[gpaw-users] Problem with compiling parallel GPAW
Michalsky Ronald
michalskyr at ethz.ch
Wed Jul 23 20:06:01 CEST 2014
This worked but running the tests:
gpaw-python `which gpaw-test` 2>&1 | tee test.log
stops at “bse_MoS2_cut.py”
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
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:
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
***********************************
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