[gpaw-users] Need help - gpaw test fails
ksaha at physics.udel.edu
ksaha at physics.udel.edu
Wed Jul 7 15:46:32 CEST 2010
Dear gpaw-users,
>
> What did you put in your $PYTHONPATH - "/home/ksaha/gpaw-07" or
> "/home/ksaha/gpaw"?
I have checked out gpaw development release ($ svn checkout
https://svn.fysik.dtu.dk/projects/gpaw/trunk gpaw) and accordingly use the
path "/home/ksaha/gpaw"
Here are the paths I put in my .bashrc file:
export PYTHONPATH=$HOME/ase:$PYTHONPATH
export PATH=$HOME/ase/tools:$PATH
export PYTHONPATH=${HOME}/gpaw:${PYTHONPATH}
export PYTHONPATH=/home/ksaha/gpaw/build/lib.linux-x86_64-2.4:${PYTHONPATH}
export
PATH=/home/ksaha/gpaw/build/bin.linux-x86_64-2.4:${HOME}/gpaw/tools:${PATH}
export GPAW_SETUP_PATH=${HOME}/gpaw-setups-setups-0.6.6300
>
> It looks like the parallel version of GPAW works OK (gpaw-python) but the
> serial version does not (_gpaw.so). How did you build the code?
After checking out the code, I have followed your installation guide given in
https://wiki.fysik.dtu.dk/gpaw/install/installationguide.html
Basically, I included required libraries and compiler name in customize.py:
compiler = 'mpiicc'
libraries += ['lapack', 'blas']
put all the pathas in .bashrc
and then executed
[gpaw]$ python setup.py build_ext 2>&1 | tee build_ext.log
> Try to
> do a "python setup.py clean" followed by a "python setup.py build_ext".
>
I followed you suggestion and you find below that the code looks compile
well:
mpicc -o build/bin.linux-x86_64-2.4//gpaw-python
build/temp.linux-x86_64-2.4/c/xc.o build/temp.linux-x86_64-2.4/c/blas.o
build/temp.linux-x86_64-2.4/c/rpbe.o build/temp.linux-x86_64-2.4/c/lfc2.o
build/temp.linux-x86_64-2.4/c/compiled_WITH_SL.o
build/temp.linux-x86_64-2.4/c/mgga.o build/temp.linux-x86_64-2.4/c/pw91.o
build/temp.linux-x86_64-2.4/c/vasiliev02prb.o
build/temp.linux-x86_64-2.4/c/lapack.o
build/temp.linux-x86_64-2.4/c/plane_wave.o
build/temp.linux-x86_64-2.4/c/libxc.o
build/temp.linux-x86_64-2.4/c/spline.o
build/temp.linux-x86_64-2.4/c/utilities.o
build/temp.linux-x86_64-2.4/c/tpss_ec.o
build/temp.linux-x86_64-2.4/c/mpi.o build/temp.linux-x86_64-2.4/c/vdw.o
build/temp.linux-x86_64-2.4/c/wigner_seitz.o
build/temp.linux-x86_64-2.4/c/_gpaw.o
build/temp.linux-x86_64-2.4/c/mlsqr.o build/temp.linux-x86_64-2.4/c/hdf5.o
build/temp.linux-x86_64-2.4/c/ensemble_gga.o
build/temp.linux-x86_64-2.4/c/transformers.o
build/temp.linux-x86_64-2.4/c/localized_functions.o
build/temp.linux-x86_64-2.4/c/lcao.o build/temp.linux-x86_64-2.4/c/lb94.o
build/temp.linux-x86_64-2.4/c/pbe.o build/temp.linux-x86_64-2.4/c/blacs.o
build/temp.linux-x86_64-2.4/c/symmetry.o
build/temp.linux-x86_64-2.4/c/tpss.o
build/temp.linux-x86_64-2.4/c/point_charges.o
build/temp.linux-x86_64-2.4/c/tpss_ex.o
build/temp.linux-x86_64-2.4/c/d2Excdn2.o
build/temp.linux-x86_64-2.4/c/cerf.o build/temp.linux-x86_64-2.4/c/bc.o
build/temp.linux-x86_64-2.4/c/lfc.o build/temp.linux-x86_64-2.4/c/plt.o
build/temp.linux-x86_64-2.4/c/operators.o
build/temp.linux-x86_64-2.4/c/io_wrappers.o
build/temp.linux-x86_64-2.4/c/bmgs/bmgs.o
build/temp.linux-x86_64-2.4/c/libxc/src/util.o
build/temp.linux-x86_64-2.4/c/libxc/src/special_functions.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_am05.o
build/temp.linux-x86_64-2.4/c/libxc/src/mgga.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_perdew.o
build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_pz.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_xc_hcth.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_am05.o
build/temp.linux-x86_64-2.4/c/libxc/src/functionals.o
build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_b3lyp.o
build/temp.linux-x86_64-2.4/c/libxc/src/mgga_c_tpss.o
build/temp.linux-x86_64-2.4/c/libxc/src/mgga_x_m06l.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_xalpha.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_pbe.o
build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_b3p86.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_b86.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_b88.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_dk87.o
build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_b3pw91.o
build/temp.linux-x86_64-2.4/c/libxc/src/mgga_c_m06l.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_lg93.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_xc_teter93.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_optx.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_pbea.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_pw86.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_rpa.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_x.o
build/temp.linux-x86_64-2.4/c/libxc/src/lca.o
build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_b1wc.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_b86_mgc.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_wigner.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_pw91.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_wc.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_pw.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_lyp.o
build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_x3lyp.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_xc_lb.o
build/temp.linux-x86_64-2.4/c/libxc/src/mgga_x_tpss.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_g96.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_ft97.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_pw91.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_mpbe.o
build/temp.linux-x86_64-2.4/c/libxc/src/mgga_c_revtpss.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_vwn.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_xc_edf1.o
build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_o3lyp.o
build/temp.linux-x86_64-2.4/c/libxc/src/mgga_x_revtpss.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_xc_xlyp.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_amgb.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_pbe.o
build/temp.linux-x86_64-2.4/c/libxc/src/lca_omc.o
build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_pbeh.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_rpbe.o
build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_hl.o
build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_p86.o
build/temp.linux-x86_64-2.4/c/libxc/src/lca_lch.o
-L/usr/lib64/python2.4/config -lblas -llapack -llapack -lblas -lpython2.4
-lpthread -ldl -lutil -lm -L/usr/kerberos/lib64 -Xlinker -export-dynamic
/usr/lib64/python2.4/config/libpython2.4.a(posixmodule.o): In function
`posix_tmpnam':
(.text+0x665): warning: the use of `tmpnam_r' is dangerous, better use
`mkstemp'
/usr/lib64/python2.4/config/libpython2.4.a(posixmodule.o): In function
`posix_tempnam':
(.text+0x748): warning: the use of `tempnam' is dangerous, better use
`mkstemp'
build/temp.linux-x86_64-2.4/c/lapack.o: warning: memset used with constant
zero length parameter; this could be due to transposed parameters
* Using standard lapack
* Compiling gpaw with mpiicc
* Architecture: linux-x86_64
* Building a custom interpreter
> Could you try to run the lxc_xc.py test directly and send us the output:
>
> cd gpaw/test
> python lxc_xc.py > output
>
Here is the output:
[ksaha at ulam test]$ python lxc_xc.py
2.0 1.0
LDA 2.90274693171e-10 dExdnb 2.90274693171e-10 dExdnb
2.0 1.0
PBE 6.32377831523e-10 dExcdsigma2 6.32377831523e-10 dExcdsigma2
2.0 1.0
revPBE 4.1867442846e-10 dExcdnb 4.1867442846e-10 dExcdnb
2.0 1.0
RPBE 2.94699376013e-10 dExcdna 2.94699376013e-10 dExcdna
2.0 1.0
LDAx 2.90274693171e-10 dExcdnb 2.90274693171e-10 dExcdnb
2.0 1.0
revPBEx 3.88416410146e-10 dExcdnb 3.88416410146e-10 dExcdnb
2.0 1.0
RPBEx 2.81688260174e-10 dExcdsigma0 2.81688260174e-10 dExcdsigma0
2.0 1.0
None-C_PW 3.09313685776e-11 dExcdna 3.09313685776e-11 dExcdna
2.0 1.0
TPSS 0.070917846674 dExcdna 0.070917846674 dExcdna
Traceback (most recent call last):
File "lxc_xc.py", line 139, in ?
assert error1[0] < 1.0e-9
AssertionError
[ksaha at ulam test]$
Also "python test.py" shows as:
[ksaha at ulam test]$ python test.py
/usr/lib64/python2.4/site-packages/scipy/misc/__init__.py:25:
DeprecationWarning: NumpyTest will be removed in the next release; please
update your code to use nose or unittest
test = NumpyTest().test
Running tests in /tmp/gpaw-test-e3Vn84
=============================================================================
ase3k_version.py 0.022 OK
numpy_core_multiarray_dot.py 0.022 OK
gemm_complex.py 0.022 OK
lapack.py 0.025 OK
mpicomm.py 0.023 OK
eigh.py 0.025 OK
setups.py 0.023 OK
xc.py 0.024 OK
xcfunc.py 0.024 OK
gradient.py 0.029 OK
pbe_pw91.py 0.023 OK
cg2.py 0.026 OK
d2Excdn2.py 0.026 OK
dot.py 0.027 OK
blas.py 0.025 OK
gp2.py 0.029 OK
non_periodic.py 0.030 OK
erf.py 0.023 OK
lf.py 0.031 OK
lxc_xc.py 0.019 FAILED!
#############################################################################
Traceback (most recent call last):
File
"/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/test/__init__.py",
line 332, in run_one
execfile(filename, {})
File "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/test/lxc_xc.py",
line 139, in ?
assert error1[0] < 1.0e-9
AssertionError
#############################################################################
lxc_fxc.py Segmentation fault
Please advise what else I shoud follow to resolve this issue. Thank you
very much!
Regards,
Kamal
>> Dear gpaw-users,
>>
>> I have installed the code in our local cluster without any problem.
>> However, when I try the following test, I get some problem. Please see
>> below:
>>
>> [ksaha at ulam gpaw]$ gpaw-python `which gpaw-test` 2>&1 | tee test.log
>> /usr/lib64/python2.4/site-packages/scipy/misc/__init__.py:25:
>> DeprecationWarning: NumpyTest will be removed in the next release;
>> please
>> update your code to use nose or unittest
>> test = NumpyTest().test
>> Running tests in /tmp/gpaw-test-ckegXA
>> ========================================================================
>> ase3k_version.py 0.023 OK
>> lapack.py 0.023 OK
>> mpicomm.py 0.023 OK
>> eigh.py 0.023 OK
>> setups.py 0.023 OK
>> xc.py 0.024 OK
>> xcfunc.py 0.024 OK
>> gradient.py 0.028 OK
>> pbe_pw91.py 0.023 OK
>> cg2.py 0.026 OK
>> d2Excdn2.py 0.026 OK
>> dot.py 0.026 OK
>> blas.py 0.025 OK
>> gp2.py 0.028 OK
>> non_periodic.py 0.030 OK
>> erf.py 0.023 OK
>> lf.py 0.031 OK
>> lxc_xc.py 0.018 FAILED!
>> ##########################################################################
>> Traceback (most recent call last):
>> File
>> "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/test/__init__.py",
>> line 325, in run_one
>> execfile(filename, {})
>> File
>> "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/test/lxc_xc.py",
>> line 139, in ?
>> assert error1[0] < 1.0e-9
>> AssertionError
>> ########################################################################
>> lxc_fxc.py [ksaha at ulam gpaw]$
>>
>>
>> Is this a bug or am I making some mistake?
>
> Could you try to run the lxc_xc.py test directly and send us the output:
>
> cd gpaw/test
> python lxc_xc.py > output
>
>> Then it also fails the following test:
>>
>> [ksaha at ulam test]$ pwd
>> /home/ksaha/gpaw/gpaw/test
>> [ksaha at ulam test]$ python test.py
>> Traceback (most recent call last):
>> File "test.py", line 9, in ?
>> import gpaw.mpi as mpi
>> File "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/__init__.py",
>> line 250, in ?
>> from gpaw.aseinterface import GPAW
>> File
>> "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/aseinterface.py",
>> line 11, in ?
>> from gpaw.paw import PAW
>> File "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/paw.py", line
>> 14,
>> in ?
>> import gpaw.io
>> File
>> "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/io/__init__.py",
>> line 10, in ?
>> import gpaw.mpi as mpi
>> File
>> "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/mpi/__init__.py",
>> line 13, in ?
>> from gpaw.utilities import is_contiguous
>> File
>> "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/utilities/__init__.py",
>> line 12, in ?
>> import _gpaw
>> ImportError: libimf.so: cannot open shared object file: No such file or
>> directory
>
> It looks like the parallel version of GPAW works OK (gpaw-python) but the
> serial version does not (_gpaw.so). How did you build the code? Try to
> do a "python setup.py clean" followed by a "python setup.py build_ext".
>
>> And also, I get different errors, when I submit a parallel job (in 2
>> processors) executing the following:
>>
>> mpirun -np 2 gpaw-python -c "import gpaw.mpi as mpi; print mpi.rank"
>>
>> See the error message:
>>
>> Traceback (most recent call last):
>> File "<string>", line 1, in ?
>> File "/home/ksaha/gpaw-0.7/gpaw/__init__.py", line 250, in ?
>> from gpaw.aseinterface import GPAW
>> Traceback (most recent call last):
>> File "<string>", line 1, in ?
>> File "/home/ksaha/gpaw-0.7/gpaw/aseinterface.py", line 9, in ?
>> File "/home/ksaha/gpaw-0.7/gpaw/__init__.py", line 250, in ?
>> from gpaw.aseinterface import GPAW
>> from ase.units import Bohr, Hartree
>> ImportError: No module named ase.units
>> File "/home/ksaha/gpaw-0.7/gpaw/aseinterface.py", line 9, in ?
>> from ase.units import Bohr, Hartree
>> ImportError: No module named ase.units
>>
>>
>> Can anyone please suggest me how to overcome this issue? Thanks in
>> advance!
>
> What did you put in your $PYTHONPATH - "/home/ksaha/gpaw-07" or
> "/home/ksaha/gpaw"? You may need to tell mpirun to export PYTHONPATH with
> "-x PYTHONPATH".
>
> Jens Jørgen
>
>> Regards,
>> Kamal
>>
>>
>> ==========================================================
>> Kamal K. Saha
>> Department of Physics and Astronomy
>> University of Delaware
>> Newark, DE 19716-2570
>> Phone: (302) 831-8519, Fax: (302) 831-1637
>>
>> http://web.physics.udel.edu/about/directory/postdoc/kamal-k-saha
>> ==========================================================
>>
>> _______________________________________________
>> gpaw-users mailing list
>> gpaw-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>
>
>
More information about the gpaw-users
mailing list