[gpaw-users] Problem with compiling parallel GPAW
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Thu Jul 24 16:24:35 CEST 2014
Hi,
On 07/23/2014 08:06 PM, Michalsky Ronald wrote:
> This worked but running the tests:
> gpaw-python `which gpaw-test` 2>&1 | tee test.log
> stops at “bse_MoS2_cut.py”
stops with an error or hangs?
>
> I assume since the parallel excetubale is not built,
> mpirun -np 2 gpaw-python -c "import gpaw.mpi as mpi; print mpi.rank"
> yields: -bash: mpirun: command not found
mpirun/mpiexec is not found - probably some environment variables not set.
Please try to get first the openmpi tests that correspond to your
compiled openmpi-1.8.1 working running on the cluster, e.g.
http://www.student.dtu.dk/~mdul/accts/accts/mpi/gcc/examples.sh
> and: mpiexec -np 4 gpaw-python `which gpaw-test` 2>&1 | tee test4.log
> yields: -bash: mpiexec: command not found
>
> The content of test.log is:
>
> [brutus1.ethz.ch:07077] mca: base: component_find: unable to open /cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/lib/openmpi/mca_ess_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored)
> --------------------------------------------------------------------------
> The OpenFabrics (openib) BTL failed to initialize while trying to
> allocate some locked memory. This typically can indicate that the
> memlock limits are set too low. For most HPC installations, the
> memlock limits should be set to "unlimited". The failure occured
> here:
>
> Local host: brutus1
> OMPI source: btl_openib.c:203
> Function: ibv_create_cq()
> Device: mlx4_0
> Memlock limit: 2097152
>
> You may need to consult with your system administrator to get this
> problem fixed. This FAQ entry on the Open MPI web site may also be
> helpful:
i see some infiniband references - have you compiled openmpi with
infiniband and batch system support?
Normally compiling own mpi on a cluster is not a good idea, better use
the provided ones.
Best regards,
Marcin
>
> http://www.open-mpi.org/faq/?category=openfabrics#ib-locked-pages
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> 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: brutus1 (PID 7077)
> 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.
> --------------------------------------------------------------------------
> python 2.7.2 GCC 4.4.6 20110731 (Red Hat 4.4.6-3) 64bit ELF on Linux x86_64 centos 6.5 Final
> Running tests in /tmp/gpaw-test-ux2iIc
> Jobs: 1, Cores: 1, debug-mode: False
> =============================================================================
> gemm_complex.py 0.019 OK
> mpicomm.py 0.022 OK
> ase3k_version.py 0.030 OK
> numpy_core_multiarray_dot.py 0.017 OK
> eigh.py 0.033 OK
> lapack.py 0.020 OK
> dot.py 0.013 OK
> lxc_fxc.py 0.017 OK
> blas.py 0.024 OK
> erf.py 0.011 OK
> gp2.py 0.014 OK
> kptpar.py 0.010 OK
> non_periodic.py 0.019 OK
> parallel/blacsdist.py 0.043 OK
> gradient.py 0.022 OK
> cg2.py 0.028 OK
> kpt.py 0.020 OK
> lf.py 0.018 OK
> gd.py 0.011 OK
> parallel/compare.py 0.010 OK
> pbe_pw91.py 0.012 OK
> fsbt.py 0.017 OK
> derivatives.py 0.034 OK
> Gauss.py 0.052 OK
> second_derivative.py 0.040 OK
> integral4.py 0.211 OK
> parallel/ut_parallel.py 0.085 OK
> transformations.py 0.049 OK
> parallel/parallel_eigh.py 0.024 OK
> spectrum.py 0.294 OK
> xc.py 0.116 OK
> zher.py 0.057 OK
> pbc.py 0.092 OK
> lebedev.py 0.042 OK
> parallel/ut_hsblacs.py 0.355 OK
> occupations.py 0.075 OK
> dump_chi0.py 0.215 OK
> cluster.py 0.351 OK
> pw/interpol.py 0.137 OK
> poisson.py 0.113 OK
> pw/lfc.py 0.300 OK
> pw/reallfc.py 0.413 OK
> XC2.py 0.285 OK
> multipoletest.py 0.476 OK
> nabla.py 0.400 OK
> noncollinear/xccorr.py 0.682 OK
> gauss_wave.py 0.621 OK
> harmonic.py 0.429 OK
> atoms_too_close.py 0.557 OK
> screened_poisson.py 0.658 OK
> yukawa_radial.py 0.017 OK
> noncollinear/xcgrid3d.py 0.655 OK
> vdwradii.py 2.071 OK
> lcao_restart.py 0.900 OK
> ase3k.py 1.287 OK
> parallel/ut_kptops.py 2.112 OK
> fileio/idiotproof_setup.py 1.029 OK
> fileio/hdf5_simple.py 0.094 SKIPPED
> fileio/hdf5_noncontiguous.py 0.022 SKIPPED
> timing.py 0.984 OK
> coulomb.py 1.438 OK
> xcatom.py 1.560 OK
> maxrss.py 1.641 OK
> proton.py 1.413 OK
> pw/moleculecg.py 5.965 OK
> keep_htpsit.py 7.162 OK
> pw/stresstest.py 2.411 OK
> aeatom.py 4.404 OK
> numpy_zdotc_graphite.py 2.449 OK
> lcao_density.py 2.264 OK
> parallel/overlap.py 2.333 OK
> restart.py 3.038 OK
> gemv.py 3.314 OK
> ylexpand.py 3.458 OK
> potential.py 3.238 OK
> wfs_io.py 4.943 OK
> fixocc.py 5.507 OK
> nonselfconsistentLDA.py 4.462 OK
> gga_atom.py 3.119 OK
> ds_beta.py 6.206 OK
> gauss_func.py 3.223 OK
> noncollinear/h.py 3.476 OK
> symmetry.py 3.655 OK
> usesymm.py 3.267 OK
> broydenmixer.py 5.569 OK
> mixer.py 5.567 OK
> pes.py 6.219 OK
> wfs_auto.py 4.546 OK
> ewald.py 4.854 OK
> refine.py 4.352 OK
> revPBE.py 5.574 OK
> nonselfconsistent.py 5.969 OK
> hydrogen.py 4.718 OK
> fileio/file_reference.py 4.291 OK
> fixdensity.py 5.568 OK
> bee1.py 5.994 OK
> spinFe3plus.py 5.925 OK
> pw/h.py 6.230 OK
> stdout.py 9.607 OK
> parallel/lcao_complicated.py 7.766 OK
> pw/slab.py 12.213 OK
> spinpol.py 6.984 OK
> plt.py 8.149 OK
> lcao_pair_and_coulomb.py 6.221 OK
> eed.py 5.338 OK
> lrtddft2.py 5.233 OK
> parallel/hamiltonian.py 6.910 OK
> ah.py 5.731 OK
> laplace.py 8.297 OK
> pw/mgo_hybrids.py 15.114 OK
> lcao_largecellforce.py 6.294 OK
> restart2.py 11.502 OK
> Cl_minus.py 11.902 OK
> fileio/restart_density.py 15.878 OK
> external_potential.py 6.671 OK
> pw/bulk.py 10.417 OK
> pw/fftmixer.py 1.736 OK
> mgga_restart.py 9.814 OK
> vdw/quick.py 12.291 OK
> partitioning.py 15.677 OK
> bulk.py 15.912 OK
> elf.py 14.620 OK
> aluminum_EELS.py 7.906 OK
> H_force.py 10.790 OK
> parallel/lcao_hamiltonian.py 9.976 OK
> fermisplit.py 11.719 OK
> parallel/ut_redist.py 16.637 OK
> lcao_h2o.py 8.878 OK
> cmrtest/cmr_test2.py 13.187 OK
> h2o_xas.py 12.424 OK
> ne_gllb.py 16.306 OK
> exx_acdf.py 10.807 OK
> asewannier.py 15.842 OK
> exx_q.py 12.657 OK
> ut_rsh.py 8.009 OK
> ut_csh.py 7.753 OK
> spin_contamination.py 12.575 OK
> davidson.py 18.177 OK
> pw/davidson_pw.py 6.337 OK
> cg.py 12.661 OK
> gllbatomic.py 20.706 OK
> lcao_force.py 15.549 OK
> neb.py 19.622 OK
> fermilevel.py 40.550 OK
> h2o_xas_recursion.py 19.107 OK
> diamond_eps.py 17.053 OK
> excited_state.py 104.577 OK
> gemm.py 18.569 OK
> rpa_energy_Ni.py 28.412 OK
> LDA_unstable.py 42.628 OK
> si.py 28.033 OK
> blocked_rmm_diis.py 12.470 OK
> lxc_xcatom.py 22.621 OK
> gw_planewave.py 26.636 OK
> degeneracy.py 22.890 OK
> apmb.py 25.843 OK
> vdw/potential.py 22.132 OK
> al_chain.py 21.149 OK
> relax.py 34.275 OK
> fixmom.py 19.754 OK
> CH4.py 26.450 OK
> diamond_absorption.py 23.281 OK
> simple_stm.py 40.956 OK
> gw_method.py 30.347 OK
> lcao_bulk.py 22.350 OK
> constant_electric_field.py 39.661 OK
> parallel/ut_invops.py 30.231 OK
> wannier_ethylene.py 42.960 OK
> parallel/lcao_projections.py 26.394 OK
> guc_force.py 35.227 OK
> test_ibzqpt.py 28.109 OK
> aedensity.py 33.635 OK
> fd2lcao_restart.py 48.761 OK
> lcao_bsse.py 30.819 OK
> pplda.py 73.708 OK
> revPBE_Li.py 60.898 OK
> si_primitive.py 33.757 OK
> complex.py 34.953 OK
> Hubbard_U.py 61.438 OK
> ldos.py 37.616 OK
> parallel/ut_hsops.py 65.933 OK
> pw/hyb.py 58.344 OK
> hgh_h2o.py 42.048 OK
> vdw/quick_spin.py 71.347 OK
> scfsic_h2.py 33.947 OK
> lrtddft.py 73.679 OK
> dscf_lcao.py 45.671 OK
> IP_oxygen.py 69.511 OK
> Al2_lrtddft.py 73.959 OK
> rpa_energy_Si.py 71.933 OK
> 2Al.py 71.388 OK
> jstm.py 48.191 OK
> tpss.py 85.009 OK
> be_nltd_ip.py 53.408 OK
> si_xas.py 74.762 OK
> atomize.py 81.544 OK
> chi0.py 328.921 OK
> ralda_energy_H2.py 14.760 OK
> ralda_energy_N2.py 44.734 OK
> ralda_energy_Ni.py 40.005 OK
> Cu.py 79.470 OK
> restart_band_structure.py 58.996 OK
> ne_disc.py 112.526 OK
> exx_coarse.py 66.586 OK
> exx_unocc.py 17.899 OK
> Hubbard_U_Zn.py 82.009 OK
> muffintinpot.py 144.672 OK
> diamond_gllb.py 155.858 OK
> h2o_dks.py 131.237 OK
> aluminum_EELS_lcao.py 70.621 OK
> gw_ppa.py 67.232 OK
> nscfsic.py 151.915 OK
> gw_static.py 29.595 OK
> exx.py 88.592 OK
> pygga.py 178.549 OK
> dipole.py 132.991 OK
> nsc_MGGA.py 97.486 OK
> mgga_sc.py 64.015 OK
> MgO_exx_fd_vs_pw.py 129.831 OK
> lb94.py 300.942 OK
> 8Si.py 108.260 OK
> td_na2.py 112.532 OK
> ehrenfest_nacl.py 62.301 OK
> rpa_energy_N2.py 129.659 OK
> beefvdw.py 252.350 OK
> nonlocalset.py 164.675 OK
> wannierk.py 138.025 OK
> rpa_energy_Na.py 212.742 OK
> coreeig.py 202.662 OK
> pw/si_stress.py 216.543 OK
> ut_tddft.py 227.711 OK
> transport.py 425.775 OK
> vdw/ar2.py 380.194 OK
> bse_sym.py 465.311 OK
> aluminum_testcell.py 436.707 OK
> au02_absorption.py 569.460 OK
> lrtddft3.py 657.319 OK
> scfsic_n2.py 307.946 OK
> bse_MoS2_cut.py
>
> ________________________________________
> From: Marcin Dulak [Marcin.Dulak at fysik.dtu.dk]
> Sent: Wednesday, July 23, 2014 10:08 AM
> To: Michalsky Ronald; gpaw-users at listserv.fysik.dtu.dk
> Subject: Re: [gpaw-users] Problem with compiling parallel GPAW
>
> Hi,
>
> On 07/23/2014 09:33 AM, Michalsky Ronald wrote:
>> This did it:
>>
>> […]
>> * Using standard lapack
>> * Architecture: linux-x86_64
>> * Building a custom interpreter
>>
>> I’ve but compiled the setups, etc., but get stuck when running the tests:
> is GPAW_SETUP_PATH exported?
>> gpaw-test -j 8
>>
>> yields: […] ImportError: libacml.so: cannot open shared object file: No such file or directory
>>
>> gpaw-python `which gpaw-test` 2>&1 | tee test.log
>>
>> yields: gpaw-python: error while loading shared libraries: libacml.so: cannot open shared object file: No such file or directory
>>
>> libacml.so is at $HOME/acm15.3.1/gfortran64/lib
>> but writing any of these does not help:
>> export PYTHONPATH=$HOME/acm15.3.1/gfortran64/lib:$PYTHONPATH
>> export PATH=$HOME/acm15.3.1/gfortran64/lib:$PATH
>> export LIBRARY_PATH=$HOME/acm15.3.1/gfortran64/lib:$LIBRARY_PATH
> you need:
>
> export LD_LIBRARY_PATH=$HOME/acm15.3.1/gfortran64/lib:$LD_LIBRARY_PATH
>
> Please remove the three exports above - they are not needed.
> Don't forget to run the tests in parallel:
> mpiexec -np 4 gpaw-python `which gpaw-test` 2>&1 | tee test4.log
> mpiexec -np 8 gpaw-python `which gpaw-test` 2>&1 | tee test8.log
>
>
>> echo $BLASLAPACK shows:
>> -L/cluster/apps/netcdf/4.1.3/x86_64/serial/gcc_4.7.2/lib -lnetcdff -lnetcdf -L/cluster/home03/mavt/ronaldm/acm15.3.1/gfortran64/lib -lacml -L/cluster/home03/mavt/ronaldm/acm15.3.1/gfortran64/lib -lacml -lgfortran
> this is not relevant for GPAW - it does not use this variable.
>
> Best regards,
>
> Marcin
>> Do you have an idea?
>> Thanks, Ronny
>>
>> ________________________________________
>> From: Marcin Dulak [Marcin.Dulak at fysik.dtu.dk]
>> Sent: Tuesday, July 22, 2014 1:39 PM
>> To: Michalsky Ronald; gpaw-users at listserv.fysik.dtu.dk
>> Subject: Re: [gpaw-users] Problem with compiling parallel GPAW
>>
>> Hi,
>>
>> On 07/22/2014 11:58 AM, Michalsky Ronald wrote:
>>> Hi,
>>>
>>> I’ve compiled ASE but have difficulties with compiling GPAW for parallel computations (CentOS 6 OS and I’m using a gcc/4.7.2 compiler). Below I describe how I’ve complied Libxc & GPAW. The initial error message (mpicc was not found) is fixed now. However, it appears the parallel executable is not compiled due to some -R option that is not recognized. I’d appreciate your advice.
>>>
>>> # Initial email at Campos mailing list:
>>>
>>>>>> Assuming Libxc is the only missing dependency:
>>> cd $HOME
>>> wget http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.0.2.tar.gz -O libxc-2.0.2.tar.gz
>>> tar xzf libxc-2.0.2.tar.gz
>>> cd libxc-2.0.2
>>> ./configure --enable-shared --prefix=$HOME/xc
>>> make
>>> make install
>>> export C_INCLUDE_PATH=~/xc/include
>>> export LIBRARY_PATH=~/xc/lib
>>> export LD_LIBRARY_PATH=~/xc/lib
>>>
>>> cd $HOME
>>> tar xzf gpaw-0.10.0.11364.tar.gz
>>>>>> Rename: $HOME/gpaw-0.10.0.11364 to $HOME/gpaw
>>> export GPAW_HOME =${HOME}/gpaw
>>> cd gpaw
>>>
>>>>>> Edit: $HOME/gpaw/customize.py:
>>> libraries = ['acml', 'gfortran']
>>> library_dirs = ['/cluster/home03/mavt/ronaldm/acm15.3.1/gfortran64/lib']
>>> mpicompiler = 'mpicc'
>>> mpilinker = 'gfortran'
>>> mpi_libraries = ['opal_wrapper']
>>>
>>> # Reply from From Marcin Dulak
>>>
>>> provide full path to mpicc. I see below from the compilation log mpicc
>>> is not in PATH.
>>>
>>> mpicompiler = '/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/bin/mpicc'
>>> mpilinker = mpicompiler
>>>
>>> mpi_libraries = ['opal_wrapper']
>>>
>>> no, this is supposed to be a library to be linked (so, for -lmpi it's
>>> just "mpi"]
>>>
>>> mpi_libraries = ['mpi']
>>>
>>>> mpi_library_dirs = ['/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/bin']
>>> '/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/lib'
>>>
>>> # My changes & notes:
>>>
>>>>>> I’ve edited in .bashrc:
>>> export PATH=/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/bin/mpicc:$PATH
>>>>>> I’ve edited in customize.py:
>>> mpicompiler = '/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/bin/mpicc'
>>> mpilinker = mpicompiler
>>> mpi_libraries = ['mpi']
>>> mpi_library_dirs = ['/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/lib']
>>>>>> this avoided the error: ‘sh: mpicc: command not found’
>>> # Continue “Initial email at Campos mailing list”:
>>>
>>> mpi_library_dirs = ['/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/bin']
>>> mpi_include_dirs = ['/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/include']
>>> mpi_runtime_library_dirs = ['/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/lib']
>>> scalapack = False
>>>
>>>>>> Note, $HOME/openmpi-1.8.1.gfortran/bin contains an ‘mpicc’ symlink to the ‘opal_wrapper’ file in the same directory
>>> python setup.py build_ext 2>&1 | tee build_ext.log
>>>
>>>>>> yielding:
>>> /usr/bin/gcc -pthread -shared build/temp.linux-x86_64-2.7/c/wigner_seitz.o build/temp.linux-x86_64-2.7/c/mpi.o build/temp.linux-x86_64-2.7/c/spline.o build/temp.linux-x86_64-2.7/c/lcao.o build/temp.linux-x86_64-2.7/c/_gpaw.o build/temp.linux-x86_64-2.7/c/plane_wave.o build/temp.linux-x86_64-2.7/c/symmetry.o build/temp.linux-x86_64-2.7/c/lfc.o build/temp.linux-x86_64-2.7/c/operators.o build/temp.linux-x86_64-2.7/c/lapack.o build/temp.linux-x86_64-2.7/c/point_charges.o build/temp.linux-x86_64-2.7/c/blacs.o build/temp.linux-x86_64-2.7/c/bc.o build/temp.linux-x86_64-2.7/c/transformers.o build/temp.linux-x86_64-2.7/c/lfc2.o build/temp.linux-x86_64-2.7/c/localized_functions.o build/temp.linux-x86_64-2.7/c/mlsqr.o build/temp.linux-x86_64-2.7/c/blas.o build/temp.linux-x86_64-2.7/c/hdf5.o build/temp.linux-x86_64-2.7/c/utilities.o build/temp.linux-x86_64-2.7/c/cerf.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/bmgs/bmgs.o build/temp.linux-x86_64-2.7/c/xc/pw91.o build/temp.linux-x86_64-2.7/c/xc/tpss.o build/temp.linux-x86_64-2.7/c/xc/revtpss.o build/temp.linux-x86_64-2.7/c/xc/revtpss_c_pbe.o build/temp.linux-x86_64-2.7/c/xc/pbe.o build/temp.linux-x86_64-2.7/c/xc/libxc.o build/temp.linux-x86_64-2.7/c/xc/rpbe.o build/temp.linux-x86_64-2.7/c/xc/m06l.o build/temp.linux-x86_64-2.7/c/xc/xc_mgga.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/ensemble_gga.o -L/cluster/home03/mavt/ronaldm/acm15.3.1/gfortran64/lib -L/cluster/apps/python/2.7.2/x86_64/lib64 -lacml -lgfortran -lpython2.7 -o build/lib.linux-x86_64-2.7/_gpaw.so
>>> sh: mpicc: command not found
>>> gfortran: error: unrecognized option '-R'
>>> mpicc -DNPY_NO_DEPRECATED_API=7 -D_GNU_SOURCE=1 -DPARALLEL=1 -DGPAW_INTERPRETER=1 -Wall -std=c99 -I/cluster/apps/python/2.7.2/x86_64/lib64/python2.7/site-packages/numpy/core/include -I/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/include -I/cluster/apps/python/2.7.2/x86_64/include/python2.7 -I/cluster/apps/python/2.7.2/x86_64/include/python2.7 -o build/temp.linux-x86_64-2.7/c/bc.o -c c/bc.c
>>> gfortran -o build/bin.linux-x86_64-2.7//gpaw-python build/temp.linux-x86_64-2.7/c/wigner_seitz.o build/temp.linux-x86_64-2.7/c/mpi.o build/temp.linux-x86_64-2.7/c/spline.o build/temp.linux-x86_64-2.7/c/lcao.o build/temp.linux-x86_64-2.7/c/_gpaw.o build/temp.linux-x86_64-2.7/c/plane_wave.o build/temp.linux-x86_64-2.7/c/symmetry.o build/temp.linux-x86_64-2.7/c/lfc.o build/temp.linux-x86_64-2.7/c/operators.o build/temp.linux-x86_64-2.7/c/lapack.o build/temp.linux-x86_64-2.7/c/point_charges.o build/temp.linux-x86_64-2.7/c/blacs.o build/temp.linux-x86_64-2.7/c/bc.o build/temp.linux-x86_64-2.7/c/transformers.o build/temp.linux-x86_64-2.7/c/lfc2.o build/temp.linux-x86_64-2.7/c/localized_functions.o build/temp.linux-x86_64-2.7/c/mlsqr.o build/temp.linux-x86_64-2.7/c/blas.o build/temp.linux-x86_64-2.7/c/hdf5.o build/temp.linux-x86_64-2.7/c/utilities.o build/temp.linux-x86_64-2.7/c/cerf.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/bmgs/bmgs.o build/temp.linux-x86_64-2.7/c/xc/pw91.o build/temp.linux-x86_64-2.7/c/xc/tpss.o build/temp.linux-x86_64-2.7/c/xc/revtpss.o build/temp.linux-x86_64-2.7/c/xc/revtpss_c_pbe.o build/temp.linux-x86_64-2.7/c/xc/pbe.o build/temp.linux-x86_64-2.7/c/xc/libxc.o build/temp.linux-x86_64-2.7/c/xc/rpbe.o build/temp.linux-x86_64-2.7/c/xc/m06l.o build/temp.linux-x86_64-2.7/c/xc/xc_mgga.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/ensemble_gga.o -L/cluster/home03/mavt/ronaldm/acm15.3.1/gfortran64/lib -L/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/bin -L/cluster/apps/python/2.7.2/x86_64/lib64/python2.7/config -lacml -lgfortran -lopal_wrapper -lpython2.7 -lpthread -ldl -lutil -lm -R/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/lib -Xlinker -export-dynamic
>>>
>>> * Using standard lapack
>>> * Architecture: linux-x86_64
>>> * Building a custom interpreter
>>> * linking FAILED! Only serial version of code will work.
>>>
>>> # Continue “Reply from From Marcin Dulak”:
>>>
>>>> sh: mpicc: command not found
>>> mpicc is missing in PATH.
>>>> gfortran: error: unrecognized option '-R'
>>> i don't see any -R option here, where does it come from?
>>> Please move the thread about building GPAW to the gpaw-users mailing
>>> list: https://wiki.fysik.dtu.dk/gpaw/mailinglists.html
>>>
>>> # My changes & notes:
>>>
>>>>>> I’ve written at ‘#Hack taken from distutils to determine option for runtime_libary_dirs’ in $HOME/gpaw/config.py:
>>> else:
>>> runtime_lib_option = '-L' # chnaged from '-R' to '-L', assuming this includes linux-x86_64
>> i guess there is a bug in this part. Just don't use
>> mpi_runtime_library_dirs or similar for the moment.
>>>>>> This yields the error copied below. Note, the error message is the same when not hacking $HOME/gpaw/config.py but instead commenting out in customize.py:
>>> # mpi_library_dirs = ['/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/lib']
>>>
>>> […]
>>> /cluster/apps/python/2.7.2/x86_64/lib64/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
>>> /tmp/Python-2.7.2/./Modules/posixmodule.c:7370: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
>>> /cluster/apps/python/2.7.2/x86_64/lib64/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
>>> /tmp/Python-2.7.2/./Modules/posixmodule.c:7317: warning: the use of `tempnam' is dangerous, better use `mkstemp'
>>> build/temp.linux-x86_64-2.7/c/xc/libxc.o: In function `lxcXCFunctional_dealloc':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:194: undefined reference to `xc_func_end'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:194: undefined reference to `xc_func_end'
>>> build/temp.linux-x86_64-2.7/c/xc/libxc.o: In function `lxcXCFunctional_CalculateFXC':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:758: undefined reference to `xc_lda_fxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:763: undefined reference to `xc_gga_fxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:763: undefined reference to `xc_gga_fxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:758: undefined reference to `xc_lda_fxc'
>>> build/temp.linux-x86_64-2.7/c/xc/libxc.o: In function `lxcXCFunctional_Calculate':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:642: undefined reference to `xc_lda_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:647: undefined reference to `xc_gga_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:647: undefined reference to `xc_gga_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:653: undefined reference to `xc_mgga_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:653: undefined reference to `xc_mgga_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:642: undefined reference to `xc_lda_exc_vxc'
>>> build/temp.linux-x86_64-2.7/c/xc/libxc.o: In function `get_fxc_fd_lda':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:38: undefined reference to `xc_lda_fxc_fd'
>>> build/temp.linux-x86_64-2.7/c/xc/libxc.o: In function `get_point':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:65: undefined reference to `xc_lda_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:69: undefined reference to `xc_gga_exc_vxc'
>>> build/temp.linux-x86_64-2.7/c/xc/libxc.o: In function `NewlxcXCFunctionalObject':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:852: undefined reference to `xc_family_from_id'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:854: undefined reference to `xc_func_init'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:861: undefined reference to `xc_family_from_id'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:863: undefined reference to `xc_func_init'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:866: undefined reference to `xc_family_from_id'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:868: undefined reference to `xc_func_init'
>>> build/temp.linux-x86_64-2.7/c/xc/libxc.o: In function `lxcXCFuncNum':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/libxc.c:907: undefined reference to `xc_functional_get_number'
>>> build/temp.linux-x86_64-2.7/c/xc/tpss.o: In function `c_tpss_12':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:292: undefined reference to `xc_gga_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:308: undefined reference to `xc_gga_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:325: undefined reference to `xc_gga_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:292: undefined reference to `xc_gga_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:308: undefined reference to `xc_gga_exc_vxc'
>>> build/temp.linux-x86_64-2.7/c/xc/tpss.o:/cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:325: more undefined references to `xc_gga_exc_vxc' follow
>>> build/temp.linux-x86_64-2.7/c/xc/tpss.o: In function `x_tpss_para':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:125: undefined reference to `xc_lda_exc_vxc'
>>> build/temp.linux-x86_64-2.7/c/xc/tpss.o: In function `tpss_end':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:544: undefined reference to `xc_func_end'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:547: undefined reference to `xc_func_end'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:548: undefined reference to `xc_func_end'
>>> build/temp.linux-x86_64-2.7/c/xc/tpss.o: In function `tpss_init':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:534: undefined reference to `xc_func_init'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:538: undefined reference to `xc_func_init'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/tpss.c:539: undefined reference to `xc_func_init'
>>> build/temp.linux-x86_64-2.7/c/xc/revtpss.o: In function `revtpss_end':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss.c:553: undefined reference to `xc_func_end'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss.c:556: undefined reference to `xc_func_end'
>>> build/temp.linux-x86_64-2.7/c/xc/revtpss.o: In function `revtpss_init':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss.c:545: undefined reference to `xc_func_init'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss.c:547: undefined reference to `xc_func_init'
>>> build/temp.linux-x86_64-2.7/c/xc/revtpss.o: In function `x_revtpss_para':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss.c:449: undefined reference to `xc_lda_exc_vxc'
>>> build/temp.linux-x86_64-2.7/c/xc/revtpss.o: In function `revtpss_end':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss.c:557: undefined reference to `xc_func_end'
>>> build/temp.linux-x86_64-2.7/c/xc/revtpss.o: In function `revtpss_init':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss.c:548: undefined reference to `xc_func_init'
>>> build/temp.linux-x86_64-2.7/c/xc/revtpss_c_pbe.o: In function `xc_perdew_params':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss_c_pbe.c:64: undefined reference to `xc_lda_exc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss_c_pbe.c:70: undefined reference to `xc_lda'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/revtpss_c_pbe.c:67: undefined reference to `xc_lda_exc_vxc'
>>> build/temp.linux-x86_64-2.7/c/xc/m06l.o: In function `m06l_end':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/m06l.c:733: undefined reference to `xc_func_end'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/m06l.c:736: undefined reference to `xc_func_end'
>>> build/temp.linux-x86_64-2.7/c/xc/m06l.o: In function `m06l_init':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/m06l.c:724: undefined reference to `xc_func_init'
>>> build/temp.linux-x86_64-2.7/c/xc/m06l.o: In function `c_m06l_para':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/m06l.c:328: undefined reference to `xc_lda_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/m06l.c:338: undefined reference to `xc_lda_exc_vxc'
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/m06l.c:372: undefined reference to `xc_lda_exc_vxc'
>>> build/temp.linux-x86_64-2.7/c/xc/m06l.o: In function `x_m06l_para':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/m06l.c:656: undefined reference to `xc_gga_exc_vxc'
>>> build/temp.linux-x86_64-2.7/c/xc/m06l.o: In function `m06l_init':
>>> /cluster/home03/mavt/ronaldm/gpaw/c/xc/m06l.c:727: undefined reference to `xc_func_init'
>>> collect2: error: ld returned 1 exit status
>>> python2.7 -I/cluster/apps/python/2.7.2/x86_64/include/python2.7 -o build/temp.linux-x86_64-2.7/c/hdf5.o -c c/hdf5.c
>>> /cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/bin/mpicc -o build/bin.linux-x86_64-2.7//gpaw-python build/temp.linux-x86_64-2.7/c/mlsqr.o build/temp.linux-x86_64-2.7/c/symmetry.o build/temp.linux-x86_64-2.7/c/lapack.o build/temp.linux-x86_64-2.7/c/lcao.o build/temp.linux-x86_64-2.7/c/blacs.o build/temp.linux-x86_64-2.7/c/plt.o build/temp.linux-x86_64-2.7/c/plane_wave.o build/temp.linux-x86_64-2.7/c/wigner_seitz.o build/temp.linux-x86_64-2.7/c/utilities.o build/temp.linux-x86_64-2.7/c/spline.o build/temp.linux-x86_64-2.7/c/point_charges.o build/temp.linux-x86_64-2.7/c/_gpaw.o build/temp.linux-x86_64-2.7/c/mpi.o build/temp.linux-x86_64-2.7/c/lfc2.o build/temp.linux-x86_64-2.7/c/bc.o build/temp.linux-x86_64-2.7/c/hdf5.o build/temp.linux-x86_64-2.7/c/cerf.o build/temp.linux-x86_64-2.7/c/transformers.o build/temp.linux-x86_64-2.7/c/blas.o build/temp.linux-x86_64-2.7/c/lfc.o build/temp.linux-x86_64-2.7/c/localized_functions.o build/temp.linux-x86_64-2.7/c/operators.o build/temp.linux-x86_64-2.7/c/fftw.o build/temp.linux-x86_64-2.7/c/bmgs/bmgs.o build/temp.linux-x86_64-2.7/c/xc/libxc.o build/temp.linux-x86_64-2.7/c/xc/xc_mgga.o build/temp.linux-x86_64-2.7/c/xc/tpss.o build/temp.linux-x86_64-2.7/c/xc/pw91.o build/temp.linux-x86_64-2.7/c/xc/pbe.o build/temp.linux-x86_64-2.7/c/xc/revtpss.o build/temp.linux-x86_64-2.7/c/xc/xc.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/vdw.o build/temp.linux-x86_64-2.7/c/xc/rpbe.o build/temp.linux-x86_64-2.7/c/xc/m06l.o -L/cluster/home03/mavt/ronaldm/acm15.3.1/gfortran64/lib -L/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/lib -L/cluster/apps/python/2.7.2/x86_64/lib64/python2.7/config -lacml -lgfortran -lmpi -lpython2.7 -lpthread -ldl -lutil -lm -L/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/lib -Xlinker -export-dynamic
>>>
>>> * Using standard lapack
>>> * Architecture: linux-x86_64
>>> * Building a custom interpreter
>>> * linking FAILED! Only serial version of code will work.
>> you miss libxc linking.
>> This is because of: libraries = ['acml', 'gfortran']
>> It should be:
>>
>> libraries += ['acml', 'gfortran']
>>
>> Best regards,
>>
>> Marcin
>>> Ronald Michalsky
>>> Postdoctoral Research Associate
>>> ETH Zürich
>>> Institute of Energy Technology
>>> ML K 23, Sonneggstr. 3
>>> 8092 Zürich, Switzerland
>>> Tel: +41-44-6338383
>>> _______________________________________________
>>> gpaw-users mailing list
>>> gpaw-users at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>
>>>
>> --
>> ***********************************
>>
>> 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
>
> ***********************************
>
>
>
>
--
***********************************
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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