[gpaw-users] can't using gpaw-python
謝其軒
z955018 at gmail.com
Thu Oct 10 15:07:42 CEST 2013
Hi,
Marcin
I'm afraid that I'd confuse you.
I compiled numpy1.7.0 myself with the recipe in
install_sun_chpc_SUSE10.sh<https://wiki.fysik.dtu.dk/gpaw/install/Linux/sun_chpc.html>
and
with python2.7 only.
Then I compiled gpaw with python2.7, too.
and do the gpaw-python test
------------
python 2.7.5 GCC 4.1.2 20080704 (Red Hat 4.1.2-52) 64bit ELF on Linux
x86_64 redhat 5.8 Final
Running tests in /tmp/gpaw-test-Htm4W4
Jobs: 1, Cores: 4, debug-mode: False
=============================================================================
gemm_complex.py 0.049 OK
mpicomm.py 0.009 OK
ase3k_version.py 0.007 OK
.........
pw/interpol.py 0.011 OK
poisson.py 0.051 OK
pw/lfc.py gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
gpaw-python: symbol lookup error:
/opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
undefined symbol: omp_get_num_procs
--------------------------------------------------------------------------
mpiexec has exited due to process rank 2 with PID 26226 on
node breadserver.physics.ntu exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
--------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------
All sound fine.
----------------
[z955018 at breadserver gpaw-0.9.1.10596]$ gpaw-python
Python 2.7.5 (default, Aug 13 2013, 16:24:20)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>>
--------------
When I start to calculate the ground state, the result works fine.
However, there's a MPI warning :
--------------------------------------------------------------------------
An MPI process has executed an operation involving a call to the
"fork()" system call to create a child process. Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your MPI job may hang, crash, or produce silent
data corruption. The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.
The process that invoked fork was:
Local host: node01 (PID 4577)
MPI_COMM_WORLD rank: 0
If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
[node01:04576] 7 more processes have sent help message help-mpi-runtime.txt
/ mpi_init:warn-fork
[node01:04576] Set MCA parameter "orte_base_help_aggregate" to 0 to see all
help / error messages
~
I can't figure out what it is.
---------------------------------------------------------
By the way, how can I find a BLAS/LAPACK library when compiling Scipy?
chi-hsuan
2013/10/10 謝其軒 <z955018 at gmail.com>
> Hi,
> Marcin
> I'm afraid that I'd confuse you.
> I compiled numpy1.7.0 myself with the recipe in
> install_sun_chpc_SUSE10.sh<https://wiki.fysik.dtu.dk/gpaw/install/Linux/sun_chpc.html> and
> with python2.7 only.
> Then I compiled gpaw with python2.7, too.
> and do the gpaw-python test
>
> ------------
> python 2.7.5 GCC 4.1.2 20080704 (Red Hat 4.1.2-52) 64bit ELF on Linux
> x86_64 redhat 5.8 Final
> Running tests in /tmp/gpaw-test-Htm4W4
> Jobs: 1, Cores: 4, debug-mode: False
>
> =============================================================================
> gemm_complex.py 0.049 OK
> mpicomm.py 0.009 OK
> ase3k_version.py 0.007 OK
> numpy_core_multiarray_dot.py 0.007 OK
> eigh.py 0.075 OK
> lapack.py 0.014 OK
> dot.py 0.012 OK
> lxc_fxc.py 0.032 OK
> blas.py 0.033 OK
> erf.py 0.008 OK
> gp2.py 0.014 OK
> kptpar.py 4.196 OK
> non_periodic.py 0.010 OK
> parallel/blacsdist.py 0.008 OK
> gradient.py 0.012 OK
> cg2.py 0.010 OK
> kpt.py 0.012 OK
> lf.py 0.012 OK
> gd.py 0.008 OK
> parallel/compare.py 0.040 OK
> pbe_pw91.py 0.008 OK
> fsbt.py 0.011 OK
> derivatives.py 0.015 OK
> Gauss.py 0.016 OK
> second_derivative.py 0.018 OK
> integral4.py 0.027 OK
> parallel/ut_parallel.py 1.075 OK
> transformations.py 0.018 OK
> parallel/parallel_eigh.py 0.008 OK
> spectrum.py 0.034 OK
> xc.py 0.045 OK
> zher.py 0.035 OK
> pbc.py 0.041 OK
> lebedev.py 0.030 OK
> parallel/ut_hsblacs.py 0.092 OK
> occupations.py 0.057 OK
> dump_chi0.py 0.040 OK
> cluster.py 0.144 OK
> pw/interpol.py 0.011 OK
> poisson.py 0.051 OK
> pw/lfc.py gpaw-python: symbol lookup error:
> /opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
> undefined symbol: omp_get_num_procs
> gpaw-python: symbol lookup error:
> /opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
> undefined symbol: omp_get_num_procs
> gpaw-python: symbol lookup error:
> /opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
> undefined symbol: omp_get_num_procs
> gpaw-python: symbol lookup error:
> /opt/intel/composerxe-2011.3.174/mkl/lib/intel64/libmkl_intel_thread.so:
> undefined symbol: omp_get_num_procs
> --------------------------------------------------------------------------
> mpiexec has exited due to process rank 2 with PID 26226 on
> node breadserver.physics.ntu exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpiexec (as reported here).
> --------------------------------------------------------------------------
>
>
>
>
> ---------------------------------------------------------------------------------------------------
>
> All sound fine.
> ----------------
> [z955018 at breadserver gpaw-0.9.1.10596]$ gpaw-python
> Python 2.7.5 (default, Aug 13 2013, 16:24:20)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>>
> --------------
>
> When I start to calculate the ground state, the result works fine.
> However, there's a MPI warning :
>
>
> --------------------------------------------------------------------------
> An MPI process has executed an operation involving a call to the
> "fork()" system call to create a child process. Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your MPI job may hang, crash, or produce silent
> data corruption. The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
>
> The process that invoked fork was:
>
> Local host: node01 (PID 4577)
> MPI_COMM_WORLD rank: 0
>
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
> [node01:04576] 7 more processes have sent help message
> help-mpi-runtime.txt / mpi_init:warn-fork
> [node01:04576] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
> ~
>
>
> I can't figure out what it is.
>
> ---------------------------------------------------------
>
> By the way, how can I find a BLAS/LAPACK library when compiling Scipy?
>
>
>
>
> chi-hsuan
>
>
> 2013/10/10 Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
>
>> On 10/10/2013 05:42 AM, 謝其軒 wrote:
>>
>> Hi,
>> Marcin
>>
>> this is the situation when compiling gpaw-python:
>> --
>>
>> mpicc -o build/bin.linux-x86_64-2.7//gpaw-python
>> build/temp.linux-x86_64-2.7/c/plane_wave.o
>> build/temp.linux-x86_64-2.7/c/point_charges.o
>> build/temp.linux-x86_64-2.7/c/wigner_seitz.o
>> build/temp.linux-x86_64-2.7/c/lapack.o
>> build/temp.linux-x86_64-2.7/c/spline.o build/temp.linux-x86_64-2.7/c/lfc2.o
>> build/temp.linux-x86_64-2.7/c/hdf5.o build/temp.linux-x86_64-2.7/c/mpi.o
>> build/temp.linux-x86_64-2.7/c/symmetry.o
>> build/temp.linux-x86_64-2.7/c/plt.o build/temp.linux-x86_64-2.7/c/fftw.o
>> build/temp.linux-x86_64-2.7/c/_gpaw.o
>> build/temp.linux-x86_64-2.7/c/transformers.o
>> build/temp.linux-x86_64-2.7/c/operators.o
>> build/temp.linux-x86_64-2.7/c/bc.o build/temp.linux-x86_64-2.7/c/cerf.o
>> build/temp.linux-x86_64-2.7/c/blacs.o
>> build/temp.linux-x86_64-2.7/c/localized_functions.o
>> build/temp.linux-x86_64-2.7/c/lfc.o build/temp.linux-x86_64-2.7/c/lcao.o
>> build/temp.linux-x86_64-2.7/c/mlsqr.o
>> build/temp.linux-x86_64-2.7/c/utilities.o
>> build/temp.linux-x86_64-2.7/c/blas.o
>> build/temp.linux-x86_64-2.7/c/bmgs/bmgs.o
>> build/temp.linux-x86_64-2.7/c/xc/pbe.o
>> build/temp.linux-x86_64-2.7/c/xc/m06l.o
>> build/temp.linux-x86_64-2.7/c/xc/vdw.o
>> build/temp.linux-x86_64-2.7/c/xc/xc.o
>> build/temp.linux-x86_64-2.7/c/xc/tpss.o
>> build/temp.linux-x86_64-2.7/c/xc/revtpss_c_pbe.o
>> build/temp.linux-x86_64-2.7/c/xc/ensemble_gga.o
>> build/temp.linux-x86_64-2.7/c/xc/libxc.o
>> build/temp.linux-x86_64-2.7/c/xc/pw91.o
>> build/temp.linux-x86_64-2.7/c/xc/rpbe.o
>> build/temp.linux-x86_64-2.7/c/xc/xc_mgga.o
>> build/temp.linux-x86_64-2.7/c/xc/revtpss.o -L/opt/libxc/lib
>> -L/home/z955018/Canopy/appdata/canopy-1.0.3.1262.rh5-x86_64/lib/python2.7/config
>> -lxc -lblas -llapack -lscalapack -lpython2.7 -lpthread -ldl -lutil -lm
>> -Wl,-rpath,'$ORIGIN/../lib' -g -L/home/z955018/Canopy/appld: cannot find
>> -lscalapack
>>
>> please do not enable scalapack in customize.py for now.
>> In the other email you sent me (please always CC to gpaw-users), i see:
>>
>> mpicc -DNPY_NO_DEPRECATED_API=7 -DGPAW_NO_UNDERSCORE_CBLACS=1 -DGPAW_NO_UNDERSCORE_CSCALAPACK=1 -DGPAW_WITH_SL=1 -DPARALLEL=1 -DGPAW_INTERPRETER=1 -Wall -std=c99 -I/home/z955018/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/numpy/core/include -I/opt/libxc/include -I/home/z955018/Canopy/appdata/canopy-1.0.3.1262.rh5-x86_64/include/python2.7 -I/home/z955018/Canopy/appdata/canopy-1.0.3.1262.rh5-x86_64/include/python2.7 -o build/temp.linux-x86_64-2.7/c/bc.o -c c/bc.c
>>
>> Is it correct? Why python comes from
>> /home/z955018/Canopy/appdata/canopy-1.0.3.1262.rh5-x86_64/include/python2.7
>> but numpy from
>> /home/z955018/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/numpy/core/include
>>
>> Best regards,
>>
>> Marcin
>>
>> -------
>> * Using standard lapack
>> * Compiling gpaw with mpicc
>> * Compiling with ScaLapack
>> * Architecture: linux-x86_64
>> * Building a custom interpreter
>> * linking FAILED! Only serial version of code will work.
>>
>>
>>
>> I can't find the "numpy/core/include" thing, where is it?
>>
>> chi-hsuan
>>
>>
>> 2013/10/9 Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
>>
>>> Hi,
>>>
>>> please continue CC to the gpaw-users list.
>>>
>>>
>>> On 10/09/2013 05:08 AM, 謝其軒 wrote:
>>>
>>> Marcin,
>>> Yes, that's the OS I use.
>>> It may take me few days to figure out what's going on.
>>> By the way, how do you relink numpy when installing gpaw if you already
>>> have a old version numpy in root?
>>>
>>> One should run gpaw-python with the numpy version that is used during
>>> gpaw-python build - during the compilation you will see lines like
>>> -I.../numpy/core/include
>>> Mixing numpy versions will result in crashes or wrong results.
>>>
>>> I'm guessing your gpaw-python is built with python 2.4 and numpy with
>>> python 2.7.
>>> It's sufficient to have your Enthought fully setup before starting GPAW
>>> compilation:
>>> both python and numpy must belong to Enthought (verify that on the
>>> command line).
>>> You will need a fresh build of gpaw-python, the best way to start is to
>>> build C-extensions only:
>>>
>>> https://wiki.fysik.dtu.dk/gpaw/devel/developer_installation.html#developer-installation
>>> Only after gpaw-test passes one can consider doing python setup.py
>>> install
>>>
>>> Best regards,
>>>
>>> Marcin
>>>
>>>
>>> sincerely,
>>> chi-hsuan
>>>
>>>
>>> 2013/10/8 Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
>>>
>>>> Please continue on the list - this will be useful for other users.
>>>>
>>>>
>>>> On 10/08/2013 03:21 AM, 謝其軒 wrote:
>>>>
>>>> Hi,
>>>> I'm on a cluster CentOS system
>>>> Using openmpi 1.4.4 numpy 1.7.0 scipy 0.12.0
>>>> The error appear when I simply started gpaw-python on the command line,
>>>> not relavant to anyother modules
>>>> the error :
>>>> ImportError: numpy.core.multiarray failed to import
>>>>
>>>>
>>>>
>>>> ----------------------------------
>>>> python -c "import numpy; print numpy.__config__.show(); print
>>>> numpy.__version__"
>>>>
>>>> lapack_opt_info:
>>>> libraries = ['mkl_lapack95_lp64', 'mkl_gf_lp64',
>>>> 'mkl_intel_thread', 'mkl_core', 'iomp5', 'pthread']
>>>> library_dirs = ['/home/vagrant/src/master-env/lib']
>>>> define_macros = [('SCIPY_MKL_H', None)]
>>>> include_dirs = ['/home/vagrant/src/master-env/include']
>>>> blas_opt_info:
>>>> libraries = ['mkl_gf_lp64', 'mkl_intel_thread', 'mkl_core',
>>>> 'iomp5', 'pthread']
>>>> library_dirs = ['/home/vagrant/src/master-env/lib']
>>>> define_macros = [('SCIPY_MKL_H', None)]
>>>> include_dirs = ['/home/vagrant/src/master-env/include']
>>>> lapack_mkl_info:
>>>> libraries = ['mkl_lapack95_lp64', 'mkl_gf_lp64',
>>>> 'mkl_intel_thread', 'mkl_core', 'iomp5', 'pthread']
>>>> library_dirs = ['/home/vagrant/src/master-env/lib']
>>>> define_macros = [('SCIPY_MKL_H', None)]
>>>> include_dirs = ['/home/vagrant/src/master-env/include']
>>>> blas_mkl_info:
>>>> libraries = ['mkl_gf_lp64', 'mkl_intel_thread', 'mkl_core',
>>>> 'iomp5', 'pthread']
>>>> library_dirs = ['/home/vagrant/src/master-env/lib']
>>>> define_macros = [('SCIPY_MKL_H', None)]
>>>> include_dirs = ['/home/vagrant/src/master-env/include']
>>>> mkl_info:
>>>> libraries = ['mkl_gf_lp64', 'mkl_intel_thread', 'mkl_core',
>>>> 'iomp5', 'pthread']
>>>> library_dirs = ['/home/vagrant/src/master-env/lib']
>>>> define_macros = [('SCIPY_MKL_H', None)]
>>>> include_dirs = ['/home/vagrant/src/master-env/include']
>>>> None
>>>> 1.7.1
>>>>
>>>>
>>>>
>>>> -------------------------------
>>>>
>>>>
>>>> ldd `python -c "from numpy.core import multiarray; print
>>>> multiarray.__file__"`
>>>> linux-vdso.so.1 => (0x00007ffffd5fd000)
>>>> libm.so.6 => /lib64/libm.so.6 (0x00002af51a2dc000)
>>>> libpython2.7.so.1.0 =>
>>>> /home/z955018/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/numpy/core/../../../../../lib/libpython2.7.so.1.0
>>>> (0x00002af51a55f000)
>>>>
>>>> this is the python used by numpy - you need to make sure that you
>>>> build gpaw-python using the same python version.
>>>>
>>>> libpthread.so.0 => /lib64/libpthread.so.0 (0x00002af51a90e000)
>>>> libc.so.6 => /lib64/libc.so.6 (0x00002af51ab2a000)
>>>> libdl.so.2 => /lib64/libdl.so.2 (0x00002af51ae81000)
>>>> libutil.so.1 => /lib64/libutil.so.1 (0x00002af51b086000)
>>>> /lib64/ld-linux-x86-64.so.2 (0x0000003836400000)
>>>>
>>>>
>>>> ----------------------------
>>>>
>>>> ldd `which gpaw-python`
>>>> linux-vdso.so.1 => (0x00007fff325d1000)
>>>> libxc.so.1 => /opt/etsf/lib/libxc.so.1 (0x00002ab9fb1e7000)
>>>> libblas.so.3 => /usr/lib64/atlas/libblas.so.3 (0x00002ab9fb495000)
>>>> liblapack.so.3 => /usr/lib64/atlas/liblapack.so.3 (0x00002ab9fbe65000)
>>>> libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003837800000)
>>>> libdl.so.2 => /lib64/libdl.so.2 (0x0000003837400000)
>>>> libutil.so.1 => /lib64/libutil.so.1 (0x0000003846600000)
>>>> libm.so.6 => /lib64/libm.so.6 (0x00000037c7000000)
>>>> librdmacm.so.1 => /usr/lib64/librdmacm.so.1 (0x0000003832200000)
>>>> libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x0000003831e00000)
>>>> libtorque.so.2 => /opt/torque//lib/libtorque.so.2 (0x00002ab9fc57e000)
>>>> libnsl.so.1 => /lib64/libnsl.so.1 (0x000000383ee00000)
>>>> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003848a00000)
>>>> libc.so.6 => /lib64/libc.so.6 (0x0000003836800000)
>>>> libgfortran.so.1 => /usr/lib64/libgfortran.so.1 (0x00002ab9fc881000)
>>>> /lib64/ld-linux-x86-64.so.2 (0x0000003836400000)
>>>> ------------------------------
>>>>
>>>> i don't see here libpython2.7.so.1.0 =>
>>>> /home/z955018/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/numpy/core/../../../../../lib/libpython2.7.so.1.0
>>>> (0x00002af51a55f000)
>>>> so i'm guessing gpaw-python is built using the default CentOS 5 python
>>>> 2.4 (is it the system you run?).
>>>>
>>>> A numpy build using mkl is a fast and good solution for standalone
>>>> numpy runs, but will most likely
>>>> fail when running with gpaw-python, and other custom python
>>>> interpreters that link their own blas/lapack.
>>>> This can be serious: I have seen cases when it does not crash, but
>>>> gives wrong numbers instead.
>>>> For the moment let's keep numpy/mkl, but if running gpaw-test fails -
>>>> try to build numpy with it's
>>>> internal blas/lapack as described here:
>>>> https://wiki.fysik.dtu.dk/gpaw/install/Linux/sun_chpc.html
>>>>
>>>> When you have gpaw-python starting,
>>>>
>>>> export OMP_NUM_THREADS=1
>>>>
>>>> and run the full tests in parallel (on 1, 2, 4, 8 cores):
>>>> mpiexec gpaw-python `which gpaw-test`
>>>>
>>>> Remember to use the version of setups that corresponds to the gpaw
>>>> version installed:
>>>>
>>>> http://listserv.fysik.dtu.dk/pipermail/gpaw-users/2013-October/002398.html
>>>> gpaw-test may show problems with numpy/mkl,
>>>> but even if all tests pass you may still expect problems in some cases.
>>>>
>>>> Best regards,
>>>>
>>>> Marcin
>>>>
>>>> I use numpy and scipy from the canopy package, funny thing is that
>>>> when I change the package to anaconda, the error message changes.
>>>>
>>>> ***********************************
>>>>
>>>
>>>
>>>
>>> --
>>> ***********************************
>>>
>>> Marcin Dulak
>>> Technical University of Denmark
>>> Department of Physics
>>> Building 307, Room 229
>>> DK-2800 Kongens Lyngby
>>> Denmark
>>> Tel.: (+45) 4525 3157
>>> Fax.: (+45) 4593 2399
>>> email: Marcin.Dulak at fysik.dtu.dk
>>>
>>> ***********************************
>>>
>>>
>>
>>
>> --
>> ***********************************
>>
>> Marcin Dulak
>> Technical University of Denmark
>> Department of Physics
>> Building 307, Room 229
>> DK-2800 Kongens Lyngby
>> Denmark
>> Tel.: (+45) 4525 3157
>> Fax.: (+45) 4593 2399
>> email: Marcin.Dulak at fysik.dtu.dk
>>
>> ***********************************
>>
>>
>
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