Dear Akimov, i encountered an "undefined symbol" problem when i installed Pyxaid2

[miller]

Dear Akimov:

I have successfully installed miniconda and Libra based on the tutorial: https://quantum-dynamics-hub.github.io/libra/installation.html

when i run python run_test.py in /root/Libra/tests/test_libra_py/test_1_init_system, it outputs: 

.........<omitted>.......

CREATE_ATOM  H

<liblibra_core.VECTOR object at 0x2ad90fd715d0> -0.0163463387301 0.102968503696 -0.184318

Number of atoms in the system =  1

Atom_id = 1

Atom_displ2 = 0

Atom_Z = 1

Atom_element = H

Atom_min_ring_size = 1

size = 1

tot_p =     -0.38832199       0.45861079       0.40525661

temp_tr= 0.0000000

target_ekin_tr= 0.0014250668

scaling_factor_tr = 0.0000000

in init_velocities...

P_tot =       0.0000000        0.0000000        0.0000000

cutt_T = 0.0000000

I think Libra is ok.

Now, when it comes Pyxaid2, i have try my best to tune the parameters and settings, but it still doesn't work.  

When i run

# cd /home/vasprun/software/pyxaid2-master/tutorials/Tut2_small/step1

# python py-scr5.py

it outputs:

Traceback (most recent call last):

  File "py-scr5.py", line 1, in <module>

    from PYXAID2 import*

ImportError: /home/vasprun/software/pyxaid2-master/PYXAID2/pyxaid_core.so: undefined symbol: _ZN8liblibra5libio9read_fileESsiRSt6vectorISsSaISsEE

The /home/vasprun/software/pyxaid2-master/PYXAID2/src_cpp/Makefile is written as:

#FLAGS= -std=c++11 -O2 -fPIC # -fno-for-scope -O2 -fPIC

FLAGS= -fPIC -O2 -fpermissive -w -g

CPP=c++

# BOOST

# UB CCR

p1=/root/miniconda2/envs/libra/include/boost

pl1=/root/miniconda2/envs/libra/lib

# PYTHON

# UB CCR

p2=/root/miniconda2/envs/libra/include/python2.7

pl2=/root/miniconda2/envs/libra/lib/python2.7

# LIBRA

p3=/root/Libra/src

pl3=/root/Libra/_build/src

pl3a=/root/Libra/_build/src/util

Could you please give me some tips where i am wrong?

Thank you very much!

Miller.

[Alexey Akimov]

Hi Miller,

It is hard to tell what exactly went wrong with your Pyxaid2 installation, but it looks like the Pyxaid2 code might not be linked to the libio library of the Libra. In principle the "libio" should be included in the libra_core, but if it isn't for some reasons, you may try to link the "libio" binary  (libio_stat.a) manually. 

Or, perhaps, you might have forgotten to define the LD_LIBRARY_PATH after Libra installation?

Best,

Alexey

[Jun Dai]

Hi Miller,

I encountered the exact same problem, have you figured out how to fix that?

Best,

[miller]

Hi Dai,

Still not resolved, I had given up hope.