5.1 cak.py analysis compile

[Victor Naden Robinson]

Dear Calypso Community,

I am having some trouble setting up the 5.1 Calypso Analysis cak.py on a new HPC (intel compilers). Can I ask:

Which version of python, numpy and spg are recommended?

I have used conda to install python 2.7 and numpy. I have installed spglib with:

conda install -c conda-forge spglib
(from https://atztogo.github.io/spglib/python-spglib.html#python-spglib)

I have changed cak.py to import spglib differently:
Perhaps I am going wrong here as the Makefile is trying to create its own libpyspg? Otherwise I am told to install spglib

    import spglib as spg
#    import libpyspg as spg


However running cak.py produces:

[/.../CALYPSO_x64/Tools/test-01/results]$ cak.py -n 10
Traceback (most recent call last):
  File "/scratch/home/mmm0037/Calypso-versions/5.1/CALYPSO_x64/Tools/CALYPSO_ANALYSIS_KIT/cak.py", line 1275, in <module>
    run()
  File "/scratch/home/mmm0037/Calypso-versions/5.1/CALYPSO_x64/Tools/CALYPSO_ANALYSIS_KIT/cak.py", line 963, in run
    Zoutput(structure, options, num_proce, prec_pool, is_refine, is_prim, hard, fdir, d2, cl, norefine, hm, bg, xrd, lsur)
  File "/scratch/home/mmm0037/Calypso-versions/5.1/CALYPSO_x64/Tools/CALYPSO_ANALYSIS_KIT/cak.py", line 989, in Zoutput
    (spgdata, recell, primcell) = findsym(structure[i][4], prec, is_refine, is_prim)
  File "/scratch/home/mmm0037/Calypso-versions/5.1/CALYPSO_x64/Tools/CALYPSO_ANALYSIS_KIT/cak.py", line 684, in findsym
    (num_spg, symbol_spg) = spg.spacegroup(l, p, numbers, prec, aprec)
AttributeError: 'module' object has no attribute 'spacegroup'

Kind Regards, Victor

[wyc]

Dear Victor,

The python 2.7 and numpy are required to install cak.py. The suitable spg will be automatically installed when you install cak.py. So please don’t change the file of Makefile, and try it again.

Sincerely

Yanchao

------------------------------------------------------
Dr. Yanchao Wang (王彦超)
State Key Lab of Superhard Materials
Jilin University
Changchun 130012
China
Email: w...@calypso.cn/wyc...@jlu.edu.cn
skype:wyanchao1225

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[Victor Naden Robinson]

Dear Yanchao,

I have tried what you said, and only linked python in the Makefile, added the path my ~/.bashrc and sourced.

Problem: when runnign cak.py in a /results/ I get:
[mmm0037@login03 /scratch/home/mmm0037/Calypso-versions/archer-calypso-attempt-2/CALYPSO_x86/Tests/results]$ cak.py
ERROR: please install libpyspg.

I am not sure if the error is with Numpy or linking the libpyspg. Any advice would be appreciated.

Full compiling log:

[mmm0037@login03 /scratch/.../CALYPSO_x86/Tools/CALYPSO_ANALYSIS_KIT]$ make
export PYTHONPATH=`pwd`/lib/python
/scratch/home/mmm0037/miniconda2/bin/python2.7 setup.py install --home=. --prefix=''
running install
running build
running build_ext
building 'libpyspg' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/c
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c libpyspg.c -o build/temp.linux-x86_64-2.7/libpyspg.o
In file included from /scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h(1788),
                 from /scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h(18),
                 from /scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h(4),
                 from libpyspg.c(3):
/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h(15): warning #1224: #warning directive: "Using deprecated NumPy API, disable it by "          "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
  #warning "Using deprecated NumPy API, disable it by " \
   ^

icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/cell.c -o build/temp.linux-x86_64-2.7/c/cell.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/debug.c -o build/temp.linux-x86_64-2.7/c/debug.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/hall_symbol.c -o build/temp.linux-x86_64-2.7/c/hall_symbol.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/kpoint.c -o build/temp.linux-x86_64-2.7/c/kpoint.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/lattice.c -o build/temp.linux-x86_64-2.7/c/lattice.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/mathfunc.c -o build/temp.linux-x86_64-2.7/c/mathfunc.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/pointgroup.c -o build/temp.linux-x86_64-2.7/c/pointgroup.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/primitive.c -o build/temp.linux-x86_64-2.7/c/primitive.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/refinement.c -o build/temp.linux-x86_64-2.7/c/refinement.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/site_symmetry.c -o build/temp.linux-x86_64-2.7/c/site_symmetry.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/sitesym_database.c -o build/temp.linux-x86_64-2.7/c/sitesym_database.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/spacegroup.c -o build/temp.linux-x86_64-2.7/c/spacegroup.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/spg_database.c -o build/temp.linux-x86_64-2.7/c/spg_database.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/spglib.c -o build/temp.linux-x86_64-2.7/c/spglib.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/spin.c -o build/temp.linux-x86_64-2.7/c/spin.o
icc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic/ -I/scratch/home/mmm0037/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/scratch/home/mmm0037/miniconda2/include/python2.7 -c c/symmetry.c -o build/temp.linux-x86_64-2.7/c/symmetry.o
creating build/lib.linux-x86_64-2.7
gcc -pthread -shared -L/home/mmm0037/miniconda2/lib -Wl,-rpath=/home/mmm0037/miniconda2/lib,--no-as-needed build/temp.linux-x86_64-2.7/libpyspg.o build/temp.linux-x86_64-2.7/c/cell.o build/temp.linux-x86_64-2.7/c/debug.o build/temp.linux-x86_64-2.7/c/hall_symbol.o build/temp.linux-x86_64-2.7/c/kpoint.o build/temp.linux-x86_64-2.7/c/lattice.o build/temp.linux-x86_64-2.7/c/mathfunc.o build/temp.linux-x86_64-2.7/c/pointgroup.o build/temp.linux-x86_64-2.7/c/primitive.o build/temp.linux-x86_64-2.7/c/refinement.o build/temp.linux-x86_64-2.7/c/site_symmetry.o build/temp.linux-x86_64-2.7/c/sitesym_database.o build/temp.linux-x86_64-2.7/c/spacegroup.o build/temp.linux-x86_64-2.7/c/spg_database.o build/temp.linux-x86_64-2.7/c/spglib.o build/temp.linux-x86_64-2.7/c/spin.o build/temp.linux-x86_64-2.7/c/symmetry.o -L/home/mmm0037/miniconda2/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/libpyspg.so
running install_lib
creating lib
creating lib/python
copying build/lib.linux-x86_64-2.7/libpyspg.so -> ./lib/python
running install_egg_info
Writing ./lib/python/libpyspg-1.4.1-py2.7.egg-info

please add " source /scratch/home/mmm0037/Calypso-versions/archer-calypso-attempt-2/CALYPSO_x86/Tools/CALYPSO_ANALYSIS_KIT/caly.sh " in /home/mmm0037/.bashrc

Kind Regards, Victor