Cannot make it work

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Josuez
Posts: 16
Joined: Thu Jun 27, 2019 6:15 am

Cannot make it work

Post by Josuez »

Hello again,

as expected I have to stop by over here. I did multiple things that failed so I will try to develop it here as clearly as possible.

First let's talk about the environment :
- My system is Linux MX 18.3 which is Debian 9 based
- I performed everything within an anaconda environment on python 3.6.10

1st case :

After setting the compilers, mpi and other basic useful libraries in the environment by calling them through the conda install system, I tried to install code_saturne 6.0.1 by letting it download and compile HDF5, CGNS, MED, SCOTCH and METIS.
This fails at the code_saturne compilation stage apparently due to a cgns problem :
Console wrote:Installation of Code_Saturne

Code_Saturne (Code_Saturne CFD tool)
version: 5.0.11
url: None
package: code_saturne
source_dir: /home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne-5.0.11
install_dir: /home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/code_saturne-5.0.11/arch/Linux_x86_64
config_opts: --with-hdf5=/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/hdf5-1.8.20/arch/Linux_x86_64 --with-cgns=/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/cgns-3.4.0/arch/Linux_x86_64 --with-med=/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/med-3.3.1/arch/Linux_x86_64 --with-metis=/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/parmetis-4.0.3/arch/Linux_x86_64 --with-scotch=/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/scotch-6.0.6/arch/Linux_x86_64 PYTHON=/home/cosmo/anaconda3/envs/SCFD3/bin/python --disable-static

o Configure...
o Compile...
Error during compile stage of Code_Saturne.
See install_saturne.log for more information.
and the end of the log file :
install_saturne.log wrote:libtool: link: /home/cosmo/anaconda3/envs/SCFD3/bin/mpicc -funroll-loops -O2 -Wuninitialized -fexcess-precision=fast -std=c99 -fms-extensions -funsigned-char -pedantic -W -Wall -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Wunused -Wfloat-equal -Wmisleading-indentation -Wduplicated-cond -fdiagnostics-color=auto -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/cosmo/anaconda3/envs/SCFD3/include -fopenmp -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath -Wl,/home/cosmo/anaconda3/envs/SCFD3/lib -Wl,-rpath-link -Wl,/home/cosmo/anaconda3/envs/SCFD3/lib -O -Wl,-export-dynamic -fopenmp -o cs_preprocess cs_preprocess-ecs_cmd.o cs_preprocess-ecs_main.o -L/home/cosmo/anaconda3/envs/SCFD3/lib ../../preprocessor/pre-post/.libs/libprepostecs.a ../../preprocessor/base/.libs/libbaseecs.a ../../preprocessor/util/.libs/libutilecs.a -L/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/med-3.3.1/arch/Linux_x86_64/lib -lmedC -L/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/cgns-3.4.0/arch/Linux_x86_64/lib -lcgns -L/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/hdf5-1.8.20/arch/Linux_x86_64/lib /home/cosmo/anaconda3/envs/SCFD3/lib/libhdf5.so -lm -lz -ldl -fopenmp -Wl,-rpath -Wl,/home/cosmo/anaconda3/envs/SCFD3/lib -Wl,-rpath -Wl,/home/cosmo/anaconda3/envs/SCFD3/lib -Wl,-rpath -Wl,/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/med-3.3.1/arch/Linux_x86_64/lib -Wl,-rpath -Wl,/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/cgns-3.4.0/arch/Linux_x86_64/lib -Wl,-rpath -Wl,/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne/hdf5-1.8.20/arch/Linux_x86_64/lib
/home/cosmo/anaconda3/envs/SCFD3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../preprocessor/pre-post/.libs/libprepostecs.a(libprepostecs_la-ecs_pre_cgns.o): in function `ecs_loc_pre_cgns__lit_ele':
ecs_pre_cgns.c:(.text.ecs_loc_pre_cgns__lit_ele+0x878): undefined reference to `cg_poly_elements_read'
collect2: error: ld returned 1 exit status
Makefile:750: recipe for target 'cs_preprocess' failed
make[3]: *** [cs_preprocess] Error 1
make[3]: Leaving directory '/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne-5.0.11.build/preprocessor/appli'
Makefile:641: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne-5.0.11.build/preprocessor'
Makefile:1462: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/cosmo/anaconda3/envs/SCFD3/opt/code_saturne-5.0.11.build'
Makefile:954: recipe for target 'all' failed
make: *** [all] Error 2
That's it for the first part, I cannot find how to make it work. I tried with the version 5.0.11 of code_saturne and ended up with the same result so it seems something in my installation is shady.

2nd case :

So to not stay on such failure, I decided to install all the necessary library beforehand through anaconda. So after

Code: Select all

conda install -c conda-forge hdf5 cgns libmed scotch metis
I retry the installation by pointing the setup file to these libraries, and surprise it works.

So I go and make a very simple test case with it, and there goes my luck. It can load the meshfile but can't even run a mesh quality analysis, says solver failed and leave a corrupted listing file so I can only show you the summary file.
I also tried this with a different version of code_saturne for the same result. Difficult to interpret since I don't have any hint on what is wrong besides a solver failed message.

By the way, I installed syrthes 4.3.5 with the same anaconda libraries and it experiences no problem so far...
Attachments
second_case.tar.gz
(4.65 MiB) Downloaded 86 times
first_case.tar.gz
(210.64 KiB) Downloaded 85 times
Yvan Fournier
Posts: 3424
Joined: Mon Feb 20, 2012 3:25 pm

Re: Cannot make it work

Post by Yvan Fournier »

Hello,

Would your CGNS version perchance be version 3.4.1 ? The CGNS developers broke upwards compatibility in 3.4.0, so to "fix" this, they decided to break it again the other way around, and code_saturne's tests may not be up to date yet ? Can you first try without CGNS ?

For your case that starts but fails, are you running in parallel or not ? Could you try a serial run first ?
Also, even if you only have a corrupted part of the run_solver.log (listing in 5.0), an a "screen" error message, could you post that ? I suspect some mix between multiple versions of some libraries.

Best regards,

Yvan
Josuez
Posts: 16
Joined: Thu Jun 27, 2019 6:15 am

Re: Cannot make it work

Post by Josuez »

Hello !

Ok, so, in order to test and eliminate as much conflicts as possible, I created a virtual machine under MX Linux 18.3.
I just performed the base package update and created one environment under python 3.6
Sorry in advance the post is going to be long due to the quotes, but I thought it might be clearer that way. I will treat each case in separate replies.

This case correspond to the automatic download and installation of libraries by install_saturne.py

Here are the packages in the environment when I attempted automatic installation :
console wrote:# packages in environment at /home/cosmo/anaconda3/envs/SCFD:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
bash 5.0.011 hcee41ef_0 conda-forge
binutils-meta 1.0.4 0 conda-forge
binutils_impl_linux-64 2.33.1 he1b5a44_7 conda-forge
binutils_linux-64 2.33.1 h9595d00_16 conda-forge
bzip2 1.0.8 h516909a_2 conda-forge
c-compiler 1.0.4 h516909a_0 conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
certifi 2019.11.28 py36_0 conda-forge
cmake 3.16.4 h28c56e5_0 conda-forge
compilers 1.0.4 0 conda-forge
cxx-compiler 1.0.4 hc9558a2_0 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
fortran-compiler 1.0.4 he991be0_0 conda-forge
gcc_impl_linux-64 7.3.0 habb00fd_1
gcc_linux-64 7.3.0 h553295d_16 conda-forge
gfortran_impl_linux-64 7.3.0 hdf63c60_5 conda-forge
gfortran_linux-64 7.3.0 h553295d_16 conda-forge
gxx_impl_linux-64 7.3.0 hdf63c60_1
gxx_linux-64 7.3.0 h553295d_16 conda-forge
icu 64.2 he1b5a44_1 conda-forge
krb5 1.16.4 h173b8e3_0
ld_impl_linux-64 2.33.1 h53a641e_7
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libcurl 7.68.0 hda55be3_0 conda-forge
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libopenblas 0.3.7 h5ec1e0e_6 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0
libuv 1.34.0 h516909a_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
mpi 1.0 openmpi conda-forge
ncurses 6.1 he6710b0_1
numpy 1.18.1 py36h95a1406_0 conda-forge
openmpi 4.0.2 hdf1f1ad_3 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
pip 20.0.2 py36_1
python 3.6.7 h357f687_1006 conda-forge
readline 8.0 hf8c457e_0 conda-forge
rhash 1.3.6 h14c3975_1001 conda-forge
setuptools 45.2.0 py36_0
sqlite 3.31.1 h7b6447c_0
tcsh 6.22.02 h46ee950_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
wheel 0.34.2 py36_0
xz 5.2.4 h14c3975_4
zlib 1.2.11 h516909a_1006 conda-forge
For this try I didn't exclude the cgns :
setup wrote:#========================================================
# Setup file for Code_Saturne installation
#========================================================
#
#--------------------------------------------------------
# Download packages ?
#--------------------------------------------------------
download yes
#
#--------------------------------------------------------
# Language
# default: "en" english
# others: "fr" french
#--------------------------------------------------------
language en
#
#--------------------------------------------------------
# Install Code_Saturne with debugging symbols
#--------------------------------------------------------
debug no
#
#--------------------------------------------------------
# Installation directory
#--------------------------------------------------------
prefix /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1
#
#--------------------------------------------------------
# Optional architecture Name (installation subdirectory)
#--------------------------------------------------------
use_arch no
arch Linux_x86_64
#
#--------------------------------------------------------
# C compiler and optional MPI wrapper
#--------------------------------------------------------
compC /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-cc
mpiCompC /home/cosmo/anaconda3/envs/SCFD/bin/mpicc
#
#--------------------------------------------------------
# Fortran compiler
#--------------------------------------------------------
compF /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-gfortran
#
#--------------------------------------------------------
# C++ compiler and MPI wrapper for optional packages
#
# Required only for static builds using the MED library
# or for build of optional modules such as MEDCoupling
# support.
#--------------------------------------------------------
compCxx /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-c++
mpiCompCxx /home/cosmo/anaconda3/envs/SCFD/bin/mpicxx
#
#--------------------------------------------------------
# Python interpreter.
#--------------------------------------------------------
python /home/cosmo/anaconda3/envs/SCFD/bin/python
#
#--------------------------------------------------------
# Disable the Graphical user Interface ?
#--------------------------------------------------------
disable_gui no
#
#--------------------------------------------------------
# Disable frontend (also disables GUI) ?
# May be useful for debug builds and HPC cluster builds
# installed side-by side with a full build.
#--------------------------------------------------------
disable_frontend no
#
#--------------------------------------------------------
# Optional SALOME platform install path.
#
# This is the path for the main SALOME directory,
# not the application directory.
#
# If Code_Saturne is built with SALOME support,
# running "code_saturne salome" will launch the
# associated application, containing the CFDSTUDY module.
#--------------------------------------------------------
salome no
#
#--------------------------------------------------------
# Optional packages:
# ------------------
#
# MED / HDF5 For MED file format support
# (used by SALOME and by Gmsh)
#
# CGNS / HDF5 For CGNS file support
# (used by many meshing tools)
#
# Scotch (includes PT-Scotch) and/or ParMetis
# for parallel partitioning
#
# For Linux workstations, HDF5, CGNS, and even MED
# packages may be available through the package manager.
# HDF5 is also often available on large systems.
# When building with SALOME, the platform distribution's
# packages may be used, by setting in the matching entry
# 'yes' under the "Use" column and simply 'salome' under
# the path column.
#
# Scotch and Pt-Scotch are available in some Linux
# distributions, but may be built with options
# incompatible with non-threaded Code_Saturne runs.
#
# To install CGNS or ParMetis, the CMake
# configuration/installation tool is required
# (it is available in most Linux distributions).
#--------------------------------------------------------
#
# Name Use Install Path
#
hdf5 yes yes None
cgns yes yes None
med yes yes None
scotch no no None
parmetis no no None
#
#========================================================
get the following console output :
console wrote:$ /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne-6.0.1/install_saturne.py

Installation of Code_Saturne
____________________________

The process will take several minutes.
You can have a look at the log file meanwhile.

Check the setup file and some utilities presence.

o Checking for x86_64-conda_cos6-linux-gnu-cc... /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-cc
o Checking for mpicc... /home/cosmo/anaconda3/envs/SCFD/bin/mpicc
o Checking for x86_64-conda_cos6-linux-gnu-gfortran... /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-gfortran
o Checking for python... /home/cosmo/anaconda3/envs/SCFD/bin/python
Python version is 3.6
o Checking for make... /usr/bin/make

Download of HDF5
(https://support.hdfgroup.org/ftp/HDF5/r ... 0.5.tar.gz)
Download of CGNS
(https://github.com/CGNS/CGNS/archive/v3.4.0.tar.gz)
Download of MED
(http://files.salome-platform.org/Salome ... 0.0.tar.gz)


HDF5 (Hierarchical Data Format)
version: 1.10.5
url: https://support.hdfgroup.org/ftp/HDF5/r ... 0.5.tar.gz
package: hdf5
source_dir: None
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64
config_opts: --enable-build-mode=production

Extract of HDF5
Installation of HDF5

HDF5 (Hierarchical Data Format)
version: 1.10.5
url: https://support.hdfgroup.org/ftp/HDF5/r ... 0.5.tar.gz
package: hdf5
source_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/hdf5-1.10.5
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64
config_opts: --enable-build-mode=production

o Configure...
o Compile...
o Install...
o Clean...


CGNS (CFD General Notation System)
version: 3.4.0
url: https://github.com/CGNS/CGNS/archive/v3.4.0.tar.gz
package: cgns
source_dir: None
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/cgns-3.4.0/arch/Linux_x86_64
config_opts: -DCGNS_ENABLE_64BIT=ON -DCGNS_ENABLE_SCOPING=ON -DCGNS_ENABLE_HDF5=ON -DCMAKE_PREFIX_PATH=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64 -DHDF5_INCLUDE_PATH=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64/include

Extract of CGNS
Installation of CGNS

CGNS (CFD General Notation System)
version: 3.4.0
url: https://github.com/CGNS/CGNS/archive/v3.4.0.tar.gz
package: cgns
source_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/CGNS-3.4.0
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/cgns-3.4.0/arch/Linux_x86_64
config_opts: -DCGNS_ENABLE_64BIT=ON -DCGNS_ENABLE_SCOPING=ON -DCGNS_ENABLE_HDF5=ON -DCMAKE_PREFIX_PATH=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64 -DHDF5_INCLUDE_PATH=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64/include

o Configure...
o Compile...
o Install...
o Clean...


MED (Model for Exchange of Data)
version: 4.0.0
url: http://files.salome-platform.org/Salome ... 0.0.tar.gz
package: med
source_dir: None
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/med-4.0.0/arch/Linux_x86_64
config_opts: --with-med_int=long --disable-fortran --disable-python --with-hdf5=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64

Extract of MED
Installation of MED

MED (Model for Exchange of Data)
version: 4.0.0
url: http://files.salome-platform.org/Salome ... 0.0.tar.gz
package: med
source_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/med-4.0.0
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/med-4.0.0/arch/Linux_x86_64
config_opts: --with-med_int=long --disable-fortran --disable-python --with-hdf5=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64

o Configure...
o Compile...
o Install...
o Clean...


scotch (PT-Scotch)
version: 6.0.6
url: https://gforge.inria.fr/frs/download.ph ... 0.6.tar.gz
package: scotch
source_dir: None
install_dir: None
config_opts:


parmetis (ParMETIS)
version: 4.0.3
url: http://glaros.dtc.umn.edu/gkhome/fetch/ ... 0.3.tar.gz
package: parmetis
source_dir: None
install_dir: None
config_opts:


Code_Saturne (Code_Saturne CFD tool)
version: 6.0.1
url: None
package: code_saturne
source_dir: None
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64
config_opts: --with-hdf5=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64 --with-cgns=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/cgns-3.4.0/arch/Linux_x86_64 --with-med=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/med-4.0.0/arch/Linux_x86_64 --without-metis --without-scotch PYTHON=/home/cosmo/anaconda3/envs/SCFD/bin/python --disable-static

Installation of Code_Saturne

Code_Saturne (Code_Saturne CFD tool)
version: 6.0.1
url: None
package: code_saturne
source_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne-6.0.1
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64
config_opts: --with-hdf5=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/hdf5-1.10.5/arch/Linux_x86_64 --with-cgns=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/cgns-3.4.0/arch/Linux_x86_64 --with-med=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/med-4.0.0/arch/Linux_x86_64 --without-metis --without-scotch PYTHON=/home/cosmo/anaconda3/envs/SCFD/bin/python --disable-static

o Configure...
Error during configure stage of Code_Saturne.
See install_saturne.log for more information.
And the error seems to be HDF5 related :
install_saturne.log wrote:checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for H5Fopen in -lhdf5-shared... no
checking for H5Fopen in -lhdf5-static... no
checking for H5Fopen in -lhdf5... no
configure: error: in `/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne-6.0.1.build':
configure: error: HDF5 support is requested, but test for HDF5 failed!
See `config.log' for more details
Attachments
install_saturne.log
(2.43 MiB) Downloaded 88 times
Josuez
Posts: 16
Joined: Thu Jun 27, 2019 6:15 am

Re: Cannot make it work

Post by Josuez »

This is the case where HDF5, CGNS and MED were installed through conda in the environment

Here are the libraries in the environment :
console wrote:# packages in environment at /home/cosmo/anaconda3/envs/SCFD:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
bash 5.0.011 hcee41ef_0 conda-forge
binutils-meta 1.0.4 0 conda-forge
binutils_impl_linux-64 2.33.1 he1b5a44_7 conda-forge
binutils_linux-64 2.33.1 h9595d00_16 conda-forge
bzip2 1.0.8 h516909a_2 conda-forge
c-compiler 1.0.4 h516909a_0 conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
certifi 2019.11.28 py36_0 conda-forge
cgns 3.2.1 h7fde49b_0 conda-forge
cmake 3.16.4 h28c56e5_0 conda-forge
compilers 1.0.4 0 conda-forge
cxx-compiler 1.0.4 hc9558a2_0 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
fortran-compiler 1.0.4 he991be0_0 conda-forge
gcc_impl_linux-64 7.3.0 habb00fd_1
gcc_linux-64 7.3.0 h553295d_16 conda-forge
gfortran_impl_linux-64 7.3.0 hdf63c60_5 conda-forge
gfortran_linux-64 7.3.0 h553295d_16 conda-forge
gxx_impl_linux-64 7.3.0 hdf63c60_1
gxx_linux-64 7.3.0 h553295d_16 conda-forge
hdf5 1.8.20 1 conda-forge
icu 64.2 he1b5a44_1 conda-forge
krb5 1.16.4 h173b8e3_0
ld_impl_linux-64 2.33.1 h53a641e_7
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libcurl 7.68.0 hda55be3_0 conda-forge
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 9.1.0 hdf63c60_0
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libmed 3.3.1 py36h9cad2ed_1001 conda-forge
libopenblas 0.3.7 h5ec1e0e_6 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0
libuv 1.34.0 h516909a_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
mpi 1.0 openmpi conda-forge
ncurses 6.1 he6710b0_1
numpy 1.18.1 py36h95a1406_0 conda-forge
openmpi 4.0.2 hdf1f1ad_3 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
pip 20.0.2 py36_1
pyqt5 5.14.1 pypi_0 pypi
pyqt5-sip 12.7.1 pypi_0 pypi
pyqtchart 5.14.0 pypi_0 pypi
python 3.6.7 h357f687_1006 conda-forge
readline 8.0 hf8c457e_0 conda-forge
rhash 1.3.6 h14c3975_1001 conda-forge
setuptools 45.2.0 py36_0
sqlite 3.31.1 h7b6447c_0
tcsh 6.22.02 h46ee950_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
wheel 0.34.2 py36_0
xz 5.2.4 h14c3975_4
zlib 1.2.11 h516909a_1006 conda-forge
Here is the setup file :
setup wrote:#========================================================
# Setup file for Code_Saturne installation
#========================================================
#
#--------------------------------------------------------
# Download packages ?
#--------------------------------------------------------
download no
#
#--------------------------------------------------------
# Language
# default: "en" english
# others: "fr" french
#--------------------------------------------------------
language en
#
#--------------------------------------------------------
# Install Code_Saturne with debugging symbols
#--------------------------------------------------------
debug no
#
#--------------------------------------------------------
# Installation directory
#--------------------------------------------------------
prefix /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1
#
#--------------------------------------------------------
# Optional architecture Name (installation subdirectory)
#--------------------------------------------------------
use_arch no
arch Linux_x86_64
#
#--------------------------------------------------------
# C compiler and optional MPI wrapper
#--------------------------------------------------------
compC /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-cc
mpiCompC /home/cosmo/anaconda3/envs/SCFD/bin/mpicc
#
#--------------------------------------------------------
# Fortran compiler
#--------------------------------------------------------
compF /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-gfortran
#
#--------------------------------------------------------
# C++ compiler and MPI wrapper for optional packages
#
# Required only for static builds using the MED library
# or for build of optional modules such as MEDCoupling
# support.
#--------------------------------------------------------
compCxx /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-c++
mpiCompCxx /home/cosmo/anaconda3/envs/SCFD/bin/mpicxx
#
#--------------------------------------------------------
# Python interpreter.
#--------------------------------------------------------
python /home/cosmo/anaconda3/envs/SCFD/bin/python
#
#--------------------------------------------------------
# Disable the Graphical user Interface ?
#--------------------------------------------------------
disable_gui no
#
#--------------------------------------------------------
# Disable frontend (also disables GUI) ?
# May be useful for debug builds and HPC cluster builds
# installed side-by side with a full build.
#--------------------------------------------------------
disable_frontend no
#
#--------------------------------------------------------
# Optional SALOME platform install path.
#
# This is the path for the main SALOME directory,
# not the application directory.
#
# If Code_Saturne is built with SALOME support,
# running "code_saturne salome" will launch the
# associated application, containing the CFDSTUDY module.
#--------------------------------------------------------
salome no
#
#--------------------------------------------------------
# Optional packages:
# ------------------
#
# MED / HDF5 For MED file format support
# (used by SALOME and by Gmsh)
#
# CGNS / HDF5 For CGNS file support
# (used by many meshing tools)
#
# Scotch (includes PT-Scotch) and/or ParMetis
# for parallel partitioning
#
# For Linux workstations, HDF5, CGNS, and even MED
# packages may be available through the package manager.
# HDF5 is also often available on large systems.
# When building with SALOME, the platform distribution's
# packages may be used, by setting in the matching entry
# 'yes' under the "Use" column and simply 'salome' under
# the path column.
#
# Scotch and Pt-Scotch are available in some Linux
# distributions, but may be built with options
# incompatible with non-threaded Code_Saturne runs.
#
# To install CGNS or ParMetis, the CMake
# configuration/installation tool is required
# (it is available in most Linux distributions).
#--------------------------------------------------------
#
# Name Use Install Path
#
hdf5 yes no /home/cosmo/anaconda3/envs/SCFD
cgns yes no /home/cosmo/anaconda3/envs/SCFD
med yes no /home/cosmo/anaconda3/envs/SCFD
scotch no no None
parmetis no no None
#
#========================================================
Installation perform with success :
console wrote:$ /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne-6.0.1/install_saturne.py

Installation of Code_Saturne
____________________________

The process will take several minutes.
You can have a look at the log file meanwhile.

Check the setup file and some utilities presence.

o Checking for x86_64-conda_cos6-linux-gnu-cc... /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-cc
o Checking for mpicc... /home/cosmo/anaconda3/envs/SCFD/bin/mpicc
o Checking for x86_64-conda_cos6-linux-gnu-gfortran... /home/cosmo/anaconda3/envs/SCFD/bin/x86_64-conda_cos6-linux-gnu-gfortran
o Checking for python... /home/cosmo/anaconda3/envs/SCFD/bin/python
Python version is 3.6
o Checking for make... /usr/bin/make



HDF5 (Hierarchical Data Format)
version: 1.10.5
url: https://support.hdfgroup.org/ftp/HDF5/r ... 0.5.tar.gz
package: hdf5
source_dir: None
install_dir: /home/cosmo/anaconda3/envs/SCFD
config_opts: --enable-build-mode=production


CGNS (CFD General Notation System)
version: 3.4.0
url: https://github.com/CGNS/CGNS/archive/v3.4.0.tar.gz
package: cgns
source_dir: None
install_dir: /home/cosmo/anaconda3/envs/SCFD
config_opts: -DCGNS_ENABLE_64BIT=ON -DCGNS_ENABLE_SCOPING=ON -DCGNS_ENABLE_HDF5=ON -DCMAKE_PREFIX_PATH=/home/cosmo/anaconda3/envs/SCFD -DHDF5_INCLUDE_PATH=/home/cosmo/anaconda3/envs/SCFD/include


MED (Model for Exchange of Data)
version: 4.0.0
url: http://files.salome-platform.org/Salome ... 0.0.tar.gz
package: med
source_dir: None
install_dir: /home/cosmo/anaconda3/envs/SCFD
config_opts: --with-med_int=long --disable-fortran --disable-python --with-hdf5=/home/cosmo/anaconda3/envs/SCFD


scotch (PT-Scotch)
version: 6.0.6
url: https://gforge.inria.fr/frs/download.ph ... 0.6.tar.gz
package: scotch
source_dir: None
install_dir: None
config_opts:


parmetis (ParMETIS)
version: 4.0.3
url: http://glaros.dtc.umn.edu/gkhome/fetch/ ... 0.3.tar.gz
package: parmetis
source_dir: None
install_dir: None
config_opts:


Code_Saturne (Code_Saturne CFD tool)
version: 6.0.1
url: None
package: code_saturne
source_dir: None
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64
config_opts: --with-hdf5=/home/cosmo/anaconda3/envs/SCFD --with-cgns=/home/cosmo/anaconda3/envs/SCFD --with-med=/home/cosmo/anaconda3/envs/SCFD --without-metis --without-scotch PYTHON=/home/cosmo/anaconda3/envs/SCFD/bin/python --disable-static

Installation of Code_Saturne

Code_Saturne (Code_Saturne CFD tool)
version: 6.0.1
url: None
package: code_saturne
source_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne-6.0.1
install_dir: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64
config_opts: --with-hdf5=/home/cosmo/anaconda3/envs/SCFD --with-cgns=/home/cosmo/anaconda3/envs/SCFD --with-med=/home/cosmo/anaconda3/envs/SCFD --without-metis --without-scotch PYTHON=/home/cosmo/anaconda3/envs/SCFD/bin/python --disable-static

o Configure...
o Compile...
o Install...
o Clean...


Before using Code_Saturne, please update your environment with:

cspath=/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64/bin
alias code_saturne="$cspath/code_saturne"

The documentation should then be available through the commands:
code_saturne info -g refcard
code_saturne info -g user

Do not forget the post-installation steps recommended in the
installation documentation, available using:
code_saturne info -g install


Thank you for choosing Code_Saturne!
Then the error occurs while testing code_saturne again on a mesh quality :
code_saturne wrote: Code_Saturne
************

Version: 6.0
Path: /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64

Result directory:
/home/cosmo/Documents/test/spike/RESU/resu



****************************
Preparing calculation data
****************************

Single processor Code_Saturne simulation.


***************************
Preprocessing calculation
***************************


**********************
Starting calculation
**********************

/home/cosmo/Documents/test/spike/RESU/resu/run_solver: line 11: 5498 Segmentation fault /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64/libexec/code_saturne/cs_solver --quality $@

*****************************
Post-calculation operations
*****************************

solver script exited with status 139.

Error running the calculation.

Check Code_Saturne log (listing) and error* files for details.

Error in calculation stage.
The full folder of the test case is in the attached tarball, with the error files.
Attachments
test_case.tar.gz
(4.81 MiB) Downloaded 88 times
Yvan Fournier
Posts: 3424
Joined: Mon Feb 20, 2012 3:25 pm

Re: Cannot make it work

Post by Yvan Fournier »

Hello,

Could you post the output of

Code: Select all

export LD_LIBRARY_PATH="/home/cosmo/anaconda3/envs/SCFD/lib":$LD_LIBRARY_PATH
ldd /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64/libexec/code_saturne/cs_solver
And attach the "run_solver.log" file from your results case ("listing" is only a symbolic link, so does not contain the backtrace) ?

Running using your "mesh_input" file, things work fine on my side, so this is certainly a build issue. The preprocessor/mesh import stage worked fine...

Best regards,

Yvan
Josuez
Posts: 16
Joined: Thu Jun 27, 2019 6:15 am

Re: Cannot make it work

Post by Josuez »

Hello,

Unfortunately there is no run_solver.log file generated. I even launched a search for it in the whole /cosmo root just in case.
And yes, listing is only a symbolic link, but it is a broken one in my case. It doesn't make reference to anything...

As for what you requested, here is the output :
console wrote:(SCFD) cosmo@simu:~/anaconda3/envs/SCFD/opt/code_saturne
$ export LD_LIBRARY_PATH="/home/cosmo/anaconda3/envs/SCFD/lib":$LD_LIBRARY_PATH
(SCFD) cosmo@simu:~/anaconda3/envs/SCFD/opt/code_saturne
$ ldd /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64/libexec/code_saturne/cs_solver
linux-vdso.so.1 (0x00007ffe79dfe000)
libcs_solver-6.0.so => /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64/lib/libcs_solver-6.0.so (0x00007f5fa45e3000)
libpthread.so.0 => /home/cosmo/anaconda3/envs/SCFD/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/libpthread.so.0 (0x00007f5fa45c4000)
libc.so.6 => /home/cosmo/anaconda3/envs/SCFD/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/libc.so.6 (0x00007f5fa4459000)
libsaturne-6.0.so => /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64/lib/libsaturne-6.0.so (0x00007f5fa2d7b000)
libple.so.2 => /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64/lib/libple.so.2 (0x00007f5fa4441000)
libcgns.so.3.2 => /home/cosmo/anaconda3/envs/SCFD/lib/libcgns.so.3.2 (0x00007f5fa2c9d000)
libmedC.so => /home/cosmo/anaconda3/envs/SCFD/lib/libmedC.so (0x00007f5fa2b6d000)
libhdf5.so.10 => /home/cosmo/anaconda3/envs/SCFD/lib/libhdf5.so.10 (0x00007f5fa2681000)
libgfortran.so.4 => /home/cosmo/anaconda3/envs/SCFD/lib/libgfortran.so.4 (0x00007f5fa2553000)
libm.so.6 => /home/cosmo/anaconda3/envs/SCFD/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/libm.so.6 (0x00007f5fa24d1000)
libquadmath.so.0 => /home/cosmo/anaconda3/envs/SCFD/lib/libquadmath.so.0 (0x00007f5fa4405000)
libz.so.1 => /home/cosmo/anaconda3/envs/SCFD/lib/libz.so.1 (0x00007f5fa24b7000)
libdl.so.2 => /home/cosmo/anaconda3/envs/SCFD/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/libdl.so.2 (0x00007f5fa4400000)
libgomp.so.1 => /home/cosmo/anaconda3/envs/SCFD/lib/libgomp.so.1 (0x00007f5fa248a000)
/lib64/ld-linux-x86-64.so.2 (0x00007f5fa43cf000)
libmpi.so.40 => /home/cosmo/anaconda3/envs/SCFD/lib/libmpi.so.40 (0x00007f5fa2368000)
libstdc++.so.6 => /home/cosmo/anaconda3/envs/SCFD/lib/./libstdc++.so.6 (0x00007f5fa21f4000)
libgcc_s.so.1 => /home/cosmo/anaconda3/envs/SCFD/lib/./libgcc_s.so.1 (0x00007f5fa21e0000)
librt.so.1 => /home/cosmo/anaconda3/envs/SCFD/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/librt.so.1 (0x00007f5fa43f4000)
libopen-rte.so.40 => /home/cosmo/anaconda3/envs/SCFD/lib/./libopen-rte.so.40 (0x00007f5fa2125000)
libopen-pal.so.40 => /home/cosmo/anaconda3/envs/SCFD/lib/./libopen-pal.so.40 (0x00007f5fa2010000)
libutil.so.1 => /home/cosmo/anaconda3/envs/SCFD/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/libutil.so.1 (0x00007f5fa200b000)
Best regards
Yvan Fournier
Posts: 3424
Joined: Mon Feb 20, 2012 3:25 pm

Re: Cannot make it work

Post by Yvan Fournier »

Hello,

The symbolic link might be broken because it is created by the script, before cs_solver starts and creates the real run_solver.log. It is more surprising that the run_solver script is not created, as this is standard script business It is usually cleaned up whe na case does not finish in error, so in the runcase file, you might add --initialize to the run command (you can also do it using the advanced settings in the GUI, "initialize only"). This prepares the run but does not start it, so you should have that file.

Otherwise, what is the output of:

Code: Select all

/home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64/libexec/code_saturne/cs_solver --system-info
? I did not notice anything strange about the ldd output.

Best regards,

Yvan
Josuez
Posts: 16
Joined: Thu Jun 27, 2019 6:15 am

Re: Cannot make it work

Post by Josuez »

Good morning,

Even with --initialize nothing is created except the preprocessor.log and summary, listing link is still broken.
Worse, the solver seems to be corrupted :
console wrote:$ /home/cosmo/anaconda3/envs/SCFD/opt/code_saturne/6.0.1/code_saturne-6.0.1/arch/Linux_x86_64/libexec/code_saturne/cs_solver --system-info
Segmentation fault
best regards
Yvan Fournier
Posts: 3424
Joined: Mon Feb 20, 2012 3:25 pm

Re: Cannot make it work

Post by Yvan Fournier »

Hello,

Is suspected the solver might be corrupted, but am not sure why. Tis type of issue usually occurs when mixing incompatible dependencies, but I did not notice anything wrong in your "ldd" output (though things may be subtle).

Did you run your install in several steps, or did you make sure you did a "clean" install, that is, run the whole code_saturne build in a previously empty directory ? If this is not the case, this is the first thing to try (I should have mentioned it before).

Otherwise, the best way to find out what is wrong is to start with a minimal install (no HDF5, MED, CGNS, Scotch, Metis) with maybe just MPI and see if the executable is OK or corrupted (the "system-info check"). If not, try removing MPI. If OK, try progressively adding the other features to see which one is causing trouble.

Best regards,

Yvan
Josuez
Posts: 16
Joined: Thu Jun 27, 2019 6:15 am

Re: Cannot make it work

Post by Josuez »

Hello !

At last, I made it.
And I come back to give some updates to all the people out there who might be eager to know what went wrong in my case.

So apparently, code_saturne do not like the full anaconda environment. I didn't push the research too far but I suspect the environment compilers.

So here is what I did :

- Started from a clean Linux MX 18.3 install
- Installed all normal updates and upgrades
- Install through apt-get if not present : gcc g++ gfortran libstdc++5 build-essential make cmake zlib1g libxml2. Maybe libxml2-dev is also needed but not sure.
- Install openmpi from tarball (openmpi-4.0.2) in a non protected direction
- export the mpi path to the LD_LIBRARY_PATH

Code: Select all

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/your/mpi/path
in the bashrc and source it
- Install anaconda for python 3 in a non protected direction (follow the website guide)

From there nothing should be done as a superuser except bashrc editing

- Install Salome-V9_3_0-univ_public.run in a non protected direction
- create a python 3.6 environment
- In the environment, install numpy through conda-forge and PyQtChart through pip (it prepares the ground for Syrthes and provide all PyQt libs)
I think that's mostly it for setting the system.

Then I followed the normal code_saturne install procedure
logically it should automatically find the usr/bin compilers and the previously installed mpi compilers.
I didn't integrate code_saturne to Salome but used Salome's HDF5, CGNS and MED for code_saturne build, it's important for mesh compatibility later.
scotch and parmetis where installed using the automatic download/install.
And voila, a working and MPI ready code_saturne.

Later I also successfully installed and coupled Syrthes in the same environment, carefully linking the tools used by code_saturne.

Thank you again Yvan and hope this helps some tortured soul out there
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