[gpaw-users] Problem with compiling parallel GPAW
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Fri Aug 1 11:04:42 CEST 2014
On 07/31/2014 06:18 PM, Michalsky Ronald wrote:
> Hi Marcin,
>
> I’ve corrected .bashrc & added a libbat.so from the cluster to $LD_LIBRARY_PATH. The OpenMPI examples pass now with only the “OpenFabrics (openib) BTL failed to initialize” warning.
you will need to ask system administrators (providing the openmpi
examples script) if they thing it's harmless.
Best regards,
Marcin
> I’ve ignored this since I’m not planning on using the BSE for now. Optimizing small molecules from the command line on the entry node and parallelized bulk optimizations converge without error.
>
> Since I’m a bit behind I won’t try compiling dacapo as well. We had stopped here:
> http://listserv.fysik.dtu.dk/pipermail/campos/2014-July/002760.html
>
> Thanks a lot for your help!
>
> Best,
> Ronny
> ______________________
> From: Marcin Dulak [Marcin.Dulak at fysik.dtu.dk]
> Sent: Friday, July 25, 2014 11:43 PM
> To: Michalsky Ronald; gpaw-users at listserv.fysik.dtu.dk
> Subject: Re: [gpaw-users] Problem with compiling parallel GPAW
>
> Hi,
>
> On 07/25/2014 09:56 PM, Michalsky Ronald wrote:
>> Yes, “bse_MoS2_cut.py” hangs; it does not yield an actual error.
> for me it looks like you installation is probably OK, but see comments
> below.
> Especially it would be nice to test the basic mpi examples so they run
> without warnings,
> or ask system administrators what they think about them.
> On most infiniband installations there are some warning printed and
> usually this is harmless.
>> I’m not sure how to test the OpenMPI but I’ve tried using the OpenMPI provided by the cluster:
>>
>> Edits: in .bashrc:
>>
>> module load open_mpi/1.6.2
> module load should result in a fully configured openmpi runtime - no further
> variable exports should be needed. Please test the default mpi
> installation with a script similar to:
> http://www.student.dtu.dk/~mdul/accts/accts/mpi/gcc/examples.sh
> Please make it run without any warnings first.
>
> The hang could be also related to:
>
> The OpenFabrics (openib) BTL failed to initialize while trying to
> allocate some locked memory.
>
> Please see http://www.open-mpi.org/faq/?category=openfabrics#ib-locked-pages-user
>
> You may need to experiment with this with system administrators.
>
> On the other hand, if you don't plan to use the BSE just ignore the hang.
> I see that most tests on 4 cores pass. The "if (i % ncalcs) == icalc" errors are known
> and already fixed in GPAW/ASE trunks.
> Again ignore this if you don't plan to use LRTDDFT.
>
>> #export MPIDIR=/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran
>> export MPIDIR=/cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2
>> #export PATH=/cluster/home03/mavt/ronaldm/openmpi-1.8.1.gfortran/bin/mpicc:$PATH
>> export PATH=/cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/bin/mpicc:$PATH
> this is incorrect - see the comment below.
>> export LD_LIBRARY_PATH=/cluster/apps/gcc/gcc472/lib64:$LD_LIBRARY_PATH # for libquadmath.so.0
>> export LD_LIBRARY_PATH=/cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_ess_lsf:$LD_LIBRARY_PATH # due to warning, that was though not prevented
>> export LD_LIBRARY_PATH=/cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_plm_lsf:$LD_LIBRARY_PATH # due to warning, that was though not prevented
>> export LD_LIBRARY_PATH=/cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_ras_lsf:$LD_LIBRARY_PATH # due to warning, that was though not prevented
> the last 3 lines are incorrect.
> Any environment variable that has a PATH in the name should point to a
> directory path
> not a file or executable, something like:
>
> export LD_LIBRARY_PATH=/cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib:$LD_LIBRARY_PATH
>
>> Edits: in .bash_profile:
>>
>> module load python/2.7.2 netcdf/4.1.3 #######
>> #module load python/2.7.2 netcdf/4.3.0 #######
>> module load gcc/4.7.2
>> module load open_mpi/1.6.2
>> export NETCDF=/cluster/apps/netcdf/4.1.3/x86_64/serial/gcc_4.7.2/lib #######
>> #export NETCDF=/cluster/apps/netcdf/4.3.0/x86_64/gcc_4.7.2/openmpi_1.6.2/lib #######
>>
>>>>> Still: gpaw-python `which gpaw-test` 2>&1 | tee test.log
>>>>> hangs at “bse_MoS2_cut.py”:
>> [brutus3.ethz.ch:35995] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_ess_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored)
> It's unlikely that the main openmpi is broken on the cluster.
> What it complains about is missing libbat.so, and I guess what is needed
> it LD_LIBRARY_PATH exported
> to the directory PATH that contains this file.
>
>> [brutus3.ethz.ch:36084] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_ess_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored)
>> [brutus3.ethz.ch:36084] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_plm_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored)
>> [brutus3.ethz.ch:36084] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_ras_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: brutus3.ethz.ch
>> OMPI source: btl_openib.c:190
>> 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: brutus3.ethz.ch (PID 35995)
>> 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-Bh4RnJ
>> Jobs: 1, Cores: 1, debug-mode: False
>> =============================================================================
>> gemm_complex.py 0.018 OK
>> […]
>>
>>>>> and: mpirun -np 2 gpaw-python -c "import gpaw.mpi as mpi; print mpi.rank"
>>>>> yields:
>> [brutus3.ethz.ch:35216] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_ess_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored)
>> [brutus3.ethz.ch:35216] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_plm_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored)
>> [brutus3.ethz.ch:35216] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_ras_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: brutus3.ethz.ch
>> OMPI source: btl_openib.c:190
>> 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
>> --------------------------------------------------------------------------
>> 0
>> 1
>> [brutus3.ethz.ch:35216] 1 more process has sent help message help-mpi-btl-openib.txt / init-fail-no-mem
>> [brutus3.ethz.ch:35216] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
>>
>>>>> while: mpiexec -np 4 gpaw-python `which gpaw-test` 2>&1 | tee test4.log
>>>>> yields:
>> [brutus2.ethz.ch:48094] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_ess_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored)
>> [brutus2.ethz.ch:48094] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_plm_lsf: libbat.so: cannot open shared object file: No such file or directory (ignored)
>> [brutus2.ethz.ch:48094] mca: base: component_find: unable to open /cluster/apps/openmpi/1.6.2/x86_64/gcc_4.7.2/lib/openmpi/mca_ras_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: brutus2.ethz.ch
>> OMPI source: btl_openib.c:190
>> 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: brutus2.ethz.ch (PID 48100)
>> 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-0Z2zMG
>> Jobs: 1, Cores: 4, debug-mode: False
>> =============================================================================
>> gemm_complex.py 0.034 OK
>> mpicomm.py 0.032 OK
>> ase3k_version.py 0.029 OK
>> numpy_core_multiarray_dot.py 0.029 OK
>> eigh.py 0.044 OK
>> lapack.py 0.026 OK
>> dot.py 0.022 OK
>> lxc_fxc.py 0.029 OK
>> blas.py 0.032 OK
>> erf.py 0.020 OK
>> gp2.py 0.022 OK
>> kptpar.py [brutus2.ethz.ch:48094] 3 more processes have sent help message help-mpi-btl-openib.txt / init-fail-no-mem
>> [brutus2.ethz.ch:48094] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
>> [brutus2.ethz.ch:48094] 3 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork
>> 6.769 OK
>> non_periodic.py 0.026 OK
>> parallel/blacsdist.py 0.030 OK
>> gradient.py 0.038 OK
>> cg2.py 0.045 OK
>> kpt.py 0.024 OK
>> lf.py 0.022 OK
>> gd.py 0.017 OK
>> parallel/compare.py 0.242 OK
>> pbe_pw91.py 0.031 OK
>> fsbt.py 0.022 OK
>> derivatives.py 0.035 OK
>> Gauss.py 0.053 OK
>> second_derivative.py 0.041 OK
>> integral4.py 0.046 OK
>> parallel/ut_parallel.py 1.170 OK
>> transformations.py 0.046 OK
>> parallel/parallel_eigh.py 0.036 OK
>> spectrum.py 0.303 OK
>> xc.py 0.099 OK
>> zher.py 0.063 OK
>> pbc.py 0.061 OK
>> lebedev.py 0.051 OK
>> parallel/ut_hsblacs.py 0.346 OK
>> occupations.py 0.093 OK
>> dump_chi0.py 0.098 OK
>> cluster.py 0.271 OK
>> pw/interpol.py 0.032 OK
>> poisson.py 0.078 OK
>> pw/lfc.py 0.291 OK
>> pw/reallfc.py 0.405 OK
>> XC2.py 0.105 OK
>> multipoletest.py 0.406 OK
>> nabla.py 0.132 OK
>> noncollinear/xccorr.py 0.600 OK
>> gauss_wave.py 0.612 OK
>> harmonic.py 0.214 OK
>> atoms_too_close.py 0.256 OK
>> screened_poisson.py 0.206 OK
>> yukawa_radial.py 0.050 OK
>> noncollinear/xcgrid3d.py 0.197 OK
>> vdwradii.py 2.275 OK
>> lcao_restart.py 0.500 OK
>> ase3k.py 0.841 OK
>> parallel/ut_kptops.py 2.128 OK
>> fileio/idiotproof_setup.py 0.682 OK
>> fileio/hdf5_simple.py 0.037 SKIPPED
>> fileio/hdf5_noncontiguous.py 0.032 SKIPPED
>> fileio/parallel.py 6.487 OK
>> timing.py 1.019 OK
>> coulomb.py 0.572 OK
>> xcatom.py 1.585 OK
>> proton.py 0.492 OK
>> keep_htpsit.py 2.049 OK
>> pw/stresstest.py 2.313 OK
>> aeatom.py 4.282 OK
>> numpy_zdotc_graphite.py 1.822 OK
>> lcao_density.py 0.845 OK
>> parallel/overlap.py 0.978 OK
>> restart.py 1.973 OK
>> gemv.py 3.267 OK
>> ylexpand.py 1.659 OK
>> wfs_io.py 1.775 OK
>> fixocc.py 4.275 OK
>> nonselfconsistentLDA.py 2.343 OK
>> gga_atom.py 3.069 OK
>> ds_beta.py 2.794 OK
>> gauss_func.py 0.894 OK
>> noncollinear/h.py 1.997 OK
>> symmetry.py 3.726 OK
>> usesymm.py 2.058 OK
>> broydenmixer.py 4.086 OK
>> mixer.py 4.097 OK
>> wfs_auto.py 1.659 OK
>> ewald.py 5.067 OK
>> refine.py 1.503 OK
>> revPBE.py 2.956 OK
>> nonselfconsistent.py 3.267 OK
>> hydrogen.py 2.043 OK
>> fileio/file_reference.py 4.062 OK
>> fixdensity.py 3.996 OK
>> bee1.py 2.605 OK
>> spinFe3plus.py 5.160 OK
>> pw/h.py 6.014 OK
>> stdout.py 3.986 OK
>> parallel/lcao_complicated.py 10.440 OK
>> pw/slab.py 9.166 OK
>> spinpol.py 4.213 OK
>> plt.py 3.010 OK
>> eed.py 2.512 OK
>> lrtddft2.py 1.868 OK
>> parallel/hamiltonian.py 2.207 OK
>> ah.py 3.870 OK
>> laplace.py 0.034 OK
>> pw/mgo_hybrids.py 12.123 OK
>> lcao_largecellforce.py 3.160 OK
>> restart2.py 3.530 OK
>> Cl_minus.py 7.130 OK
>> fileio/restart_density.py 10.020 OK
>> external_potential.py 2.266 OK
>> pw/bulk.py 8.433 OK
>> pw/fftmixer.py 1.472 OK
>> mgga_restart.py 3.698 OK
>> vdw/quick.py 11.911 OK
>> partitioning.py 8.147 OK
>> bulk.py 12.549 OK
>> elf.py 6.431 OK
>> aluminum_EELS.py 5.776 OK
>> H_force.py 5.329 OK
>> parallel/lcao_hamiltonian.py 8.331 OK
>> fermisplit.py 5.849 OK
>> parallel/ut_redist.py 15.330 OK
>> lcao_h2o.py 2.746 OK
>> cmrtest/cmr_test2.py 5.257 OK
>> h2o_xas.py 5.350 OK
>> ne_gllb.py 10.771 OK
>> exx_acdf.py 6.887 OK
>> ut_rsh.py 2.145 OK
>> ut_csh.py 2.205 OK
>> spin_contamination.py 6.899 OK
>> davidson.py 9.190 OK
>> cg.py 7.258 OK
>> gllbatomic.py 22.057 OK
>> lcao_force.py 12.172 OK
>> fermilevel.py 12.780 OK
>> h2o_xas_recursion.py 7.836 OK
>> excited_state.py /cluster/home03/mavt/ronaldm/gpaw/gpaw/lrtddft/excited_state.py:176: RuntimeWarning: divide by zero encountered in remainder
>> if (i % ncalcs) == icalc:
>> /cluster/home03/mavt/ronaldm/gpaw/gpaw/lrtddft/excited_state.py:176: RuntimeWarning: divide by zero encountered in remainder
>> if (i % ncalcs) == icalc:
>> /cluster/home03/mavt/ronaldm/gpaw/gpaw/lrtddft/excited_state.py:176: RuntimeWarning: divide by zero encountered in remainder
>> if (i % ncalcs) == icalc:
>> /cluster/home03/mavt/ronaldm/gpaw/gpaw/lrtddft/excited_state.py:176: RuntimeWarning: divide by zero encountered in remainder
>> if (i % ncalcs) == icalc:
>> 2.423 FAILED! (rank 0,1,2,3)
>> #############################################################################
>> RANK 0,1,2,3:
>> Traceback (most recent call last):
>> File "/cluster/home03/mavt/ronaldm/gpaw/gpaw/test/__init__.py", line 514, in run_one
>> execfile(filename, loc)
>> File "/cluster/home03/mavt/ronaldm/gpaw/gpaw/test/excited_state.py", line 39, in <module>
>> forces = exst.get_forces(H2)
>> File "/cluster/home03/mavt/ronaldm/gpaw/gpaw/lrtddft/excited_state.py", line 176, in get_forces
>> if (i % ncalcs) == icalc:
>> ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
>> #############################################################################
>> gemm.py 18.840 OK
>> rpa_energy_Ni.py 15.612 OK
>> LDA_unstable.py 20.611 OK
>> si.py 7.939 OK
>> blocked_rmm_diis.py 5.108 OK
>> lxc_xcatom.py 22.004 OK
>> gw_planewave.py 9.671 OK
>> degeneracy.py 9.305 OK
>> apmb.py 9.745 OK
>> vdw/potential.py 0.041 OK
>> al_chain.py 13.172 OK
>> relax.py 12.406 OK
>> fixmom.py 10.716 OK
>> CH4.py 12.639 OK
>> diamond_absorption.py 12.034 OK
>> simple_stm.py 22.820 OK
>> gw_method.py 18.060 OK
>> lcao_bulk.py 14.978 OK
>> constant_electric_field.py 15.148 OK
>> parallel/ut_invops.py 14.622 OK
>> parallel/lcao_projections.py 7.506 OK
>> guc_force.py 24.147 OK
>> test_ibzqpt.py 16.916 OK
>> aedensity.py 16.705 OK
>> fd2lcao_restart.py 23.504 OK
>> lcao_bsse.py 9.762 OK
>> pplda.py 33.445 OK
>> revPBE_Li.py 35.922 OK
>> si_primitive.py 17.008 OK
>> complex.py 10.706 OK
>> Hubbard_U.py 30.096 OK
>> ldos.py 38.696 OK
>> parallel/ut_hsops.py 58.648 OK
>> pw/hyb.py 35.228 OK
>> hgh_h2o.py 13.953 OK
>> vdw/quick_spin.py 52.983 OK
>> scfsic_h2.py 16.912 OK
>> lrtddft.py 31.377 OK
>> dscf_lcao.py 24.880 OK
>> IP_oxygen.py 36.677 OK
>> Al2_lrtddft.py 22.078 OK
>> rpa_energy_Si.py 32.897 OK
>> 2Al.py 29.983 OK
>> jstm.py 19.824 OK
>> tpss.py 42.180 OK
>> be_nltd_ip.py 17.267 OK
>> si_xas.py 30.602 OK
>> atomize.py 37.679 OK
>> chi0.py 162.184 OK
>> Cu.py 48.385 OK
>> restart_band_structure.py 41.443 OK
>> ne_disc.py 36.857 OK
>> exx_coarse.py 32.540 OK
>> exx_unocc.py 8.875 OK
>> Hubbard_U_Zn.py 41.355 OK
>> diamond_gllb.py 73.924 OK
>> h2o_dks.py 70.194 OK
>> aluminum_EELS_lcao.py 26.350 OK
>> gw_ppa.py 21.388 OK
>> gw_static.py 10.340 OK
>> exx.py 30.104 OK
>> pygga.py 89.949 OK
>> dipole.py 39.430 OK
>> nsc_MGGA.py 48.030 OK
>> mgga_sc.py 39.634 OK
>> MgO_exx_fd_vs_pw.py 79.017 OK
>> lb94.py 170.687 OK
>> 8Si.py 42.790 OK
>> td_na2.py 33.487 OK
>> ehrenfest_nacl.py 19.010 OK
>> rpa_energy_N2.py 149.873 OK
>> beefvdw.py 114.234 OK
>> nonlocalset.py 108.888 OK
>> wannierk.py 68.999 OK
>> rpa_energy_Na.py 79.209 OK
>> pw/si_stress.py 139.633 OK
>> ut_tddft.py 69.103 OK
>> transport.py 163.823 OK
>> vdw/ar2.py 120.665 OK
>> aluminum_testcell.py 162.975 OK
>> au02_absorption.py 231.149 OK
>> lrtddft3.py 212.349 OK
>> scfsic_n2.py 146.630 OK
>> parallel/lcao_parallel.py 8.294 OK
>> parallel/fd_parallel.py 6.368 OK
>> bse_aluminum.py 16.704 OK
>> bse_diamond.py 47.535 OK
>> bse_vs_lrtddft.py 116.312 OK
>> parallel/pblas.py 0.051 OK
>> parallel/scalapack.py 0.041 OK
>> parallel/scalapack_diag_simple.py 0.055 OK
>> parallel/scalapack_mpirecv_crash.py 11.156 OK
>> parallel/realspace_blacs.py 0.050 OK
>> AA_exx_enthalpy.py 303.890 OK
>> cmrtest/cmr_test.py 0.383 SKIPPED
>> cmrtest/cmr_test3.py 0.025 SKIPPED
>> cmrtest/cmr_test4.py 0.031 SKIPPED
>> cmrtest/cmr_append.py 0.016 SKIPPED
>> cmrtest/Li2_atomize.py 0.017 SKIPPED
>> =============================================================================
>> Ran 230 tests out of 237 in 4885.5 seconds
>> Tests skipped: 7
>> Tests failed: 1
>> =============================================================================
>>
>>>>> Trying addtitinoally: in .bashrc & .bash_profile:
>> #module load python/2.7.2 netcdf/4.1.3 #######
>> module load python/2.7.2 netcdf/4.3.0 #######
> Best regards,
>
> Marcin
>> #export NETCDF=/cluster/apps/netcdf/4.1.3/x86_64/serial/gcc_4.7.2/lib #######
>> export NETCDF=/cluster/apps/netcdf/4.3.0/x86_64/gcc_4.7.2/openmpi_1.6.2/lib #######
>>
>> Serial: yields the same hanging at “bse_MoS2_cut.py”
>> Parallel: The same error messages as above
>>
>
>
>
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