resolved by then. Like this, @rubendibattista can also help out if I'm not responding. The benefit of working it out here is that potentially others can find the solution useful in the future.
rdbisme
commented
3 years ago Oups, sorry @jbscoggi :).
jbscoggi
commented
3 years ago No problem @rubendibattista, thanks for helping!
CatarinaGarbacz
commented
3 years ago @rubendibattista sounds good, thanks a lot for getting back to me in a detailed way. Not sure if I will be able to respond to every point, because of the way I did things, but I will explain precisely what I did. And if you have more questions please ask!
a)I did this in the past, with cmake/make, and things worked perfectly well b) now with meson/ninja, in an automatic way
a)
git clone https://github.com/mutationpp/Mutationpp.git
install and compile eigen3
cd mutationpp/thirdparty/eigen; mkdir build_dir; cd build_dir; cmake .. ; make install;
at the end of this step I have eigen here: /usr/local/include/eigen3
install and compile mutation
cd Mutationpp; mkdir build; cd build; cmake -DCMAKE_INSTALL_PREFIX:PATH=$(realpath ../install) .. ; make -j N install
add lines to ~/.bashrc file
export MPP_DIRECTORY=<path_to_mutation++_directory>
export MPP_DATA_DIRECTORY=$MPP_DIRECTORY/data
export PATH=$MPP_DIRECTORY/install/bin:$PATH
export LD_LIBRARY_PATH=$MPP_DIRECTORY/install/lib:$LD_LIBRARY_PATHcreate symbolic links to link to SU2 later on
cd mutationpp/install/lib; ln -s libmutation++.so libmutation++.a; ln -s libmutation++.a libmutation++.dylib
I modify the configure.ac file of SU2, adding:
# check for lib
Mutationpplib=libmutation++.a
Mutationppheader=mutation++.h
have_MPP="no"
if test "$with_Mutationpp_lib" != "no"
then
AC_CHECK_FILE([$with_Mutationpp_lib/$Mutationpplib],[have_MPP="yes"],[have_MPP="no"])
if test "$have_MPP" == "no"
then
AC_MSG_ERROR([Mutation++ requested but library file not found.])
fi
fi
# check for header
if test "$have_MPP" != "no"
then
if test "$with_Mutationpp_include" != "no"
then
AC_CHECK_FILE([$with_Mutationpp_include/$Mutationppheader],[have_MPP='yes'],[have_MPP='no'])
if test "$have_MPP" == "no"
then
AC_MSG_ERROR([Mutation++ requested but header file not found.])
fi
else
have_MPP="no"
fi
fi
if test "$have_MPP" != "no"
then
AM_CONDITIONAL(BUILD_MUTATIONPP,true,test x$enablempp = xyes -a x$have_MPP = xyes)
MUTATIONPP_CXX="-DHAVE_MPP -I"$with_Mutationpp_include""
MUTATIONPP_LD="$with_Mutationpp_lib"/$Mutationpplib
else
AM_CONDITIONAL(BUILD_MUTATIONPP,false)
MUTATIONPP_CXX=
MUTATION_LD=
fi
AC_SUBST([MUTATIONPP_CXX])
AC_SUBST([MUTATIONPP_LD])if BUILD_MUTATIONPP
lib_cxxflags += @MUTATIONPP_CXX@
lib_ldadd += @MUTATIONPP_LD@
endif./configure --prefix=<path_to_su2_nemo> CXXFLAGS="-O3 -std=c++0x -I <path_to_mutationpp>/install/include -I <path_to_eigen3>" --with-Mutationpp-lib=<path_to_mutationpp>/install/lib --with-Mutationpp-include=<path_to_mutationpp>/install/include/mutation++
b) with meson/ninja things work differently. I don't know exactly how the linking process should be done, this is what I am trying to figure out. The point of using meson/ninja is: instead of doing all these manual steps, simply configuring SU2 in the following way:
./meson.py --prefix=<path_to_su2> -Denable-mpp=true
so simply tell the configure string we want to enable mutation++, and all the rest would be done automatically.
# Mutation++
if get_option('enable-mpp')
subdir('externals/Mutationpp-meson')
su2_deps += mpp_dep
su2_cpp_args += '-DHAVE_MPP'
endif mpp_c_args = []
mpp_default_warnings = []
mpp_src = ['../Mutationpp/src/fortran/cwrapper.cpp',
'../Mutationpp/src/general/bprime.cpp',
'../Mutationpp/src/general/checkmix.cpp',
'../Mutationpp/src/general/Mixture.cpp',
'../Mutationpp/src/general/MixtureOptions.cpp',
'../Mutationpp/src/general/mppequil.cpp',
'../Mutationpp/src/gsi/DiffusionVelocityCalculator.cpp',
'../Mutationpp/src/gsi/GasFourierHeatFluxCalculator.cpp',
'../Mutationpp/src/gsi/GasSurfaceInteraction.cpp',
'../Mutationpp/src/gsi/GSIRateLawGammaConst.cpp',
'../Mutationpp/src/gsi/GSIRateLawGammaT.cpp',
'../Mutationpp/src/gsi/GSIRateLawSublimation.cpp',
'../Mutationpp/src/gsi/GSIRateManagerPhenomenological.cpp',
'../Mutationpp/src/gsi/GSIReactionAblation.cpp',
'../Mutationpp/src/gsi/GSIReactionCatalysis.cpp',
'../Mutationpp/src/gsi/GSIStoichiometryManager.cpp',
'../Mutationpp/src/gsi/MassBlowingRateAblation.cpp',
'../Mutationpp/src/gsi/MassBlowingRateNull.cpp',
'../Mutationpp/src/gsi/SolidPropertiesNull.cpp',
'../Mutationpp/src/gsi/SolidPropertiesSteadyState.cpp',
'../Mutationpp/src/gsi/SurfaceBalanceSolverMass.cpp',
'../Mutationpp/src/gsi/SurfaceBalanceSolverMassEnergy.cpp',
'../Mutationpp/src/gsi/SurfaceChemistry.cpp',
'../Mutationpp/src/gsi/SurfacePropertiesAblation.cpp',
'../Mutationpp/src/gsi/SurfacePropertiesNull.cpp',
'../Mutationpp/src/gsi/SurfaceRadiation.cpp',
'../Mutationpp/src/gsi/SurfaceState.cpp',
'../Mutationpp/src/kinetics/JacobianManager.cpp',
'../Mutationpp/src/kinetics/Kinetics.cpp',
'../Mutationpp/src/kinetics/RateLaws.cpp',
'../Mutationpp/src/kinetics/RateManager.cpp',
'../Mutationpp/src/kinetics/Reaction.cpp',
'../Mutationpp/src/kinetics/ReactionType.cpp',
'../Mutationpp/src/kinetics/StoichiometryManager.cpp',
'../Mutationpp/src/numerics/Interpolators.cpp',
'../Mutationpp/src/thermo/ChemNonEqStateModel.cpp',
'../Mutationpp/src/thermo/ChemNonEqTTvStateModel.cpp',
'../Mutationpp/src/thermo/Composition.cpp',
'../Mutationpp/src/thermo/EquilStateModel.cpp',
'../Mutationpp/src/thermo/MultiPhaseEquilSolver.cpp',
'../Mutationpp/src/thermo/Nasa7DB.cpp',
'../Mutationpp/src/thermo/Nasa7Polynomial.cpp',
'../Mutationpp/src/thermo/Nasa9DB.cpp',
'../Mutationpp/src/thermo/Nasa9Polynomial.cpp',
'../Mutationpp/src/thermo/ParticleRRHO.cpp',
'../Mutationpp/src/thermo/RrhoDB.cpp',
'../Mutationpp/src/thermo/Species.cpp',
'../Mutationpp/src/thermo/SpeciesListDescriptor.cpp',
'../Mutationpp/src/thermo/SpeciesNameFSM.cpp',
'../Mutationpp/src/thermo/ThermoDB.cpp',
'../Mutationpp/src/thermo/Thermodynamics.cpp',
'../Mutationpp/src/transfer/MillikanWhite.cpp',
'../Mutationpp/src/transfer/OmegaCE.cpp',
'../Mutationpp/src/transfer/OmegaCElec.cpp',
'../Mutationpp/src/transfer/OmegaCV.cpp',
'../Mutationpp/src/transfer/OmegaET.cpp',
'../Mutationpp/src/transfer/OmegaI.cpp',
'../Mutationpp/src/transfer/OmegaVT.cpp',
'../Mutationpp/src/transport/CapitelliIntegrals.cpp',
'../Mutationpp/src/transport/CollisionDB.cpp',
'../Mutationpp/src/transport/CollisionGroup.cpp',
'../Mutationpp/src/transport/CollisionIntegral.cpp',
'../Mutationpp/src/transport/CollisionPair.cpp',
'../Mutationpp/src/transport/CoulombIntegrals.cpp',
'../Mutationpp/src/transport/ElectronSubSystem.cpp',
'../Mutationpp/src/transport/ExactDiffMat.cpp',
'../Mutationpp/src/transport/LangevinIntegrals.cpp',
'../Mutationpp/src/transport/RamshawDiffMat.cpp',
'../Mutationpp/src/transport/ThermalConductivityChapmannEnskog.cpp',
'../Mutationpp/src/transport/ThermalConductivityWilke.cpp',
'../Mutationpp/src/transport/Transport.cpp',
'../Mutationpp/src/transport/ViscosityChapmannEnskog.cpp',
'../Mutationpp/src/transport/ViscosityGuptaYos.cpp',
'../Mutationpp/src/transport/ViscosityWilke.cpp',
'../Mutationpp/src/utilities/StringUtils.cpp',
'../Mutationpp/src/utilities/TemporaryFile.cpp',
'../Mutationpp/src/utilities/Units.cpp',
'../Mutationpp/src/utilities/XMLite.cpp']
mpp_include = include_directories(['../Mutationpp/thirdparty/eigen',
'../Mutationpp/src',
'../Mutationpp/src/general',
'../Mutationpp/src/thermo',
'../Mutationpp/src/kinetics',
'../Mutationpp/src/transfer',
'../Mutationpp/src/transport',
'../Mutationpp/src/utilities',
'../Mutationpp/src/fortran',
'../Mutationpp/src/gsi',
'../Mutationpp/src/numerics'])
mpp_lib = static_library('mpp',
mpp_src,
include_directories : mpp_include,
c_args: mpp_c_args + mpp_default_warnings)
mpp_dep = declare_dependency(link_with : mpp_lib,
include_directories : mpp_include)I configure SU2 with
./meson.py --prefix=<path_to_su2> -Denable-mpp=true
output:
The Meson build system
Version: 0.54.999
Source dir: /home/catarina/Desktop/PhD/Codes/SU2
Build dir: /home/catarina/Desktop/PhD/Codes/SU2/build
Build type: native build
Project name: SU2
Project version: 7.0.7 "Blackbird"
C compiler for the host machine: cc (gcc 7.5.0 "cc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0")
C linker for the host machine: cc ld.bfd 2.30
C++ compiler for the host machine: c++ (gcc 7.5.0 "c++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0")
C++ linker for the host machine: c++ ld.bfd 2.30
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python3 found: YES (/usr/bin/python3)
Found pkg-config: /usr/bin/pkg-config (0.29.1)
mpicc found: NO
Run-time dependency MPI for c found: NO (tried pkgconfig and config-tool)
mpic++ found: NO
Run-time dependency MPI for cpp found: NO (tried pkgconfig and config-tool)
Message: Boost sources found.
Run-time dependency threads found: YES
Message: -------------------------------------------------------------------------
| ___ _ _ ___ |
| / __| | | |_ ) Release 7.0.7 "Blackbird" |
| \__ \ |_| |/ / |
| |___/\___//___| Meson Configuration Summary |
| |
-------------------------------------------------------------------------
Option Value
---------------------
TecIO: true
CGNS: true
AD (reverse): false
AD (forward): false
Python Wrapper: false
Intel-MKL: false
OpenBlas: false
PaStiX: false
Mixed Float: false
Mutation++: true
Please be sure to add the $SU2_HOME and $SU2_RUN environment variables,
and update your $PATH (and $PYTHONPATH if applicable) with $SU2_RUN
Based on the input to this configuration, add these lines to your .bashrc file:
export SU2_RUN=/home/catarina/Desktop/PhD/Codes/SU2/bin
export SU2_HOME=/home/catarina/Desktop/PhD/Codes/SU2
export PATH=$PATH:$SU2_RUN
export PYTHONPATH=$PYTHONPATH:$SU2_RUN
Use './ninja -C build install' to compile and install SU2
Build targets in project: 11
Found ninja-1.10.0.git at /home/catarina/Desktop/PhD/Codes/SU2/ninja
I compile SU2 with
./ninja -C build install -- all good
I run the code :
..........SU2 non-relevant output.............
M++ error: invalid input.
input: key = NASA-9
Provider <NASA-9> for type ThermoDB is not registered. Possible providers are:
Was trying to load the thermodynamic database.note that I never compiled mutation++ explicitly, which could have been the problem. So to check if this is the actual problem, manually I go to SU2/externals/Mutationpp and I install and compile mutation explicity following steps a)1-5.
I re-run meson as in 3. - same output
$env
MPP_DIRECTORY=/home/catarina/Desktop/PhD/Codes/SU2/externals/Mutationpp
CLUTTER_IM_MODULE=xim
LD_LIBRARY_PATH=/home/catarina/Desktop/PhD/Codes/SU2/externals/Mutationpp/install/lib:/home/catarina/Desktop/PhD/Codes/Mutationpp/install/lib:
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:*.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:
LC_MEASUREMENT=pt_PT.UTF-8
LESSCLOSE=/usr/bin/lesspipe %s %s
LC_PAPER=pt_PT.UTF-8
LC_MONETARY=pt_PT.UTF-8
XDG_MENU_PREFIX=gnome-
LANG=en_US.UTF-8
DISPLAY=:0
OLDPWD=/home/catarina/Desktop/PhD/Codes
MPP_DATA_DIRECTORY=/home/catarina/Desktop/PhD/Codes/SU2/externals/Mutationpp/data
GNOME_SHELL_SESSION_MODE=ubuntu
COLORTERM=truecolor
USERNAME=catarina
XDG_VTNR=2
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
MANDATORY_PATH=/usr/share/gconf/ubuntu.mandatory.path
LC_NAME=pt_PT.UTF-8
XDG_SESSION_ID=2
USER=catarina
DESKTOP_SESSION=ubuntu
QT4_IM_MODULE=xim
TEXTDOMAINDIR=/usr/share/locale/
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/27720672_6db5_436f_9f83_1648ad513fd3
DEFAULTS_PATH=/usr/share/gconf/ubuntu.default.path
PWD=/home/catarina/Desktop/PhD/Codes/SU2
HOME=/home/catarina
SU2_HOME=/home/catarina/Desktop/PhD/Codes/SU2
LC_CTYPE=pt_PT.UTF-8
TEXTDOMAIN=im-config
SSH_AGENT_PID=2703
QT_ACCESSIBILITY=1
XDG_SESSION_TYPE=x11
XDG_DATA_DIRS=/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop
XDG_SESSION_DESKTOP=ubuntu
LC_ADDRESS=pt_PT.UTF-8
GJS_DEBUG_OUTPUT=stderr
LC_NUMERIC=pt_PT.UTF-8
SU2_RUN=/home/catarina/Desktop/PhD/Codes/SU2/bin
GTK_MODULES=gail:atk-bridge
WINDOWPATH=2
VTE_VERSION=5202
TERM=xterm-256color
SHELL=/bin/bash
QT_IM_MODULE=ibus
XMODIFIERS=@im=ibus
IM_CONFIG_PHASE=2
XDG_CURRENT_DESKTOP=ubuntu:GNOME
GPG_AGENT_INFO=/run/user/1000/gnupg/S.gpg-agent:0:1
GNOME_TERMINAL_SERVICE=:1.116
XDG_SEAT=seat0
SHLVL=1
PYTHONPATH=:/home/catarina/Desktop/PhD/Codes/SU2/bin:/home/catarina/Desktop/PhD/Codes/SU2/bin
LC_TELEPHONE=pt_PT.UTF-8
GDMSESSION=ubuntu
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
LOGNAME=catarina
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
XDG_RUNTIME_DIR=/run/user/1000
XAUTHORITY=/run/user/1000/gdm/Xauthority
XDG_CONFIG_DIRS=/etc/xdg/xdg-ubuntu:/etc/xdg
PATH=/home/catarina/Desktop/PhD/Codes/SU2/externals/Mutationpp/install/bin:/home/catarina/Desktop/PhD/Codes/Mutationpp/install/bin:/home/catarina/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/catarina/Desktop/PhD/Codes/SU2/bin:/home/catarina/Desktop/PhD/Codes/SU2/bin
LC_IDENTIFICATION=pt_PT.UTF-8
GJS_DEBUG_TOPICS=JS ERROR;JS LOG
SESSION_MANAGER=local/catarina-VivoBook-ASUSLaptop-X580GD-N580GD:@/tmp/.ICE-unix/2607,unix/catarina-VivoBook-ASUSLaptop-X580GD-N580GD:/tmp/.ICE-unix/2607
LESSOPEN=| /usr/bin/lesspipe %s
GTK_IM_MODULE=ibus
LC_TIME=pt_PT.UTF-8
_=/usr/bin/env
re-run ninja as in 4. - all good
run SU2, same error as in 6.
$uname -a
Linux catarina-VivoBook-ASUSLaptop-X580GD-N580GD 4.15.0-123-generic #126-Ubuntu SMP Wed Oct 21 09:40:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
rdbisme
commented
3 years ago Ehi @CatarinaGarbacz, I think the problem is in the meson files. Is your code available somewhere? Is it standard SU2?
CatarinaGarbacz
commented
3 years ago it is. not standard SU2, but you can checkout to this branch: https://github.com/su2code/SU2/tree/feature_NEMO_streamline
rdbisme
commented
3 years ago The right way of using Mutation++ with meson should be:
(Build and) install Mutation where you want it to be using cmake. (When you install it, Mutation++ exports a mutation++Config.cmake file that is called "Export file" and it's the way a CMake project provides discoverability)
Example meson.build for a simple main.cpp file:
project('example', 'cpp')
mutation = dependency('mutation++', method: 'cmake')
exe = executable('main', 'main.cpp', dependencies : mutation)Theoretically meson should be able to discover the dependency and link your code against it.
Unfortunately meson is missing support for CMake export files so this does not work.
The Meson build system
Version: 0.56.0
Source dir: /tmp/mutation-meson
Build dir: /tmp/mutation-meson/builddir
Build type: native build
Project name: example
Project version: undefined
Using 'CXX' from environment with value: '/home2/softmassot/spack2/linux-centos7-x86_64/gcc-4.8.5/gcc-9.2.0-wqdecm4rkyyhejagxwmnabt6lscgm45d/bin/g++'
C++ compiler for the host machine: /home2/softmassot/spack2/linux-centos7-x86_64/gcc-4.8.5/gcc-9.2.0-wqdecm4rkyyhejagxwmnabt6lscgm45d/bin/g++ (gcc 9.2.0 "g++ (Spack GCC) 9.2.0")
C++ linker for the host machine: /home2/softmassot/spack2/linux-centos7-x86_64/gcc-4.8.5/gcc-9.2.0-wqdecm4rkyyhejagxwmnabt6lscgm45d/bin/g++ ld.bfd 2.27-44
Using 'CXX' from environment with value: '/home2/softmassot/spack2/linux-centos7-x86_64/gcc-4.8.5/gcc-9.2.0-wqdecm4rkyyhejagxwmnabt6lscgm45d/bin/g++'
Host machine cpu family: x86_64
Host machine cpu: x86_64
Found CMake: /home2/softmassot/spack2/linux-centos7-x86_64/gcc-9.2.0/cmake-3.18.2-lcjefgbrqg7tz2ebfyvi4n7fun55dg2f/bin/cmake (3.18.2)
Using 'CMAKE_PREFIX_PATH' from environment with value: '/home2/softmassot/spack2/linux-centos7-x86_64/gcc-9.2.0/mutationpp-1.0.0-trlaixpf72tamrff77xmifg2stg2knlh/lib64/cmake/mutation++:/home2/softmassot/spack2/linux-centos7-x86_64/gcc-9.2.0/cmake-3.18.2-lcjefgbrqg7tz2ebfyvi4n7fun55dg2f:/home2/softmassot/spack2/linux-centos7-x86_64/gcc-9.2.0/mutationpp-1.0.0-trlaixpf72tamrff77xmifg2stg2knlh:/home2/softmassot/spack2/linux-centos7-x86_64/gcc-9.2.0/texlive-live-5an722qp4yuxlnee66g6x6mfreoeilee:/home2/softmassot/spack2/linux-centos7-x86_64/gcc-9.2.0/pinentry-1.1.0-orjum2gylyfzrnedepgxhcpuki4v6eel:/home2/softmassot/spack2/linux-centos7-x86_64/gcc-9.2.0/gnupg-2.2.19-nou273k7da4p6yzhx2i2uolryhkwpy72:/home2/softmassot/spack2/linux-centos7-x86_64/gcc-9.2.0/git-2.25.0-df2wwwxta5mifluyheox4nui6zu2yicw:/home2/softmassot/spack2/linux-centos7-x86_64/gcc-4.8.5/gcc-9.2.0-wqdecm4rkyyhejagxwmnabt6lscgm45d'
Run-time dependency mutation++ found: NO (tried cmake)
meson.build:2:0: ERROR: Dependency "mutation++" not found, tried cmakePossible workarounds:
I'm not familiar with meson, but it looks like a limitation. I cannot be of better help, let me know if you're able to implement a workaround
rdbisme
commented
3 years ago Ok, it seems to work.
subprojects folder in the repository rootMutationpp folder in ${SU2_ROOT}/subprojects (probably as a git submodule)meson.build with this:
# Mutation++
if get_option('enable-mpp')
cmake = import('cmake')
mpp_subproj = cmake.subproject('Mutationpp')
mpp_dep = mpp_subproj.dependency('mutation++')
su2_deps += mpp_dep
su2_cpp_args += '-DHAVE_MPP'
endifexport MPP_DATA_DIRECTORY="${SU2_ROOT}/subprojects/Mutationpp/data"TestCases/nonequilibrium/invwedge test case like this:
diff --git TestCases/nonequilibrium/invwedge/invwedge.cfg TestCases/nonequilibrium/invwedge/invwedge.cfg
index ccc48f23f2..45dba0d328 100644
--- TestCases/nonequilibrium/invwedge/invwedge.cfg
+++ TestCases/nonequilibrium/invwedge/invwedge.cfg
@@ -16,7 +16,7 @@
% POISSON_EQUATION)
SOLVER= NEMO_EULER
%
-GAS_MODEL= AIR-5
+GAS_MODEL= air_5
%
GAS_COMPOSITION= (0.77, 0.23, 0.0, 0.0, 0.0)
%
@@ -56,7 +56,7 @@ FREESTREAM_TEMPERATURE_VE= 288.15
%
% Fluid model (STANDARD_AIR, IDEAL_GAS, VW_GAS, PR_GAS,
% CONSTANT_DENSITY, INC_IDEAL_GAS, INC_IDEAL_GAS_POLY, MUTATIONPP, USER_DEFINED_NONEQ)
-FLUID_MODEL= USER_DEFINED_NONEQ
+FLUID_MODEL= MUTATIONPP
%
% -------------------- BOUNDARY CONDITION DEFINITION --------------------------%
%
(END)../../../builddir/SU2_CFD/src/SU2_CFD invwedge.cfgThis gives me the following output:
[...]
+------------------------------------------------------------------------------+
-- Initial and free-stream conditions:
+------------------------------------------------------------------------------+
| Name| Dim. value| Ref. value| Unit|Non-dim. value|
+------------------------------------------------------------------------------+
| Static Pressure| 101325| 1| Pa| 101325|
| Density| 0.609849| 1| kg/m^3| 0.609849|
| T-R Temperature| 288.15| 1| K| 288.15|
| V-E Temperature| 288.15| 1| K| 288.15|
| Total Energy| 3.28354e+07| 1| m^2/s^2| 3.28354e+07|
| Velocity-X| 2631.12| 1| m/s| 2631.12|
| Velocity-Y| 0| 1| m/s| 0|
| Velocity Magnitude| 2631.12| 1| m/s| 2631.12|
+------------------------------------------------------------------------------+
| Mach Number| -| -| -| 5|
+------------------------------------------------------------------------------+
Explicit Scheme. No Jacobian structure (Euler). MG level: 0.
------------------- Numerics Preprocessing ( Zone 0 ) -------------------
----------------- Integration Preprocessing ( Zone 0 ) ------------------
------------------- Iteration Preprocessing ( Zone 0 ) ------------------
Euler/Navier-Stokes/RANS fluid iteration.
------------------------------ Begin Solver -----------------------------
Simulation Run using the Single-zone Driver
+---------------------------------------------------------------------------------------------------------------------------------+
| Inner_Iter| rms[Rho_0]| rms[Rho_1]| rms[Rho_2]| rms[Rho_3]| rms[Rho_4]| rms[RhoU]| rms[RhoV]| rms[RhoE]| rms[RhoEve]|
+---------------------------------------------------------------------------------------------------------------------------------+
| 0| 3.942598| 2.745529| 2.309800| 3.937851| 2.651051| 2.502827| -13.260262| 6.601220| 5.237562|
| 1| -0.622880| -1.147643| -0.931788| 0.696263| -0.590537| 3.768063| 3.839363| 7.009293| 7.931364|
Warning, didn't converge temperatures: f = 8.03751e+18
Warning, didn't converge temperatures: f = 2.61814e+17
Warning, didn't converge temperatures: f = 5.21711e+12
Warning, didn't converge temperatures: f = 1.36784e+17
Warning, didn't converge temperatures: f = 5.17945e+16
| 2| 3.318968| 1.978563| 1.527387| 3.315993| 1.890395| 3.663803| 3.736285| 7.013566| 8.957421|
Warning!! Instances of NaN in the following source terms:
Axisymmetry: 0
Chemical: 25830
Vib. Relax: 25830
Error in "void CSolver::SetResidual_RMS(CGeometry*, CConfig*)":
-------------------------------------------------------------------------
SU2 has diverged. (NaN detected)
------------------------------ Error Exit -------------------------------It explodes, but at least it seems to not complain about Mutation.
What do you think @CatarinaGarbacz?
CatarinaGarbacz
commented
3 years ago Uau I'm very impressed, that was quick! it definitely works perfectly well in term of linking mutation with SU2 :D
Probably the reason why it explodes is simply because in MPP we have N,O,NO,N2,O2 as the list of species and in the userdefined model we have N2,O2,N,O,NO, so you're giving 0.77, 0.23 mass fractions to N and O. which shoud be fine generally, but this test-case was only configured and tested for 0.77 N2 and 0.23 O2 so might give some issues if we change that. in any case, I will implement this and test with the right mass fractions.
and let you know how it went. But many thanks, this is incredibly helpful. I can tell you understand more about this scripting/compilation/installation stuff than I do, so very much appreciated.
rdbisme
commented
3 years ago Amazing! 👍
I'll close this issue since it's resolved in terms of build systems shenanigans, feel free to drop a message to let us know if you manage to make the simulation work as expected.
PS: I should probably checkout SU2, sooner or later, it looks a cool project! :)
Up to now, we were linking mpp to SU2 by means of: 1.install mpp - with cmake 2.compile mpp - with make 3.configure su2 with linking flags to mpp 4.compile su2 - with make
now SU2 has a new way of configuring/compiling, that uses building software called meson/ninja. So I have been working on making the previous process completely automatic within this software. The idea is: 1.configure su2 with meson, with flag mutationpp=true 2.compile su2 with ninja and everything else is done in the background with meson scripting.
It is generally going well. I specify the sources in the meson.build file (all .cpp files in Mutationpp/src/), as well as and include folders (all folders in Mutationpp/src/), and su2 configures and compiles well. However, when I run the code, I get the following error:
**M++ error: invalid input. input: key = RRHO Provider for type ThermoDB is not registered. Possible providers are:
Was trying to load the thermodynamic database.**
In the attempt to solve this, I tried also including all the folders in Mutationpp/data/ but as expected this did not work. Could you explain to me the origin of this error and perhaps any guess of what is missing in the meson.build linking files?
Thank you