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 :
and the end of the log file :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.
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.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 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
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
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...