SU2-7.0.1 on ubuntu 18.04

hyunko · February 28, 2020, 01:24

Hi all,

I am trying to build 7.0.1 in ubuntu 18.04.
I got the following messages when I run meson build.

I have installed mpi & python 3.7.1.

please give an advice for that.

Thanks.

================================================== =================
hero@dndn64c:~/Downloads/su2-701$ ./meson.py build
git command not found. Using fall-back method to init submodules
Downloading CoDiPack '501dcf0305df147481630f20ce37c2e624fb351f'
Traceback (most recent call last):
File "./meson.py", line 71, in <module>
init_submodules('auto')
File "/home/hero/Downloads/su2-701/meson_scripts/init.py", line 85, in init_submodules
download_module(codi_name, alt_name_codi, github_repo_codi, sha_version_codi)
File "/home/hero/Downloads/su2-701/meson_scripts/init.py", line 165, in download_module
urllib.request.urlretrieve (url, commit_sha + '.zip')
File "/usr/local/lib/python3.7/urllib/request.py", line 247, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "/usr/local/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/usr/local/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/usr/local/lib/python3.7/urllib/request.py", line 548, in _open
'unknown_open', req)
File "/usr/local/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/usr/local/lib/python3.7/urllib/request.py", line 1387, in unknown_open
raise URLError('unknown url type: %s' % type)
urllib.error.URLError: <urlopen error unknown url type: https>

kett · February 28, 2020, 02:07

Try running the following first

Code:

sudo apt install git

hyunko · February 28, 2020, 03:19

Hi kett,

Tried, but only "git command" related thing is vanished.
Still as follows.

hero@dndn64c:~/Downloads/su2-701$ ./meson.py build
Downloading CoDiPack '501dcf0305df147481630f20ce37c2e624fb351f'
Traceback (most recent call last):
File "./meson.py", line 71, in <module>
init_submodules('auto')
File "/home/hero/Downloads/su2-701/meson_scripts/init.py", line 85, in init_submodules
download_module(codi_name, alt_name_codi, github_repo_codi, sha_version_codi)
File "/home/hero/Downloads/su2-701/meson_scripts/init.py", line 165, in download_module
urllib.request.urlretrieve (url, commit_sha + '.zip')
File "/usr/local/lib/python3.7/urllib/request.py", line 247, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "/usr/local/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/usr/local/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/usr/local/lib/python3.7/urllib/request.py", line 548, in _open
'unknown_open', req)
File "/usr/local/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/usr/local/lib/python3.7/urllib/request.py", line 1387, in unknown_open
raise URLError('unknown url type: %s' % type)
urllib.error.URLError: <urlopen error unknown url type: https>

hyunko · February 28, 2020, 03:45

I tried to use git command.

>>git clone https://github.com/su2code/SU2.git

meson & ninja worked.

But, when I run a simulation with mpirun or parallel_computation.py,
I got the same output messages as the number of cores I used.
And finally ABORTED!!!. see the following messages.
For single core run, it works. but fails in parallel runs.

Thanks in advances.

======= screen outputs ============================================
------------------- Geometry Preprocessing ( Zone 0 ) -------------------
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
Three dimensional problem.
3303775 grid points.
7133068 volume elements.
--------------------------------------------------------------------------
mpirun noticed that process rank 58 with PID 0 on node dndn64c exited on signal 6 (Aborted).
--------------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/local/bin/parallel_computation.py", line 106, in <module>
main()
File "/usr/local/bin/parallel_computation.py", line 57, in main
options.compute )
File "/usr/local/bin/parallel_computation.py", line 84, in parallel_computation
info = SU2.run.CFD(config)
File "/usr/local/bin/SU2/run/interface.py", line 112, in CFD
run_command( the_Command )
File "/usr/local/bin/SU2/run/interface.py", line 292, in run_command
raise exception(message)
RuntimeError: Path = /home/hero/test/,
Command = mpirun -n 64 /usr/local/bin/SU2_CFD config_CFD.cfg
SU2 process returned error '134'
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'St9bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
terminate called after throwing an instance of 'std::bad_alloc'

hyunko · February 28, 2020, 03:50

Followings are the messages when I used meson & ninja

hero@dndn64c:~/Downloads/SU2$ ./meson.py build
Initialize submodule /home/hero/Downloads/SU2/externals/codi using git ...
Submodule 'externals/codi' (https://github.com/scicompkl/CoDiPack) registered for path 'externals/codi'
Cloning into '/home/hero/Downloads/SU2/externals/codi'...
Submodule path 'externals/codi': checked out '501dcf0305df147481630f20ce37c2e624fb351f'
Initialize submodule /home/hero/Downloads/SU2/externals/medi using git ...
Submodule 'externals/medi' (https://github.com/SciCompKL/MeDiPack) registered for path 'externals/medi'
Cloning into '/home/hero/Downloads/SU2/externals/medi'...
Submodule path 'externals/medi': checked out 'edde14f9ac4026b72b1e130f61c0a78e8652afa5'
Initialize submodule /home/hero/Downloads/SU2/externals/meson using git ...
Submodule 'externals/meson' (https://github.com/mesonbuild/meson) registered for path 'externals/meson'
Cloning into '/home/hero/Downloads/SU2/externals/meson'...
Submodule path 'externals/meson': checked out '0435691e83fb7172e2a9635d2eb32d5521089916'
Initialize submodule /home/hero/Downloads/SU2/externals/ninja using git ...
Submodule 'externals/ninja' (https://github.com/ninja-build/ninja) registered for path 'externals/ninja'
Cloning into '/home/hero/Downloads/SU2/externals/ninja'...
Submodule path 'externals/ninja': checked out '2d15b04e411229cb902332957281622119025e77'
ninja executable not found. Building ...
bootstrapping ninja...
warning: A compatible version of re2c (>= 0.11.3) was not found; changes to src/*.in.cc will not affect your build.
wrote build.ninja.
bootstrap complete. rebuilding...
[29/29] LINK ninja
The Meson build system
Version: 0.52.999
Source dir: /home/hero/Downloads/SU2
Build dir: /home/hero/Downloads/SU2/build
Build type: native build
Project name: SU2
Project version: 7.0.1
C compiler for the host machine: cc (gcc 7.4.0 "cc (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0")
C linker for the host machine: GNU ld.bfd 2.30
C++ compiler for the host machine: c++ (gcc 7.4.0 "c++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0")
C++ linker for the host machine: GNU ld.bfd 2.30
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python3 found: YES (/usr/local/bin/python3)
Run-time dependency MPI for c found: YES
Run-time dependency MPI for cpp found: YES
Message: Extracting boost ...
Message: -------------------------------------------------------------------------
| ___ _ _ ___ |
| / __| | | |_ ) Release 7.0.1 "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

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=/usr/local/bin
export SU2_HOME=/home/hero/Downloads/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-1.9.0.git at /home/hero/Downloads/SU2/ninja
hero@dndn64c:~/Downloads/SU2$ ./ninja -C build install
ninja: Entering directory `build'
[84/389] Compiling C object 'externals/cgns/d6f0b8a@@cgns@sta/cgns_io.c.o'.
../externals/cgns/cgns_io.c: In function ‘cgio_check_file’:
../externals/cgns/cgns_io.c:606:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread (buf, 1, sizeof(buf), fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[102/389] Compiling C object 'externals/cgns/d6f0b8a@@cgns@sta/adf_ADF_interface.c.o'.
../externals/cgns/adf/ADF_interface.c: In function ‘ADF_Database_Valid’:
../externals/cgns/adf/ADF_interface.c:1022:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread (header, sizeof(char), 32, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[158/389] Compiling C object 'externals/metis/15213e7@@metis@sta/GKlib_gkregex.c.o'.
../externals/metis/GKlib/gkregex.c: In function ‘init_dfa’:
../externals/metis/GKlib/gkregex.c:3434:7: warning: implicit declaration of function ‘strcasecmp’ [-Wimplicit-function-declaration]
if (strcasecmp (codeset_name, "UTF-8") == 0
^~~~~~~~~~
[388/389] Installing files.
Installation failed due to insufficient permissions.
Attempting to use polkit to gain elevated privileges...
Installing SU2_CFD/src/SU2_CFD to /usr/local/bin
Installing SU2_DOT/src/SU2_DOT to /usr/local/bin
Installing SU2_DEF/src/SU2_DEF to /usr/local/bin
Installing SU2_GEO/src/SU2_GEO to /usr/local/bin
Installing SU2_MSH/src/SU2_MSH to /usr/local/bin
Installing SU2_SOL/src/SU2_SOL to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/continuous_adjoint.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/compute_uncertainty.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/finite_differences.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/mesh_deformation.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/parallel_computation.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/parallel_computation_fsi.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/package_tests.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/shape_optimization.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/merge_solution.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/set_ffd_design_var.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/compute_polar.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/compute_multipoint.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/discrete_adjoint.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/direct_differentiation.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/fsi_computation.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/SU2_CFD.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/__init__.py to /usr/local/bin/SU2
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/design.py to /usr/local/bin/SU2/eval
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/functions.py to /usr/local/bin/SU2/eval
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/gradients.py to /usr/local/bin/SU2/eval
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/__init__.py to /usr/local/bin/SU2/eval
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/config.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/config_options.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/data.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/filelock.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/redirect.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/state.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/tools.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/historyMap.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/__init__.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/mesh/adapt.py to /usr/local/bin/SU2/mesh
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/mesh/tools.py to /usr/local/bin/SU2/mesh
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/mesh/__init__.py to /usr/local/bin/SU2/mesh
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/opt/project.py to /usr/local/bin/SU2/opt
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/opt/scipy_tools.py to /usr/local/bin/SU2/opt
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/opt/__init__.py to /usr/local/bin/SU2/opt
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/adaptation.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/adjoint.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/deform.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/direct.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/interface.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/merge.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/geometry.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/projection.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/__init__.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/bunch.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/filter_adjoint.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/lhc_unif.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/misc.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/mp_eval.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/ordered_bunch.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/ordered_dict.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/plot.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/polarSweepLib.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/which.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/switch.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/__init__.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/__init__.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/FSIInterface.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/PitchPlungeAirfoilStructuralTester.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/io/__init__.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/io/FSI_config.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/util/__init__.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/util/switch.py to /usr/local/bin/FSI

hyunko · February 28, 2020, 21:44

1. The problem is related to mpirun.
when I check the mpirun, it was openmpi version mpirun.
So I changed it into mpich version mpirun.

2. I suggest to use careful when apply mpi related dependency.

Best

Umuteng · March 15, 2020, 09:38

Quote:

Originally Posted by hyunko

Followings are the messages when I used meson & ninja

hero@dndn64c:~/Downloads/SU2$ ./meson.py build
Initialize submodule /home/hero/Downloads/SU2/externals/codi using git ...
Submodule 'externals/codi' (https://github.com/scicompkl/CoDiPack) registered for path 'externals/codi'
Cloning into '/home/hero/Downloads/SU2/externals/codi'...
Submodule path 'externals/codi': checked out '501dcf0305df147481630f20ce37c2e624fb351f'
Initialize submodule /home/hero/Downloads/SU2/externals/medi using git ...
Submodule 'externals/medi' (https://github.com/SciCompKL/MeDiPack) registered for path 'externals/medi'
Cloning into '/home/hero/Downloads/SU2/externals/medi'...
Submodule path 'externals/medi': checked out 'edde14f9ac4026b72b1e130f61c0a78e8652afa5'
Initialize submodule /home/hero/Downloads/SU2/externals/meson using git ...
Submodule 'externals/meson' (https://github.com/mesonbuild/meson) registered for path 'externals/meson'
Cloning into '/home/hero/Downloads/SU2/externals/meson'...
Submodule path 'externals/meson': checked out '0435691e83fb7172e2a9635d2eb32d5521089916'
Initialize submodule /home/hero/Downloads/SU2/externals/ninja using git ...
Submodule 'externals/ninja' (https://github.com/ninja-build/ninja) registered for path 'externals/ninja'
Cloning into '/home/hero/Downloads/SU2/externals/ninja'...
Submodule path 'externals/ninja': checked out '2d15b04e411229cb902332957281622119025e77'
ninja executable not found. Building ...
bootstrapping ninja...
warning: A compatible version of re2c (>= 0.11.3) was not found; changes to src/*.in.cc will not affect your build.
wrote build.ninja.
bootstrap complete. rebuilding...
[29/29] LINK ninja
The Meson build system
Version: 0.52.999
Source dir: /home/hero/Downloads/SU2
Build dir: /home/hero/Downloads/SU2/build
Build type: native build
Project name: SU2
Project version: 7.0.1
C compiler for the host machine: cc (gcc 7.4.0 "cc (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0")
C linker for the host machine: GNU ld.bfd 2.30
C++ compiler for the host machine: c++ (gcc 7.4.0 "c++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0")
C++ linker for the host machine: GNU ld.bfd 2.30
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python3 found: YES (/usr/local/bin/python3)
Run-time dependency MPI for c found: YES
Run-time dependency MPI for cpp found: YES
Message: Extracting boost ...
Message: -------------------------------------------------------------------------
| ___ _ _ ___ |
| / __| | | |_ ) Release 7.0.1 "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

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=/usr/local/bin
export SU2_HOME=/home/hero/Downloads/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-1.9.0.git at /home/hero/Downloads/SU2/ninja
hero@dndn64c:~/Downloads/SU2$ ./ninja -C build install
ninja: Entering directory `build'
[84/389] Compiling C object 'externals/cgns/d6f0b8a@@cgns@sta/cgns_io.c.o'.
../externals/cgns/cgns_io.c: In function ‘cgio_check_file’:
../externals/cgns/cgns_io.c:606:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread (buf, 1, sizeof(buf), fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[102/389] Compiling C object 'externals/cgns/d6f0b8a@@cgns@sta/adf_ADF_interface.c.o'.
../externals/cgns/adf/ADF_interface.c: In function ‘ADF_Database_Valid’:
../externals/cgns/adf/ADF_interface.c:1022:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
fread (header, sizeof(char), 32, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[158/389] Compiling C object 'externals/metis/15213e7@@metis@sta/GKlib_gkregex.c.o'.
../externals/metis/GKlib/gkregex.c: In function ‘init_dfa’:
../externals/metis/GKlib/gkregex.c:3434:7: warning: implicit declaration of function ‘strcasecmp’ [-Wimplicit-function-declaration]
if (strcasecmp (codeset_name, "UTF-8") == 0
^~~~~~~~~~
[388/389] Installing files.
Installation failed due to insufficient permissions.
Attempting to use polkit to gain elevated privileges...
Installing SU2_CFD/src/SU2_CFD to /usr/local/bin
Installing SU2_DOT/src/SU2_DOT to /usr/local/bin
Installing SU2_DEF/src/SU2_DEF to /usr/local/bin
Installing SU2_GEO/src/SU2_GEO to /usr/local/bin
Installing SU2_MSH/src/SU2_MSH to /usr/local/bin
Installing SU2_SOL/src/SU2_SOL to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/continuous_adjoint.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/compute_uncertainty.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/finite_differences.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/mesh_deformation.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/parallel_computation.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/parallel_computation_fsi.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/package_tests.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/shape_optimization.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/merge_solution.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/set_ffd_design_var.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/compute_polar.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/compute_multipoint.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/discrete_adjoint.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/direct_differentiation.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/fsi_computation.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/SU2_CFD.py to /usr/local/bin
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/__init__.py to /usr/local/bin/SU2
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/design.py to /usr/local/bin/SU2/eval
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/functions.py to /usr/local/bin/SU2/eval
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/gradients.py to /usr/local/bin/SU2/eval
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/__init__.py to /usr/local/bin/SU2/eval
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/config.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/config_options.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/data.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/filelock.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/redirect.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/state.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/tools.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/historyMap.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/__init__.py to /usr/local/bin/SU2/io
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/mesh/adapt.py to /usr/local/bin/SU2/mesh
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/mesh/tools.py to /usr/local/bin/SU2/mesh
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/mesh/__init__.py to /usr/local/bin/SU2/mesh
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/opt/project.py to /usr/local/bin/SU2/opt
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/opt/scipy_tools.py to /usr/local/bin/SU2/opt
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/opt/__init__.py to /usr/local/bin/SU2/opt
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/adaptation.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/adjoint.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/deform.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/direct.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/interface.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/merge.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/geometry.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/projection.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/__init__.py to /usr/local/bin/SU2/run
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/bunch.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/filter_adjoint.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/lhc_unif.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/misc.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/mp_eval.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/ordered_bunch.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/ordered_dict.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/plot.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/polarSweepLib.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/which.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/switch.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/__init__.py to /usr/local/bin/SU2/util
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/__init__.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/FSIInterface.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/PitchPlungeAirfoilStructuralTester.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/io/__init__.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/io/FSI_config.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/util/__init__.py to /usr/local/bin/FSI
Installing /home/hero/Downloads/SU2/SU2_PY/FSI/util/switch.py to /usr/local/bin/FSI

I think it is related to permission. It actually gives you "Installation failed due to insufficient permissions." error. Be a superuser, try it again. it should help

hyunko · March 16, 2020, 04:37

Thank you Umuteng.

I have tried already about the superuser related stuff.

The main reason of "multiple outputs for parallel run" was related to mpirun.

I have cleared mpirun related error with using MPICH version mpirun.

Thanks.

February 28, 2020, 01:24	SU2-7.0.1 on ubuntu 18.04	#1
hyunko Member Hyun Ko Join Date: Jun 2009 Posts: 32 Rep Power: 16	Hi all, I am trying to build 7.0.1 in ubuntu 18.04. I got the following messages when I run meson build. I have installed mpi & python 3.7.1. please give an advice for that. Thanks. ================================================== ================= hero@dndn64c:~/Downloads/su2-701$ ./meson.py build git command not found. Using fall-back method to init submodules Downloading CoDiPack '501dcf0305df147481630f20ce37c2e624fb351f' Traceback (most recent call last): File "./meson.py", line 71, in <module> init_submodules('auto') File "/home/hero/Downloads/su2-701/meson_scripts/init.py", line 85, in init_submodules download_module(codi_name, alt_name_codi, github_repo_codi, sha_version_codi) File "/home/hero/Downloads/su2-701/meson_scripts/init.py", line 165, in download_module urllib.request.urlretrieve (url, commit_sha + '.zip') File "/usr/local/lib/python3.7/urllib/request.py", line 247, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/usr/local/lib/python3.7/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/usr/local/lib/python3.7/urllib/request.py", line 525, in open response = self._open(req, data) File "/usr/local/lib/python3.7/urllib/request.py", line 548, in _open 'unknown_open', req) File "/usr/local/lib/python3.7/urllib/request.py", line 503, in _call_chain result = func(*args) File "/usr/local/lib/python3.7/urllib/request.py", line 1387, in unknown_open raise URLError('unknown url type: %s' % type) urllib.error.URLError: <urlopen error unknown url type: https>

February 28, 2020, 02:07		#2
kett New Member Andrew Join Date: Nov 2013 Posts: 1 Rep Power: 0	Try running the following first Code: sudo apt install git

February 28, 2020, 21:44	Solved	#6
hyunko Member Hyun Ko Join Date: Jun 2009 Posts: 32 Rep Power: 16	1. The problem is related to mpirun. when I check the mpirun, it was openmpi version mpirun. So I changed it into mpich version mpirun. 2. I suggest to use careful when apply mpi related dependency. Best

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February 28, 2020, 03:19		#3
hyunko Member Hyun Ko Join Date: Jun 2009 Posts: 32 Rep Power: 16	Hi kett, Tried, but only "git command" related thing is vanished. Still as follows. hero@dndn64c:~/Downloads/su2-701$ ./meson.py build Downloading CoDiPack '501dcf0305df147481630f20ce37c2e624fb351f' Traceback (most recent call last): File "./meson.py", line 71, in <module> init_submodules('auto') File "/home/hero/Downloads/su2-701/meson_scripts/init.py", line 85, in init_submodules download_module(codi_name, alt_name_codi, github_repo_codi, sha_version_codi) File "/home/hero/Downloads/su2-701/meson_scripts/init.py", line 165, in download_module urllib.request.urlretrieve (url, commit_sha + '.zip') File "/usr/local/lib/python3.7/urllib/request.py", line 247, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/usr/local/lib/python3.7/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/usr/local/lib/python3.7/urllib/request.py", line 525, in open response = self._open(req, data) File "/usr/local/lib/python3.7/urllib/request.py", line 548, in _open 'unknown_open', req) File "/usr/local/lib/python3.7/urllib/request.py", line 503, in _call_chain result = func(*args) File "/usr/local/lib/python3.7/urllib/request.py", line 1387, in unknown_open raise URLError('unknown url type: %s' % type) urllib.error.URLError: <urlopen error unknown url type: https>

February 28, 2020, 03:45		#4
hyunko Member Hyun Ko Join Date: Jun 2009 Posts: 32 Rep Power: 16	I tried to use git command. >>git clone https://github.com/su2code/SU2.git meson & ninja worked. But, when I run a simulation with mpirun or parallel_computation.py, I got the same output messages as the number of cores I used. And finally ABORTED!!!. see the following messages. For single core run, it works. but fails in parallel runs. Thanks in advances. ======= screen outputs ============================================ ------------------- Geometry Preprocessing ( Zone 0 ) ------------------- Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. Three dimensional problem. 3303775 grid points. 7133068 volume elements. -------------------------------------------------------------------------- mpirun noticed that process rank 58 with PID 0 on node dndn64c exited on signal 6 (Aborted). -------------------------------------------------------------------------- Traceback (most recent call last): File "/usr/local/bin/parallel_computation.py", line 106, in <module> main() File "/usr/local/bin/parallel_computation.py", line 57, in main options.compute ) File "/usr/local/bin/parallel_computation.py", line 84, in parallel_computation info = SU2.run.CFD(config) File "/usr/local/bin/SU2/run/interface.py", line 112, in CFD run_command( the_Command ) File "/usr/local/bin/SU2/run/interface.py", line 292, in run_command raise exception(message) RuntimeError: Path = /home/hero/test/, Command = mpirun -n 64 /usr/local/bin/SU2_CFD config_CFD.cfg SU2 process returned error '134' terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'St9bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc terminate called after throwing an instance of 'std::bad_alloc'

February 28, 2020, 03:50		#5
hyunko Member Hyun Ko Join Date: Jun 2009 Posts: 32 Rep Power: 16	Followings are the messages when I used meson & ninja hero@dndn64c:~/Downloads/SU2$ ./meson.py build Initialize submodule /home/hero/Downloads/SU2/externals/codi using git ... Submodule 'externals/codi' (https://github.com/scicompkl/CoDiPack) registered for path 'externals/codi' Cloning into '/home/hero/Downloads/SU2/externals/codi'... Submodule path 'externals/codi': checked out '501dcf0305df147481630f20ce37c2e624fb351f' Initialize submodule /home/hero/Downloads/SU2/externals/medi using git ... Submodule 'externals/medi' (https://github.com/SciCompKL/MeDiPack) registered for path 'externals/medi' Cloning into '/home/hero/Downloads/SU2/externals/medi'... Submodule path 'externals/medi': checked out 'edde14f9ac4026b72b1e130f61c0a78e8652afa5' Initialize submodule /home/hero/Downloads/SU2/externals/meson using git ... Submodule 'externals/meson' (https://github.com/mesonbuild/meson) registered for path 'externals/meson' Cloning into '/home/hero/Downloads/SU2/externals/meson'... Submodule path 'externals/meson': checked out '0435691e83fb7172e2a9635d2eb32d5521089916' Initialize submodule /home/hero/Downloads/SU2/externals/ninja using git ... Submodule 'externals/ninja' (https://github.com/ninja-build/ninja) registered for path 'externals/ninja' Cloning into '/home/hero/Downloads/SU2/externals/ninja'... Submodule path 'externals/ninja': checked out '2d15b04e411229cb902332957281622119025e77' ninja executable not found. Building ... bootstrapping ninja... warning: A compatible version of re2c (>= 0.11.3) was not found; changes to src/.in.cc will not affect your build. wrote build.ninja. bootstrap complete. rebuilding... [29/29] LINK ninja The Meson build system Version: 0.52.999 Source dir: /home/hero/Downloads/SU2 Build dir: /home/hero/Downloads/SU2/build Build type: native build Project name: SU2 Project version: 7.0.1 C compiler for the host machine: cc (gcc 7.4.0 "cc (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0") C linker for the host machine: GNU ld.bfd 2.30 C++ compiler for the host machine: c++ (gcc 7.4.0 "c++ (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.0") C++ linker for the host machine: GNU ld.bfd 2.30 Host machine cpu family: x86_64 Host machine cpu: x86_64 Program python3 found: YES (/usr/local/bin/python3) Run-time dependency MPI for c found: YES Run-time dependency MPI for cpp found: YES Message: Extracting boost ... Message: ------------------------------------------------------------------------- \| ___ _ _ ___ \| \| / __\| \| \| \|_ ) Release 7.0.1 "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 Please be sure to add the $SU2_HOME and $SU2_RUN environment variables, and update your $PATH (and $PYTHONPATH if applicable) with $SU2_RUN Based on the input to this configuration, add these lines to your .bashrc file: export SU2_RUN=/usr/local/bin export SU2_HOME=/home/hero/Downloads/SU2 export PATH=$PATH:$SU2_RUN export PYTHONPATH=$PYTHONPATH:$SU2_RUN Use './ninja -C build install' to compile and install SU2 Build targets in project: 11 Found ninja-1.9.0.git at /home/hero/Downloads/SU2/ninja hero@dndn64c:~/Downloads/SU2$ ./ninja -C build install* ninja: Entering directory `build' [84/389] Compiling C object 'externals/cgns/d6f0b8a@@cgns@sta/cgns_io.c.o'. ../externals/cgns/cgns_io.c: In function ‘cgio_check_file’: ../externals/cgns/cgns_io.c:606:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread (buf, 1, sizeof(buf), fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [102/389] Compiling C object 'externals/cgns/d6f0b8a@@cgns@sta/adf_ADF_interface.c.o'. ../externals/cgns/adf/ADF_interface.c: In function ‘ADF_Database_Valid’: ../externals/cgns/adf/ADF_interface.c:1022:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread (header, sizeof(char), 32, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [158/389] Compiling C object 'externals/metis/15213e7@@metis@sta/GKlib_gkregex.c.o'. ../externals/metis/GKlib/gkregex.c: In function ‘init_dfa’: ../externals/metis/GKlib/gkregex.c:3434:7: warning: implicit declaration of function ‘strcasecmp’ [-Wimplicit-function-declaration] if (strcasecmp (codeset_name, "UTF-8") == 0 ^~~~~~~~~~ [388/389] Installing files. Installation failed due to insufficient permissions. Attempting to use polkit to gain elevated privileges... Installing SU2_CFD/src/SU2_CFD to /usr/local/bin Installing SU2_DOT/src/SU2_DOT to /usr/local/bin Installing SU2_DEF/src/SU2_DEF to /usr/local/bin Installing SU2_GEO/src/SU2_GEO to /usr/local/bin Installing SU2_MSH/src/SU2_MSH to /usr/local/bin Installing SU2_SOL/src/SU2_SOL to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/continuous_adjoint.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/compute_uncertainty.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/finite_differences.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/mesh_deformation.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/parallel_computation.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/parallel_computation_fsi.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/package_tests.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/shape_optimization.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/merge_solution.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/set_ffd_design_var.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/compute_polar.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/compute_multipoint.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/discrete_adjoint.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/direct_differentiation.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/fsi_computation.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/SU2_CFD.py to /usr/local/bin Installing /home/hero/Downloads/SU2/SU2_PY/SU2/__init__.py to /usr/local/bin/SU2 Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/design.py to /usr/local/bin/SU2/eval Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/functions.py to /usr/local/bin/SU2/eval Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/gradients.py to /usr/local/bin/SU2/eval Installing /home/hero/Downloads/SU2/SU2_PY/SU2/eval/__init__.py to /usr/local/bin/SU2/eval Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/config.py to /usr/local/bin/SU2/io Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/config_options.py to /usr/local/bin/SU2/io Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/data.py to /usr/local/bin/SU2/io Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/filelock.py to /usr/local/bin/SU2/io Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/redirect.py to /usr/local/bin/SU2/io Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/state.py to /usr/local/bin/SU2/io Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/tools.py to /usr/local/bin/SU2/io Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/historyMap.py to /usr/local/bin/SU2/io Installing /home/hero/Downloads/SU2/SU2_PY/SU2/io/__init__.py to /usr/local/bin/SU2/io Installing /home/hero/Downloads/SU2/SU2_PY/SU2/mesh/adapt.py to /usr/local/bin/SU2/mesh Installing /home/hero/Downloads/SU2/SU2_PY/SU2/mesh/tools.py to /usr/local/bin/SU2/mesh Installing /home/hero/Downloads/SU2/SU2_PY/SU2/mesh/__init__.py to /usr/local/bin/SU2/mesh Installing /home/hero/Downloads/SU2/SU2_PY/SU2/opt/project.py to /usr/local/bin/SU2/opt Installing /home/hero/Downloads/SU2/SU2_PY/SU2/opt/scipy_tools.py to /usr/local/bin/SU2/opt Installing /home/hero/Downloads/SU2/SU2_PY/SU2/opt/__init__.py to /usr/local/bin/SU2/opt Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/adaptation.py to /usr/local/bin/SU2/run Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/adjoint.py to /usr/local/bin/SU2/run Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/deform.py to /usr/local/bin/SU2/run Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/direct.py to /usr/local/bin/SU2/run Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/interface.py to /usr/local/bin/SU2/run Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/merge.py to /usr/local/bin/SU2/run Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/geometry.py to /usr/local/bin/SU2/run Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/projection.py to /usr/local/bin/SU2/run Installing /home/hero/Downloads/SU2/SU2_PY/SU2/run/__init__.py to /usr/local/bin/SU2/run Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/bunch.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/filter_adjoint.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/lhc_unif.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/misc.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/mp_eval.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/ordered_bunch.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/ordered_dict.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/plot.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/polarSweepLib.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/which.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/switch.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/SU2/util/__init__.py to /usr/local/bin/SU2/util Installing /home/hero/Downloads/SU2/SU2_PY/FSI/__init__.py to /usr/local/bin/FSI Installing /home/hero/Downloads/SU2/SU2_PY/FSI/FSIInterface.py to /usr/local/bin/FSI Installing /home/hero/Downloads/SU2/SU2_PY/FSI/PitchPlungeAirfoilStructuralTester.py to /usr/local/bin/FSI Installing /home/hero/Downloads/SU2/SU2_PY/FSI/io/__init__.py to /usr/local/bin/FSI Installing /home/hero/Downloads/SU2/SU2_PY/FSI/io/FSI_config.py to /usr/local/bin/FSI Installing /home/hero/Downloads/SU2/SU2_PY/FSI/util/__init__.py to /usr/local/bin/FSI Installing /home/hero/Downloads/SU2/SU2_PY/FSI/util/switch.py to /usr/local/bin/FSI

March 16, 2020, 04:37		#8
hyunko Member Hyun Ko Join Date: Jun 2009 Posts: 32 Rep Power: 16	Thank you Umuteng. I have tried already about the superuser related stuff. The main reason of "multiple outputs for parallel run" was related to mpirun. I have cleared mpirun related error with using MPICH version mpirun. Thanks.