[gpaw-users] Installation question. Lapack and scalapack.
Aleksei
alekcey92 at inbox.ru
Tue Nov 28 21:14:58 CET 2017
Hello all,
On 23.11.2017 10:12, Jens Jørgen Mortensen wrote:
> Den 22-11-2017 kl. 13:37 skrev Aleksei via gpaw-users:
>> Hello Gaël,
>>
>>
>> On 20.11.2017 16:25, Gaël Donval via gpaw-users wrote:
>>> Hi Aleksei,
>>>> Hello Gaël,
>>>>
>>>> Thank you for your reply.
>>>>
>>>>>> /home/aleksei/anaconda3/compiler_compat/ld:
>>>>>> /home/aleksei/Programs/scalapack/lib/../lib/liblapack.a(zlarf.o):
>>>>>> relocation R_X86_64_32 against `.rodata' can not be used when
>>>>>> making
>>>>>> a
>>>>>> shared object; recompile with -fPIC
>>>>>> /home/aleksei/anaconda3/compiler_compat/ld: final link failed:
>>>>>> Nonrepresentable section on output
>>>>>> collect2: error: ld returned 1 exit status
>>>>>> error: command 'gcc' failed with exit status 1
>>>>>>
>>>>>> Has anybody seen these errors and do you know solution around
>>>>>> this?
>>>>> Did you try to... recompile with -fPIC? :)
>>>> :)
>>>>
>>>> I am so bad at this that I did not realize that I had to add -fPIC to
>>>> extra_compile_args, right?
>>> I don't know if that's required in that file (the installer could add
>>> it itself).
>>>
>>> Anyway, you need to compile blas/lapack/scalapack with -fPIC, not only
>>> GPAW... well, if you indeed need it (see comments below).
>>>
>>>> As you suggested before, I installed intel mkl library. Then I found
>>>> in gpaw archive customize.py file and changed it a bit (see attached)
>>>> with intel compiler and gpaw was installed without any errors. Also I
>>>> use now intel distribution of python, even just 'python
>>>> gpaw_script.py' uses 4 cores and calculations are much more faster.
>>>> But, for some reason it seems that scalapck is not used. At least
>>>> gpaw -info shows it. Also, when I type 'gpaw-python $(which gpaw)
>>>> info' I get this error:
>>> I have a limited experience with Intel libs but to my knowledge, they
>>> provide their own scalapack. If you go with Intel, it's far easier to
>>> use their full stack. You most likely want to use and link to that
>>> library instead of compiling your own.
>>>
>>> Two important comments:
>>>
>>> * Scalapack is harmful (performance-wise) for small systems and is
>>> definitely unnecessary if you don't use "many" CPU cores. So you
>>> may
>>> want it but you might not actually need it.
>>> * Compiling and setting things up is, most of the time, not a very
>>> involved process and yet it requires quite a lot of knowledge and
>>> experience! In other words, setting things up yourself is insanely
>>> hard if you don't know precisely what you are doing. Don't worry,
>>> you won't blow up your computer if you make a mistake! :) But you
>>> will go through an endless stream of weird errors that won't make
>>> any sense to you. In your case, all the new errors you describe
>>> stem
>>> from a misconfiguration of your Python environment (so nothing
>>> to do
>>> with GPAW or scalapack anymore). You can try to solve it
>>> yourself if
>>> you want, but I won't help you with it.
>>>
>>
>> Yes, the problem now is with a misconfiguration of my Python
>> environment. Interesting that I do not have any problems when I run
>> gpaw calculations (or any other calculations) using python
>> interpreter, but I can not use only gpaw-python. In requirements it
>> says that I need to have python 2.7-3.5, but I use python 3.6.3. I
>> was wondering if it can be the reason.
>
> Python 3.6.3 should be fine.
I found out that my python console in pycharm use this path
/home/aleksei/anaconda3/envs/idp/lib/python3.6/lib-dynload. Therefore,
after I added this path to my bashrc file, gpaw-python has started
working! In summary, (just in a case if someone has similar issues) I
have three additional pathes in the bashrc file:
export PYTHONHOME="/home/aleksei/anaconda3/envs/idp:$PYTHONHOME"
export
PYTHONPATH="/home/aleksei/anaconda3/envs/idp/lib/python3.6:$PYTHONPATH"
export
PYTHONPATH="/home/aleksei/anaconda3/envs/idp/lib/python3.6/lib-dynload:$PYTHONPATH"
Now I performed some calculations with 4 cores successfully. My question
is for how long the tests with 4 cores should usually execute? I run
'gpaw -P 4 test' but after more then 6 hours I terminated it since I
could not wait longer. I think that during the last few hours it
performed 'pathological/nonlocalset.py'. (see output below). Is it OK? I
checked that 'pathological/nonlocalset.py' were executed quiet quickly
in 'gpaw test -j 4'.
Best wishes,
Aleksei
gpaw -P 4 test
python-3.6.3
/home/aleksei/Programs/gpaw/build/bin.linux-x86_64-3.6/gpaw-python
gpaw-1.3.1b1 /home/aleksei/Programs/gpaw/gpaw/
ase-3.15.0 /home/aleksei/anaconda3/envs/idp/lib/python3.6/site-packages/ase/
numpy-1.13.3
/home/aleksei/anaconda3/envs/idp/lib/python3.6/site-packages/numpy/
scipy-0.19.1
/home/aleksei/anaconda3/envs/idp/lib/python3.6/site-packages/scipy/
_gpaw built-in
parallel /home/aleksei/Programs/gpaw/build/bin.linux-x86_64-3.6/gpaw-python
FFTW yes
scalapack yes
libvdwxc no
PAW-datasets 1: /home/aleksei/Programs/gpaw_setups/gpaw-setups-0.9.20000
2: /usr/local/share/gpaw-setups
3: /usr/share/gpaw-setups
Running tests in /tmp/gpaw-test-wvo8ogg8
Jobs: 1, Cores: 4, debug-mode: False
=============================================================================
linalg/gemm_complex.py 0.121 OK
ase_features/ase3k_version.py 0.044 OK
kpt.py 0.242 OK
mpicomm.py 0.022 OK
pathological/numpy_core_multiarray_dot.py 0.048 OK
eigen/cg2.py 0.076 OK
fd_ops/laplace.py 0.000 SKIPPED
linalg/lapack.py 0.093 OK
linalg/eigh.py 0.158 OK
parallel/submatrix_redist.py 0.171 OK
lfc/second_derivative.py 0.111 OK
parallel/parallel_eigh.py 0.018 OK
lfc/gp2.py 0.019 OK
linalg/blas.py 0.086 OK
Gauss.py 0.045 OK
symmetry/check.py 0.545 OK
fd_ops/nabla.py 0.126 OK
linalg/dot.py 0.019 OK
linalg/mmm.py 0.019 OK
xc/lxc_fxc.py 0.090 OK
xc/pbe_pw91.py 0.022 OK
fd_ops/gradient.py 0.027 OK
maths/erf.py 0.018 OK
lfc/lf.py 0.019 OK
maths/fsbt.py 0.256 OK
parallel/compare.py 0.024 OK
vdw/libvdwxc_functionals.py 0.000 SKIPPED
radial/integral4.py 0.111 OK
linalg/zher.py 0.050 OK
fd_ops/gd.py 0.021 OK
pw/interpol.py 0.039 OK
poisson/screened_poisson.py 0.371 OK
xc/xc.py 0.093 OK
xc/XC2.py 0.053 OK
radial/yukawa_radial.py 0.028 OK
vdw/potential.py 0.020 OK
radial/lebedev.py 0.025 OK
occupations.py 0.072 OK
lfc/derivatives.py 0.032 OK
parallel/realspace_blacs.py 0.019 OK
pw/reallfc.py 0.443 OK
parallel/pblas.py 0.038 OK
fd_ops/non_periodic.py 0.022 OK
spectrum.py 0.041 OK
pw/lfc.py 0.111 OK
gauss_func.py 0.302 OK
multipoletest.py 0.209 OK
cluster.py 0.210 OK
poisson/poisson.py 0.176 OK
poisson/poisson_asym.py 0.153 OK
parallel/arraydict_redist.py 0.030 OK
parallel/overlap.py 0.555 OK
parallel/scalapack.py 0.059 OK
gauss_wave.py 0.272 OK
fd_ops/transformations.py 0.025 OK
parallel/blacsdist.py 0.020 OK
pbc.py 0.556 OK
atoms_too_close.py 0.652 OK
ext_potential/harmonic.py 0.714 OK
generic/proton.py 3.675 OK
atoms_mismatch.py 0.041 OK
setup_basis_spec.py 0.038 OK
overlap.py 1.902 OK
pw/direct.py 0.051 OK
vdw/libvdwxc_spin.py 0.000 SKIPPED
timing.py 0.278 OK
parallel/ut_parallel.py 0.106 OK
lcao/density.py 0.869 OK
parallel/hamiltonian.py 1.176 OK
pw/stresstest.py 0.593 OK
pw/fftmixer.py 1.013 OK
symmetry/usesymm.py 1.161 OK
coulomb.py 0.355 OK
xc/xcatom.py 0.659 OK
force_as_stop.py 0.724 OK
vdwradii.py 0.824 OK
ase_features/ase3k.py 1.144 OK
pathological/numpy_zdotc_graphite.py 0.950 OK
utilities/eed.py 1.273 OK
lcao/dos.py 1.285 OK
solvation/nan_radius.py 0.681 OK
solvation/pbc_pos_repeat.py 0.500 OK
linalg/gemv.py 1.677 OK
fileio/idiotproof_setup.py 2.305 OK
radial/ylexpand.py 1.428 OK
eigen/keep_htpsit.py 1.669 OK
xc/gga_atom.py 1.309 OK
generic/hydrogen.py 4.374 OK
aeatom.py 0.773 OK
ase_features/plt.py 1.826 OK
ds_beta.py 1.855 OK
multipoleH2O.py 2.083 OK
spinorbit_Kr.py 0.000 SKIPPED
stdout.py 2.297 OK
lcao/largecellforce.py 1.571 OK
parallel/scalapack_diag_simple.py 0.030 OK
fixdensity.py 2.623 OK
pseudopotential/ah.py 2.244 OK
lcao/restart.py 1.999 OK
lcao/tddft.py 1.512 OK
lcao/gllb_si.py 1.133 OK
fileio/wfs_io.py 2.298 OK
lrtddft/2.py 2.444 OK
fileio/file_reference.py 1.757 OK
fileio/restart.py 1.814 OK
broydenmixer.py 3.235 OK
pw/fulldiagk.py 3.720 OK
ext_potential/external.py 3.044 OK
lcao/atomic_corrections.py 2.573 OK
vdw/libvdwxc_h2.py 0.000 SKIPPED
generic/mixer.py 2.451 OK
parallel/lcao_projections.py 3.853 OK
lcao/h2o.py 3.858 OK
corehole/h2o.py 4.423 OK
fileio/wfs_auto.py 2.774 OK
pw/fulldiag.py 2.668 OK
symmetry/symmetry_ft.py 2.806 OK
response/aluminum_EELS_RPA.py 2.335 OK
poisson/poisson_extended.py 2.966 OK
solvation/vacuum.py 5.028 OK
vdw/libvdwxc_mbeef.py 0.000 SKIPPED
pseudopotential/sg15_hydrogen.py 3.586 OK
parallel/augment_grid.py 7.749 OK
utilities/ewald.py 3.023 OK
symmetry/symmetry.py 3.042 OK
xc/revPBE.py 3.254 OK
xc/nonselfconsistentLDA.py 3.836 OK
response/aluminum_EELS_ALDA.py 3.676 OK
spin/spin_contamination.py 3.968 OK
inducedfield_lrtddft.py 4.366 OK
generic/H_force.py 2.629 OK
symmetry/usesymm2.py 3.306 OK
mgga/mgga_restart.py 3.467 OK
fixocc.py 4.103 OK
spin/spinFe3plus.py 2.927 OK
fermisplit.py 3.652 OK
generic/Cl_minus.py 3.547 OK
lrtddft/pes.py 2.930 OK
corehole/h2o_recursion.py 4.345 OK
xc/nonselfconsistent.py 4.267 OK
spin/spinpol.py 4.020 OK
eigen/cg.py 4.264 OK
parallel/kptpar.py 4.243 OK
utilities/elf.py 4.333 OK
eigen/blocked_rmm_diis.py 4.004 OK
pw/slab.py 4.251 OK
generic/si.py 7.280 OK
lcao/bsse.py 8.574 OK
parallel/lcao_hamiltonian.py 3.876 OK
xc/degeneracy.py 5.122 OK
fileio/refine.py 3.781 OK
solvation/pbc.py 1.951 OK
generic/asym_box.py 5.978 OK
linalg/gemm.py 0.220 OK
generic/al_chain.py 6.089 OK
fileio/parallel.py 3.548 OK
fixmom.py 4.731 OK
exx/unocc.py 6.290 OK
eigen/davidson.py 10.765 OK
vdw/H_Hirshfeld.py 4.682 OK
parallel/redistribute_grid.py 3.953 OK
aedensity.py 7.713 OK
pw/h.py 4.708 OK
lrtddft/apmb.py 6.710 OK
pseudopotential/hgh_h2o.py 10.934 OK
fdtd/ed_wrapper.py 6.697 OK
fdtd/ed_shapes.py 5.477 OK
fdtd/ed.py 10.447 OK
fdtd/ed_inducedfield.py 11.504 OK
inducedfield_td.py 4.837 OK
pw/bulk.py 5.518 OK
gllb/ne.py 9.229 OK
lcao/force.py 4.253 OK
xc/pplda.py 5.826 OK
response/test_unit_sphere_area.py 30.063 OK
fileio/restart_density.py 2.627 OK
rpa/rpa_energy_Ni.py 6.478 OK
tddft/be_nltd_ip.py 13.968 OK
ibzqpt.py 7.153 OK
generic/si_primitive.py 3.309 OK
tddft/ehrenfest_nacl.py 13.678 OK
lcao/fd2lcao_restart.py 12.166 OK
ext_potential/constant_e_field.py 1.515 OK
complex.py 8.489 OK
vdw/quick.py 4.235 OK
lrtddft2/H2O-lcao.py 6.312 OK
lrtddft2/Al2.py 14.352 OK
ralda/ralda_energy_N2.py 7.264 OK
parallel/lcao_complicated.py 10.976 OK
generic/bulk.py 7.785 OK
sic/scfsic_h2.py 11.671 OK
lcao/bulk.py 10.964 OK
reuse_wfs.py 16.181 OK
generic/2Al.py 11.840 OK
lrtddft/kssingles_Be.py 9.617 OK
generic/relax.py 14.863 OK
solvation/adm12.py 4.967 OK
solvation/lrtddft.py 4.654 OK
dscf/dscf_lcao.py 12.492 OK
generic/8Si.py 17.615 OK
utilities/partitioning.py 12.278 OK
xc/lxc_xcatom.py 8.420 OK
solvation/sfgcm06.py 4.685 OK
solvation/sss09.py 4.544 OK
gllb/atomic.py 9.292 OK
generic/guc_force.py 8.453 OK
ralda/ralda_energy_Ni.py 16.877 OK
utilities/simple_stm.py 14.874 OK
ofdft/ofdft_pbc.py 6.319 OK
gllb/restart_band_structure.py 15.167 OK
exx/exx.py 58.485 OK
Hubbard_U.py 9.637 OK
rpa/rpa_energy_Si.py 15.478 OK
dipole.py 23.083 OK
generic/IP_oxygen.py 18.223 OK
rpa/rpa_energy_Na.py 21.125 OK
parallel/fd_parallel.py 15.977 OK
solvation/poisson.py 5.061 OK
solvation/water_water.py 4.601 OK
xc/pygga.py 11.941 OK
parallel/lcao_parallel.py 19.125 OK
xc/atomize.py 5.592 OK
lrtddft/excited_state.py 43.018 OK
gllb/ne_disc.py 21.711 OK
ofdft/ofdft.py 7.160 OK
response/bse_silicon.py 16.503 OK
tpss.py 6.955 OK
tddft/td_na2.py 25.766 OK
exx/coarse.py 37.130 OK
corehole/si.py 5.428 OK
mgga/mgga_sc.py 27.317 OK
Hubbard_U_Zn.py 4.611 OK
lrtddft/1.py 39.561 OK
gllb/spin.py 20.787 OK
parallel/fd_parallel_kpt.py 21.234 OK
generic/Cu.py 16.715 OK
vdw/ts09.py 14.154 OK
response/na_plasmon.py 75.898 OK
fermilevel.py 7.764 OK
ralda/ralda_energy_H2.py 13.187 OK
response/diamond_absorption.py 21.969 OK
ralda/ralda_energy_Si.py 65.092 OK
jellium.py 10.433 OK
utilities/ldos.py 21.322 OK
solvation/swap_atoms.py 8.081 OK
xc/revPBE_Li.py 9.111 OK
ofdft/ofdft_scale.py 12.075 OK
parallel/lcao_parallel_kpt.py 34.550 OK
corehole/h2o_dks.py 33.203 OK
mgga/nsc_MGGA.py 29.838 OK
solvation/spinpol.py 14.635 OK
gllb/diamond.py 25.107 OK
vdw/quick_spin.py 17.098 OK
pw/expert_diag.py 2.705 OK
pathological/LDA_unstable.py 7.861 OK
response/bse_aluminum.py 7.878 OK
response/au02_absorption.py 56.769 OK
xc/tb09.py 35.059 OK
ext_potential/point_charge.py 10.282 OK
ase_features/wannierk.py 43.338 OK
ut_tddft.py 0.053 OK
response/pair.py 0.000 SKIPPED
rpa/rpa_energy_N2.py 60.714 OK
vdw/ar2.py 62.919 OK
solvation/forces_symmetry.py 24.284 OK
parallel/diamond_gllb.py 68.633 OK
beef.py 264.436 OK
response/chi0.py 78.288 OK
sic/scfsic_n2.py 109.392 OK
lrtddft/3.py 112.180 OK
pathological/nonlocalset.py
> Jens Jørgen
>
>> Anyway, I will try to figure out how I can use gpaw-python since I
>> need to run parallel calculations on my laptop.
>>
>>> So what should you do?
>>>
>>> * If you are on your own computer, just activate your anaconda3
>>> environment and type `pip install -U gpaw` to install gpaw. Then
>>> use
>>> as it is: in that case scalapack is definitely unnecessary.
>>
>> Before I always did this way, but I could not get 'gpaw-python' (I
>> had mpi and other dependences installed with intel distribution) and
>> I could not run parallel calculations, so I decided to try to install
>> it myself.
>>
>> Thank you for clarifying the situation.
>>
>> Best wishes,
>> Aleksei
>>> * If you are on a HPC cluster, ask your local HPC services for
>>> support: chances are high that almost everything required is
>>> already
>>> there and they'll know what to do.
>>> * Or learn yourself, step by step, what you are doing when
>>> "installing" GPAW and related packages so that you make everything
>>> work.
>>>
>>> Best regards,
>>> Gaël
>>>
>>>
>>>
>>>
>>>
>>>> Could not find platform independent libraries <prefix>
>>>> Could not find platform dependent libraries <exec_prefix>
>>>> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
>>>> Fatal Python error: Py_Initialize: Unable to get the locale encoding
>>>> ModuleNotFoundError: No module named 'encodings'
>>>>
>>>> Current thread 0x00007f91d4861700 (most recent call first):
>>>> Aborted (core dumped)
>>>>
>>>> Seems that I need to set PYHTONHOME like this
>>>>
>>>> export PYTHONHOME="/home/aleksei/anaconda3/envs/idp:$PYTHONHOME"
>>>>
>>>> but while this error is fixed I obtain another:
>>>>
>>>> File "/home/aleksei/anaconda3/envs/idp/lib/python3.6/struct.py", line
>>>> 13, in <module>
>>>> from _struct import *
>>>> ModuleNotFoundError: No module named '_struct'
>>>>
>>>>
>>>> So, I am trying to fix it but always obtain one or another error and
>>>> can not run gpaw-python.
>>>>
>>>> Have you seen similar issues?
>>>>
>>>>
>>>> Best wishes,
>>>> Aleksei
>>>>
>>>>
>>>>
>>>>> Best regards,
>>>>> Gaël
>>>>>
>>>>>
>>>>>> Thanks for help and your time!
>>>>>>
>>>>>> Best wishes,
>>>>>>
>>>>>> Aleksei
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> gpaw-users mailing list
>>>>>> gpaw-users at listserv.fysik.dtu.dk
>>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>>> _______________________________________________
>>>>> gpaw-users mailing list
>>>>> gpaw-users at listserv.fysik.dtu.dk
>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>> _______________________________________________
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>>> _______________________________________________
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>>
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