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libadept.so.0 can't find in Functional testing #49

@syoukera

Description

@syoukera

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

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