Hi!
I currently try to run "Functional testing" in example.rst.
But, I got an error after caluculation of psr.
My environment is WSL working on windows.
And, I installed pyJac using conda.
I think it is caused from installation of Adept.
I installed Adept using command shown in README on Adept github repository.
Does anyone know the way to solve this issue?
~/github/pyJac$ python -m pyjac.functional_tester --mech data/h2o2.cti --lang c --pasr_output h2_pasr_output.npy
/usr/bin/gcc
User specified last species not found or not specified. Attempting to find a default species
Warning: Neither a user specified or default last species could be found. Proceeding using the last species in the base mechanism: N2
User specified last species not found or not specified. Attempting to find a default species
Warning: Neither a user specified or default last species could be found. Proceeding using the last species in the base mechanism: N2
gcc -std=c99 -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/chem_utils.c -o /home/syoukera/github/pyJac/obj/chem_utils.o
gcc -std=c99 -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/dydt.c -o /home/syoukera/github/pyJac/obj/dydt.o
gcc -std=c99 -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/spec_rates.c -o /home/syoukera/github/pyJac/obj/spec_rates.o
gcc -std=c99 -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/rxn_rates.c -o /home/syoukera/github/pyJac/obj/rxn_rates.o
gcc -std=c99 -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/mechanism.c -o /home/syoukera/github/pyJac/obj/mechanism.o
gcc -std=c99 -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/mass_mole.c -o /home/syoukera/github/pyJac/obj/mass_mole.o
gcc -std=c99 -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/rxn_rates_pres_mod.c -o /home/syoukera/github/pyJac/obj/rxn_rates_pres_mod.o
gcc -std=c99 -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/jacob.c -o /home/syoukera/github/pyJac/obj/jacob.o
ar rcs /home/syoukera/github/pyJac/build/temp.linux-x86_64-3.6/libc_pyjac.a /home/syoukera/github/pyJac/obj/chem_utils.o /home/syoukera/github/pyJac/obj/dydt.o /home/syoukera/github/pyJac/obj/spec_rates.o /home/syoukera/github/pyJac/obj/rxn_rates.o /home/syoukera/github/pyJac/obj/mechanism.o /home/syoukera/github/pyJac/obj/mass_mole.o /home/syoukera/github/pyJac/obj/rxn_rates_pres_mod.o /home/syoukera/github/pyJac/obj/jacob.o
running build_ext
skipping '/home/syoukera/github/pyJac/pyjac/pywrap/pyjacob_wrapper.c' Cython extension (up-to-date)
g++ -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/ad_dydt.c -o /home/syoukera/github/pyJac/obj/ad_dydt.o
g++ -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/ad_rxn_rates.c -o /home/syoukera/github/pyJac/obj/ad_rxn_rates.o
g++ -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/ad_spec_rates.c -o /home/syoukera/github/pyJac/obj/ad_spec_rates.o
g++ -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/ad_chem_utils.c -o /home/syoukera/github/pyJac/obj/ad_chem_utils.o
g++ -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/ad_jac.c -o /home/syoukera/github/pyJac/obj/ad_jac.o
g++ -O3 -mtune=native -fPIC -I/home/syoukera/github/pyJac/out -I/usr/local/include/ -c /home/syoukera/github/pyJac/out/ad_rxn_rates_pres_mod.c -o /home/syoukera/github/pyJac/obj/ad_rxn_rates_pres_mod.o
ar rcs /home/syoukera/github/pyJac/build/temp.linux-x86_64-3.6/libad_pyjac.a /home/syoukera/github/pyJac/obj/ad_dydt.o /home/syoukera/github/pyJac/obj/ad_rxn_rates.o /home/syoukera/github/pyJac/obj/ad_spec_rates.o /home/syoukera/github/pyJac/obj/ad_chem_utils.o /home/syoukera/github/pyJac/obj/ad_jac.o /home/syoukera/github/pyJac/obj/ad_rxn_rates_pres_mod.o
running build_ext
skipping '/home/syoukera/github/pyJac/pyjac/pywrap/adjacob_wrapper.cpp' Cython extension (up-to-date)
Could not load saved pasr data... re-running
/home/syoukera/github/pyJac/pyjac/functional_tester/partially_stirred_reactor.py:967: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
pars = yaml.load(f)
Time [ms] Temperature [K]
0.00 2387.6
0.10 2387.6
0.20 2387.6
0.30 2387.6
0.40 2387.6
0.50 2387.6
0.60 2187.7
0.70 2026.3
0.80 2064.9
0.90 2324.2
1.00 2351.7
1.10 2357.3
1.20 2366.3
1.30 2375.8
1.40 2378.8
1.50 2381.3
1.60 2182.9
1.70 2024.6
1.80 2064.1
1.90 2323.5
2.00 2351.3
2.10 2364.3
2.20 2371.2
2.30 2375.2
2.40 2378.4
2.50 2380.5
2.60 2182.9
2.70 2024.9
2.80 2064.4
2.90 2323.8
3.00 2351.5
3.10 2357.1
3.20 2366.1
3.30 2375.7
3.40 2378.8
3.50 2378.6
3.60 2180.8
3.70 2023.1
3.80 2063.0
3.90 2278.1
4.00 2329.2
4.10 2360.2
4.20 2368.3
4.30 2374.5
4.40 2377.9
4.50 2378.0
4.60 2183.0
4.70 2025.0
4.80 2064.4
4.90 2282.2
5.00 2331.0
5.10 2361.7
5.20 2369.4
5.30 2375.1
5.40 2378.3
5.50 2378.3
5.60 2182.6
5.70 2022.9
5.80 2062.5
5.90 2322.4
6.00 2350.4
6.10 2363.8
6.20 2370.8
6.30 2370.7
6.40 2375.1
6.50 2380.7
6.60 2185.0
6.70 2024.9
6.80 2064.0
6.90 2310.9
7.00 2343.7
7.10 2363.3
7.20 2370.5
7.30 2375.7
7.40 2378.8
7.50 2381.2
7.60 2185.4
7.70 2025.4
7.80 2064.6
7.90 2324.0
8.00 2351.6
8.10 2364.7
8.20 2371.5
8.30 2373.8
8.40 2377.3
8.50 2380.9
8.60 2182.5
8.70 2024.4
8.80 2064.0
8.90 2323.2
9.00 2351.0
9.10 2353.5
9.20 2363.8
9.30 2370.6
9.40 2375.0
9.50 2378.3
9.60 2380.6
9.70 2383.6
9.80 2384.5
9.90 2384.5
10.00 2385.2
10.00 2385.8
Traceback (most recent call last):
File "/home/syoukera/miniconda3/envs/pyjac/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/home/syoukera/miniconda3/envs/pyjac/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/syoukera/github/pyJac/pyjac/functional_tester/__main__.py", line 110, in <module>
args.do_not_remove, args.condition_numbers
File "/home/syoukera/github/pyJac/pyjac/functional_tester/test.py", line 1294, in test
ajac = AutodiffJacob(pres, pyjacob.fwd_spec_map)
File "/home/syoukera/github/pyJac/pyjac/functional_tester/test.py", line 193, in __init__
import adjacob
ImportError: libadept.so.0: cannot open shared object file: No such file or directory
Hi!
I currently try to run "Functional testing" in example.rst.
But, I got an error after caluculation of psr.
My environment is WSL working on windows.
And, I installed pyJac using conda.
I think it is caused from installation of Adept.
I installed Adept using command shown in README on Adept github repository.
Does anyone know the way to solve this issue?