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ftherrien / p2ptrans

An algorithm to match crystal structures atom-to-atom
http://p2ptrans.rtfd.io
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Facing error during p2ptrans --help #34

Closed SANAULLAHMIR closed 7 months ago

SANAULLAHMIR commented 8 months ago

I have successfully installed the p2ptrans, but whenever i am going "p2ptrans --help", it give me the following error: Please expert need your help in this regard: p2ptrans --help Traceback (most recent call last): File "/home/SanaUllah/anaconda3/bin/p2ptrans", line 6, in from p2ptrans import * File "/home/SanaUllah/anaconda3/lib/python3.9/site-packages/p2ptrans/init.py", line 5, in from . import interfaces File "/home/SanaUllah/anaconda3/lib/python3.9/site-packages/p2ptrans/interfaces.py", line 10, in from .core import makeSphere, find_cell, makeStructures, switchDispStruc, find_periodicity File "/home/SanaUllah/anaconda3/lib/python3.9/site-packages/p2ptrans/core.py", line 8, in from .fmodules import hungarian as lap ImportError: cannot import name 'hungarian' from 'p2ptrans.fmodules' (/home/SanaUllah/anaconda3/lib/python3.9/site-packages/p2ptrans/fmodules.cpython-39-x86_64-linux-gnu.so)

ftherrien commented 8 months ago

Hi @SANAULLAHMIR, I can't really tell from this error message. Could you show me how you installed p2ptrans and what output you got?

SANAULLAHMIR commented 8 months ago

Hello @ftherrien I have successfully installed the p2ptrans through Conda by clicking the command pip install git+https://github.com/ftherrien/p2ptrans It show me that p2ptrans is successfully installed, as you can see in the below snap

image

But further, when i am going to get help, by clicking command p2ptrans --help,,,, it give me the following error: 111

ftherrien commented 8 months ago

Can you check that /home/SanaUllah/anaconda3/lib/python3.9/site-packages/p2ptrans/fmodules.cpython-39-x86_64-linux-gnu.so actually exists? If it does, can you try:


cd /home/SanaUllah/anaconda3/lib/python3.9/site-packages/p2ptrans/
python -c "import fmodules"
samtsevich commented 7 months ago

@SANAULLAHMIR If you fixed that, please, let me know.

Otherwise, @ftherrien , please try to install it from the scratch on another machine and you will face with the same error (99% sure). I have faced with the same error on Ubuntu, MacOS.

I do try to install it as it is written in README.md. And when I try to just run p2ptrans -h it gives me the same error as in the initial post of this issue.

I did try to dig deeply and tried to compile .so library by hands (direct run of f2py) and still the error is there. I did try different gfortran-s, intel compilers, different versions of python and numpy, but error is still there.

Here is the output when I tried to just run make in the root folder:

rmbadname1: Replacing "char" with "char_bn".
rmbadname1: Replacing "char" with "char_bn".
appenddecl: "dimension" not implemented.
appenddecl: "dimension" not implemented.
appenddecl: "dimension" not implemented.
appenddecl: "dimension" not implemented.

And some more here


python3 -m numpy.f2py -c --f90exec=gfortran --fcompiler=gnu95 --f90flags="-Wall -g -Og -fbacktrace -fopenmp" -lgomp  -m p2ptrans.fmodules source/lap.f90 source/utils.f90 source/tiling.f90 source/potential.f90 source/transform.f90 only: munkres free_trans rot_mat center eye norm split det sort sphere circle distance derivative closest fixed_tmat fixed_tmat_int intoptimization fastoptimization optimize_vec
running build
running config_cc
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
INFO: build_src
INFO: building extension "p2ptrans.fmodules" sources
INFO: f2py options: ['only:', 'munkres', 'free_trans', 'rot_mat', 'center', 'eye', 'norm', 'split', 'det', 'sort', 'sphere', 'circle', 'distance', 'derivative', 'closest', 'fixed_tmat', 'fixed_tmat_int', 'intoptimization', 'fastoptimization', 'optimize_vec', ':']
INFO: f2py:> /tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fmodulesmodule.c
creating /tmp/tmp7klu8d34/src.linux-x86_64-3.10
creating /tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans
Reading fortran codes...
    Reading file 'source/lap.f90' (format:free)
    Reading file 'source/utils.f90' (format:free)
    Reading file 'source/tiling.f90' (format:free)
    Reading file 'source/potential.f90' (format:free)
    Reading file 'source/transform.f90' (format:free)
Post-processing...
    Block: fmodules
            Block: hungarian
                Block: munkres
            Block: utils
                Block: free_trans
                Block: rot_mat
                Block: center
                Block: eye
                Block: norm
                Block: split
                Block: det
In: :fmodules:source/utils.f90:utils:det
analyzevars: prefix ('recursive') were not used
                Block: sort
            Block: tiling
                Block: sphere
In: :fmodules:source/tiling.f90:tiling:sphere
get_parameters: got "eval() arg 1 must be a string, bytes or code object" on 8
                Block: circle
In: :fmodules:source/tiling.f90:tiling:circle
get_parameters: got "eval() arg 1 must be a string, bytes or code object" on 8
            Block: potential
                Block: distance
                Block: derivative
            Block: transform
In: :fmodules:source/transform.f90:transform
get_parameters: got "eval() arg 1 must be a string, bytes or code object" on 8
                Block: closest
                Block: optimize_vec
                Block: fastoptimization
In: :fmodules:source/transform.f90:transform:fastoptimization
get_parameters: got "eval() arg 1 must be a string, bytes or code object" on 8
                Block: fixed_tmat
In: :fmodules:source/transform.f90:transform:fixed_tmat
get_parameters: got "eval() arg 1 must be a string, bytes or code object" on 8
                Block: intoptimization
In: :fmodules:source/transform.f90:transform:intoptimization
get_parameters: got "eval() arg 1 must be a string, bytes or code object" on 8
                Block: fixed_tmat_int
In: :fmodules:source/transform.f90:transform:fixed_tmat_int
get_parameters: got "eval() arg 1 must be a string, bytes or code object" on 8
Post-processing (stage 2)...
    Block: fmodules
        Block: unknown_interface
            Block: hungarian
                Block: munkres
            Block: utils
                Block: free_trans
                Block: rot_mat
                Block: center
                Block: eye
                Block: norm
                Block: split
                Block: det
                Block: sort
            Block: tiling
                Block: sphere
                Block: circle
            Block: potential
                Block: distance
                Block: derivative
            Block: transform
                Block: closest
                Block: optimize_vec
                Block: fastoptimization
                Block: fixed_tmat
                Block: intoptimization
                Block: fixed_tmat_int
Building modules...
    Building module "fmodules"...
        Constructing F90 module support for "hungarian"...
            Constructing wrapper function "hungarian.munkres"...
              sumsol,jsol = munkres(c,[n])
        Constructing F90 module support for "utils"...
        Creating wrapper for Fortran function "free_trans"("free_trans")...
            Constructing wrapper function "utils.free_trans"...
              free_trans = free_trans(pos,mat,vec)
        Creating wrapper for Fortran function "rot_mat"("rot_mat")...
            Constructing wrapper function "utils.rot_mat"...
              r = rot_mat(angles)
            Constructing wrapper function "utils.center"...
              center(pos,[n])
        Creating wrapper for Fortran function "eye"("eye")...
            Constructing wrapper function "utils.eye"...
              a = eye()
        Creating wrapper for Fortran function "norm"("norm")...
            Constructing wrapper function "utils.norm"...
              norm = norm(a)
        Creating wrapper for Fortran function "split"("split")...
            Constructing wrapper function "utils.split"...
              split = split(a,char_bn)
        Creating wrapper for Fortran function "det"("det")...
            Constructing wrapper function "utils.det"...
              accumulation = det(a,[n])
        Creating wrapper for Fortran function "sort"("sort")...
            Constructing wrapper function "utils.sort"...
              idx = sort(array)
        Constructing F90 module support for "tiling"...
            Constructing wrapper function "tiling.sphere"...
              asc = sphere(acell,ncell,center)
            Constructing wrapper function "tiling.circle"...
              asc = circle(acell,ncell,center)
        Constructing F90 module support for "potential"...
        Creating wrapper for Fortran function "distance"("distance")...
            Constructing wrapper function "potential.distance"...
              distance = distance(apos,bpos,mat,vec,pot,param)
        Creating wrapper for Fortran function "derivative"("derivative")...
            Constructing wrapper function "potential.derivative"...
              e = derivative(apos,bpos,mat,vec,pot,param)
        Constructing F90 module support for "transform"...
            Constructing wrapper function "transform.closest"...
              cost = closest(apos,bpos,[n])
            Constructing wrapper function "transform.optimize_vec"...
              vec_out = optimize_vec(apos,bpos,vec,filename,[n])
            Constructing wrapper function "transform.fastoptimization"...
              apos_out,bpos_out,bpos_out_stretch,n_out,n_a,classes_list_out,tmat,dmin,vec = fastoptimization(apos,bpos,acell,iacell,atoms,filename,outdir,[na,nb,n_atoms])
            Constructing wrapper function "transform.fixed_tmat"...
              apos_out,bpos_out,bpos_out_stretch,n_out,n_a,classes_list_out,tmat,dmin,vec = fixed_tmat(apos,bpos,tmat_in,vec_in,atoms,filename,outdir,[na,nb,n_atoms])
            Constructing wrapper function "transform.intoptimization"...
              apos_out,bpos_out,bpos_out_stretch,n_out,n_a,classes_list_out,ttrans,rtrans,dmin,stats,n_peaks,peak_thetas = intoptimization(sym,n_iter,apos,bpos,acell,iacell,atoms,switched,filename,outdir,[na,nb,n_atoms])
            Constructing wrapper function "transform.fixed_tmat_int"...
              apos_out,bpos_out,bpos_out_stretch,n_out,n_a,classes_list_out,vec,dmin = fixed_tmat_int(apos,bpos,ttrans,atoms,switched,filename,outdir,[na,nb,n_atoms])
    Wrote C/API module "fmodules" to file "/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fmodulesmodule.c"
    Fortran 90 wrappers are saved to "/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fmodules-f2pywrappers2.f90"
INFO:   adding '/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fortranobject.c' to sources.
INFO:   adding '/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans' to include_dirs.
copying /home/asamt/.pyenv/versions/3.10.8/lib/python3.10/site-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans
copying /home/asamt/.pyenv/versions/3.10.8/lib/python3.10/site-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans
INFO:   adding '/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fmodules-f2pywrappers2.f90' to sources.
INFO: build_src: building npy-pkg config files
running build_ext
INFO: customize UnixCCompiler
INFO: customize UnixCCompiler using build_ext
INFO: customize Gnu95FCompiler
INFO: Found executable /usr/bin/gfortran
INFO: customize Gnu95FCompiler using build_ext
INFO: building 'p2ptrans.fmodules' extension
INFO: compiling C sources
INFO: C compiler: gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

creating /tmp/tmp7klu8d34/tmp
creating /tmp/tmp7klu8d34/tmp/tmp7klu8d34
creating /tmp/tmp7klu8d34/tmp/tmp7klu8d34/src.linux-x86_64-3.10
creating /tmp/tmp7klu8d34/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans
INFO: compile options: '-DNPY_DISABLE_OPTIMIZATION=1 -I/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans -I/home/asamt/.pyenv/versions/3.10.8/lib/python3.10/site-packages/numpy/core/include -I/home/asamt/.pyenv/versions/3.10.8/include/python3.10 -c'
INFO: gcc: /tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fmodulesmodule.c
INFO: gcc: /tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fortranobject.c
INFO: compiling Fortran 90 module sources
creating /tmp/tmp7klu8d34/p2ptrans
INFO: Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: gfortran -Wall -g -Og -fbacktrace -fopenmp -fPIC -O3 -funroll-loops
Fortran fix compiler: gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -Og -fbacktrace -fopenmp -fPIC -O3 -funroll-loops
creating /tmp/tmp7klu8d34/source
INFO: compile options: '-I/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans -I/home/asamt/.pyenv/versions/3.10.8/lib/python3.10/site-packages/numpy/core/include -I/home/asamt/.pyenv/versions/3.10.8/include/python3.10 -c'
extra options: '-J/tmp/tmp7klu8d34/p2ptrans -I/tmp/tmp7klu8d34/p2ptrans'
INFO: gfortran:f90: source/lap.f90
INFO: gfortran:f90: source/utils.f90
INFO: gfortran:f90: source/tiling.f90
INFO: gfortran:f90: source/potential.f90
INFO: gfortran:f90: source/transform.f90
INFO: compiling Fortran sources
INFO: Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops
Fortran f90 compiler: gfortran -Wall -g -Og -fbacktrace -fopenmp -fPIC -O3 -funroll-loops
Fortran fix compiler: gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -Og -fbacktrace -fopenmp -fPIC -O3 -funroll-loops
INFO: compile options: '-I/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans -I/home/asamt/.pyenv/versions/3.10.8/lib/python3.10/site-packages/numpy/core/include -I/home/asamt/.pyenv/versions/3.10.8/include/python3.10 -c'
extra options: '-J/tmp/tmp7klu8d34/p2ptrans -I/tmp/tmp7klu8d34/p2ptrans'
INFO: gfortran:f90: /tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fmodules-f2pywrappers2.f90
INFO: /usr/bin/gfortran -Wall -g -Wall -g -shared /tmp/tmp7klu8d34/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fmodulesmodule.o /tmp/tmp7klu8d34/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fortranobject.o /tmp/tmp7klu8d34/source/lap.o /tmp/tmp7klu8d34/source/utils.o /tmp/tmp7klu8d34/source/tiling.o /tmp/tmp7klu8d34/source/potential.o /tmp/tmp7klu8d34/source/transform.o /tmp/tmp7klu8d34/tmp/tmp7klu8d34/src.linux-x86_64-3.10/p2ptrans/fmodules-f2pywrappers2.o -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/home/asamt/.pyenv/versions/3.10.8/lib -lgomp -lgfortran -o ./p2ptrans/fmodules.cpython-310-x86_64-linux-gnu.so
Removing build directory /tmp/tmp7klu8d34

I hope that will help to fix this issue.

ftherrien commented 7 months ago

Thanks @samtsevich, let me look into it, I will get back to you soon.

samtsevich commented 7 months ago

@ftherrien

Any news about that bug? If so, maybe I can help somehow.

ftherrien commented 7 months ago

I will allocate some time on it today

ftherrien commented 7 months ago

@samtsevich and @SANAULLAHMIR

I have created an issue on Numpy in the mean time, it should work if you use Numpy 1.26.2 or less

ftherrien commented 7 months ago

@samtsevich and @SANAULLAHMIR

You can install pre-released versions of numpy that fix this issue through pip install --pre numpy. Basically it works with any recent version of numpy except for 1.26.3 and 1.26.4