[MOAB-dev] Error message when compiling the mbcoupler_test.cpp
Grindeanu, Iulian R.
iulian at mcs.anl.gov
Fri May 13 17:16:48 CDT 2016
Another possible cause is that you do not have a clean build.
can you do a make clean in your moab src and test folder, and then make and make check again. (this assumes that your configuration was successful already, as you reported)
I cannot explain why your MPI calls would have problems
________________________________________
From: Jie Wu [jie.voo at gmail.com]
Sent: Friday, May 13, 2016 3:41 PM
To: Vijay S. Mahadevan
Cc: Grindeanu, Iulian R.; moab-dev at mcs.anl.gov
Subject: Re: [MOAB-dev] Error message when compiling the mbcoupler_test.cpp
Hi Vijay,
Thank you so much for your help! 'Make install’ works good on my laptop.
I am looking forward to seeing the possible causes of the failing tests.
Best,
Jie
> On May 13, 2016, at 4:08 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>
> Ok, looks like your MPI installation and MOAB+MPI are configured and
> working fine. We will look at the tests and see why they are failing.
> I haven't been able to replicate the errors locally but I think we
> should be able to find the issue soon.
>
> If "make install" works (you should configure with a
> --prefix=$INSTALL_DIR option), you can start using the library now.
> I'll update you once we find the root cause for the issues you found.
>
> Vijay
>
> On Fri, May 13, 2016 at 2:12 PM, Jie Wu <jie.voo at gmail.com> wrote:
>> Hi there,
>>
>> Thank you for your directions! Here is the results I get after issuing make
>> -k check at directory test/parallel, and I think they look good.
>>
>> dyn-160-39-10-173:parallel jiewu$ make -k check
>> /Applications/Xcode.app/Contents/Developer/usr/bin/make pcomm_unit scdtest
>> pcomm_serial par_spatial_locator_test parallel_unit_tests scdpart
>> read_nc_par ucdtrvpart mpastrvpart gcrm_par parallel_hdf5_test
>> mhdf_parallel parallel_write_test uber_parallel_test parallel_adj
>> parmerge_test augment_with_ghosts imeshp_test mbparallelcomm_test partcheck
>> structured3 parmerge
>> CXX pcomm_unit.o
>> CXXLD pcomm_unit
>> CXX scdtest.o
>> CXXLD scdtest
>> CXX pcomm_serial.o
>> CXXLD pcomm_serial
>> CXX par_spatial_locator_test.o
>> CXXLD par_spatial_locator_test
>> CXX parallel_unit_tests.o
>> CXXLD parallel_unit_tests
>> CXX scdpart.o
>> CXXLD scdpart
>> CXX ../io/read_nc.o
>> CXXLD read_nc_par
>> CXX ucdtrvpart.o
>> CXXLD ucdtrvpart
>> CXX mpastrvpart.o
>> CXXLD mpastrvpart
>> CXX gcrm_par.o
>> CXXLD gcrm_par
>> CXX parallel_hdf5_test.o
>> CXXLD parallel_hdf5_test
>> CC mhdf_parallel.o
>> CCLD mhdf_parallel
>> CXX parallel_write_test.o
>> CXXLD parallel_write_test
>> CXX uber_parallel_test.o
>> CXXLD uber_parallel_test
>> CXX ../adj_moab_test.o
>> CXXLD parallel_adj
>> CXX parmerge_test.o
>> CXXLD parmerge_test
>> CXX augment_with_ghosts.o
>> CXXLD augment_with_ghosts
>> PPFC imeshp_test.o
>> FCLD imeshp_test
>> CXX mbparallelcomm_test.o
>> CXXLD mbparallelcomm_test
>> CXX partcheck.o
>> CXXLD partcheck
>> CXX structured3.o
>> CXXLD structured3
>> CXX parmerge.o
>> CXXLD parmerge
>> /Applications/Xcode.app/Contents/Developer/usr/bin/make check-TESTS
>> PASS: pcomm_unit
>> PASS: scdtest
>> PASS: pcomm_serial
>> PASS: par_spatial_locator_test
>> PASS: parallel_unit_tests
>> PASS: scdpart
>> PASS: read_nc_par
>> PASS: ucdtrvpart
>> PASS: mpastrvpart
>> PASS: gcrm_par
>> PASS: parallel_hdf5_test
>> PASS: mhdf_parallel
>> PASS: parallel_write_test
>> PASS: uber_parallel_test
>> PASS: parallel_adj
>> PASS: parmerge_test
>> PASS: augment_with_ghosts
>> PASS: imeshp_test
>> ============================================================================
>> Testsuite summary for MOAB 4.9.2pre
>> ============================================================================
>> # TOTAL: 18
>> # PASS: 18
>> # SKIP: 0
>> # XFAIL: 0
>> # FAIL: 0
>> # XPASS: 0
>> # ERROR: 0
>> ============================================================================
>>
>> Following is an example I run with mpiexec, and I think it also goes well.
>>
>> Thank you very much for your help! Any help deal with the failing tests will
>> be much appreciated.
>>
>> Best,
>> Jie
>>
>> dyn-160-39-10-173:mbcoupler jiewu$ mpiexec -np 2 mbcoupler_test -meshes
>> /Users/wujie/SourceCode/moab/MeshFiles/unittest/64bricks_1khex.h5m
>> /Users/wujie/SourceCode/moab/MeshFiles/unittest/64bricks_12ktet.h5m -itag
>> vertex_field -outfile dum.h5m
>> ReadHDF5: 0.0324039
>> get set meta 0.00103188
>> partial subsets 0.000803947
>> partition time 2.14577e-06
>> get set ids 0.000556946
>> set contents 0.00107098
>> polyhedra 2.5034e-05
>> elements 0.00174189
>> nodes 0.0014832
>> node adjacency 0
>> side elements 0.000672817
>> update connectivity 0.000102043
>> adjacency 0
>> delete non_adj 0.00338697
>> recursive sets 0
>> find contain_sets 0.000369072
>> read sets 0.00147104
>> read tags 0.01667
>> store file ids 0.00191593
>> read qa records 0.000133038
>> Parallel Read times:
>> 0.0473361 PARALLEL READ PART
>> 0.0138111 PARALLEL RESOLVE_SHARED_ENTS
>> 0.0113361 PARALLEL EXCHANGE_GHOSTS
>> 0.00113177 PARALLEL RESOLVE_SHARED_SETS
>> 0.00648403 PARALLEL_AUGMENT_SETS_WITH_GHOSTS
>> 0.079994 PARALLEL TOTAL
>> ReadHDF5: 0.0714378
>> get set meta 0.000261784
>> partial subsets 0.000660181
>> partition time 9.53674e-07
>> get set ids 0.00101304
>> set contents 0.000728846
>> polyhedra 0.000128031
>> elements 0.0155201
>> nodes 0.00354886
>> node adjacency 6.19888e-06
>> side elements 0.00422001
>> update connectivity 0.00184798
>> adjacency 0
>> delete non_adj 0.0100739
>> recursive sets 0
>> find contain_sets 0.00218511
>> read sets 0.00258899
>> read tags 0.0235598
>> store file ids 0.0044961
>> read qa records 9.5129e-05
>> Parallel Read times:
>> 0.0779119 PARALLEL READ PART
>> 0.0667319 PARALLEL RESOLVE_SHARED_ENTS
>> 0.0397439 PARALLEL EXCHANGE_GHOSTS
>> 0.00435901 PARALLEL RESOLVE_SHARED_SETS
>> 0.0243261 PARALLEL_AUGMENT_SETS_WITH_GHOSTS
>> 0.209468 PARALLEL TOTAL
>> Proc 1 iface entities:
>> 446 0d iface entities.
>> 1080 1d iface entities.
>> Proc 0636 2d iface entities.
>> 0 3d iface entities.
>> iface entities:
>> 446 0d iface entities.
>> 108 (446 verts adj to other iface ents)
>> 0 1d iface entities.
>> 636 2d iface entities.
>> 0 3d iface entities.
>> (446 verts adj to other iface ents)
>> rank 0 points of interest: 6155
>> rank 1 points of interest: 6155
>>
>> Max time : 0.101124 0.0461781 0.00104499 (inst loc interp -- 2 procs)
>> WriteHDF5: 0.0779669
>> gather mesh: 0.00237203
>> create file: 0.0655501
>> create nodes: 0.00201201
>> negotiate types: 2.19345e-05
>> create elem: 0.000785828
>> file id exch: 0.0234561
>> create adj: 0.000414848
>> create set: 0.019654
>> shared ids: 6.19888e-05
>> shared data: 0.014715
>> set offsets: 0.00447798
>> create tags: 0.0160849
>> coordinates: 0.00199103
>> connectivity: 0.00162005
>> sets: 0.0010829
>> set descrip: 0.00019598
>> set content: 0.000527859
>> set parent: 0.000226021
>> set child: 0.000128984
>> adjacencies: 5.96046e-06
>> tags: 0.00700402
>> dense data: 0.00127792
>> sparse data: 0.00569224
>> var-len data: 0
>> Wrote dum.h5m
>> mbcoupler_test complete.
>>
>>
>>
>> On May 13, 2016, at 2:58 PM, Grindeanu, Iulian R. <iulian at mcs.anl.gov>
>> wrote:
>>
>> yes, can you try make -k check ?
>> It will not stop at the first failed test, it will try to test everything
>> ________________________________________
>> From: Vijay S. Mahadevan [vijay.m at gmail.com]
>> Sent: Friday, May 13, 2016 1:53 PM
>> To: Jie Wu
>> Cc: Grindeanu, Iulian R.; moab-dev at mcs.anl.gov
>> Subject: Re: [MOAB-dev] Error message when compiling the mbcoupler_test.cpp
>>
>> Jie,
>>
>> We are looking into the failing tests and will update in case there is
>> a bug in the code. Our nightly tests are running cleanly and so I'm
>> curious to see if other tests are failing. Can you go to test/parallel
>> and run "make check" there to verify if the parallel job launch is
>> working correctly ? Also, can you verify if you can run MPI programs
>> with mpiexec ?
>>
>> Vijay
>>
>>
>>
>> Vijay
>>
>> On Fri, May 13, 2016 at 1:31 PM, Jie Wu <jie.voo at gmail.com> wrote:
>>
>> Hi Vijay,
>>
>> Deleting the auto-installed packages under sandbox before issue new
>> configurations works good! No error message emerged until I input the
>> command make check, which is as following.
>>
>> Do you have any idea for this problem?
>>
>> Best,
>> Jie
>>
>> PASS: reorder_test
>> FAIL: test_prog_opt
>> PASS: coords_connect_iterate
>> PASS: elem_eval_test
>> PASS: spatial_locator_test
>> PASS: test_boundbox
>> PASS: adj_moab_test
>> PASS: uref_mesh_test
>> PASS: verdict_test
>> PASS: test_Matrix3
>> PASS: mbfacet_test
>> PASS: gttool_test
>> PASS: cropvol_test
>> FAIL: mergemesh_test
>> PASS: mbground_test
>> PASS: lloyd_smoother_test
>> ============================================================================
>> Testsuite summary for MOAB 4.9.2pre
>> ============================================================================
>> # TOTAL: 36
>> # PASS: 34
>> # SKIP: 0
>> # XFAIL: 0
>> # FAIL: 2
>> # XPASS: 0
>> # ERROR: 0
>> ============================================================================
>> See test/test-suite.log
>> Please report to moab-dev at mcs.anl.gov
>> ============================================================================
>> make[4]: *** [test-suite.log] Error 1
>> make[3]: *** [check-TESTS] Error 2
>> make[2]: *** [check-am] Error 2
>> make[1]: *** [check-recursive] Error 1
>> make: *** [check-recursive] Error 1
>>
>>
>>
>>
>> On May 13, 2016, at 1:08 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>
>> Jie, since you now changed the compilers used to configure the stack,
>> I would advise deleting the auto-installed packages under sandbox
>> directory and then re-configuring. This will force the rebuild of
>> HDF5/NetCDF packages with the parallel MPI compilers and you should
>> get the HDF5-parallel support enabled after that. Makes sense ?
>>
>> Vijay
>>
>> On Fri, May 13, 2016 at 11:27 AM, Jie Wu <jie.voo at gmail.com> wrote:
>>
>> Hi Vijay,
>>
>> Thank you for your reply. The new configuration do works. Here shows the
>> command I inputed and the message while I input: make check.
>>
>> dyn-160-39-10-173:moab jiewu$ ./configure --with-mpi=/usr/local
>> CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpic++ FC=/usr/local/bin/mpif90
>> F77=/usr/local/bin/mpif77 --download-metis --download-hdf5 --download-netcdf
>> --enable-docs --with-doxygen=/Applications/Doxygen.app/Contents/Resources/
>>
>> The results are
>>
>> configure: WARNING:
>> *************************************************************************
>> * MOAB has been configured with parallel and HDF5 support
>> * but the configured HDF5 library does not support parallel IO.
>> * Some parallel IO capabilities will be disabled.
>> *************************************************************************
>>
>> After that, I inputted the command, make -j4, and then command make check.
>> Here are the results it shows
>>
>> /Applications/Xcode.app/Contents/Developer/usr/bin/make check-TESTS
>> PASS: elem_util_test
>> PASS: element_test
>> FAIL: datacoupler_test
>> FAIL: mbcoupler_test
>> FAIL: parcoupler_test
>> ============================================================================
>> Testsuite summary for MOAB 4.9.2pre
>> ============================================================================
>> # TOTAL: 5
>> # PASS: 2
>> # SKIP: 0
>> # XFAIL: 0
>> # FAIL: 3
>> # XPASS: 0
>> # ERROR: 0
>> ============================================================================
>> See tools/mbcoupler/test-suite.log
>> Please report to moab-dev at mcs.anl.gov
>> ============================================================================
>> make[4]: *** [test-suite.log] Error 1
>> make[3]: *** [check-TESTS] Error 2
>> make[2]: *** [check-am] Error 2
>> make[1]: *** [check-recursive] Error 1
>> make: *** [check-recursive] Error 1
>>
>> Then I was trying to run the mbcouple_test with command
>> dyn-160-39-10-173:mbcoupler jiewu$ mpiexec -np 2 mbcoupler_test -meshes
>> /Users/wujie/SourceCode/moab/MeshFiles/unittest/64bricks_1khex.h5m
>> /Users/wujie/SourceCode/moab/MeshFiles/unittest/64bricks_12ktet.h5m -itag
>> vertex_field -outfile dum.h5m
>> Now the results look like,
>>
>> [0]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]MOAB ERROR: MOAB not configured with parallel HDF5 support!
>> [0]MOAB ERROR: set_up_read() line 355 in src/io/ReadHDF5.cpp
>> [0]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]MOAB ERROR: NULL file handle.!
>> [0]MOAB ERROR: is_error() line 133 in src/io/ReadHDF5.hpp
>> [1]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [1]MOAB ERROR: MOAB not configured with parallel HDF5 support!
>> [1]MOAB ERROR: set_up_read() line 355 in src/io/ReadHDF5.cpp
>> [1]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [1]MOAB ERROR: NULL file handle.!
>> [1]MOAB ERROR: is_error() line 133 in src/io/ReadHDF5.hpp
>> [0]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]MOAB ERROR: Failed to load file after trying all possible readers!
>> [0]MOAB ERROR: serial_load_file() line 635 in src/Core.cpp
>> [0]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [0]MOAB ERROR: Failed in step PARALLEL READ PART!
>> [0]MOAB ERROR: load_file() line 553 in src/parallel/ReadParallel.cpp
>> [0]MOAB ERROR: load_file() line 252 in src/parallel/ReadParallel.cpp
>> [0]MOAB ERROR: load_file() line 515 in src/Core.cpp
>> [1]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [1]MOAB ERROR: Failed to load file after trying all possible readers!
>> [1]MOAB ERROR: serial_load_file() line 635 in src/Core.cpp
>> [1]MOAB ERROR: --------------------- Error Message
>> ------------------------------------
>> [1]MOAB ERROR: Failed in step PARALLEL READ PART!
>> [1]MOAB ERROR: load_file() line 553 in src/parallel/ReadParallel.cpp
>> [0]MOAB ERROR: main() line 172 in mbcoupler_test.cpp
>> [1]MOAB ERROR: load_file() line 252 in src/parallel/ReadParallel.cpp
>> [1]MOAB ERROR: load_file() line 515 in src/Core.cpp
>> [1]MOAB ERROR: main() line 172 in mbcoupler_test.cpp
>> --------------------------------------------------------------------------
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 16.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> --------------------------------------------------------------------------
>> [dyn-160-39-11-172.dyn.columbia.edu:26361] 1 more process has sent help
>> message help-mpi-api.txt / mpi-abort
>> [dyn-160-39-11-172.dyn.columbia.edu:26361] Set MCA parameter
>> "orte_base_help_aggregate" to 0 to see all help / error messages
>> The other excitable file in mbcoupler folder, like ./element_test now can
>> run successfully.
>>
>> Any direction for this was deeply appreciated!
>>
>> Best,
>> Jie
>>
>>
>> On May 13, 2016, at 11:54 AM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>
>> I also forgot to mention that you can be more explicit in the
>> specification of compilers during configuration, if you really want.
>> This would avoid headaches since the user specified wrappers will
>> directly be used. For example:
>>
>> ./configure --with-mpi=/usr/local CC=/usr/local/bin/mpicc
>> CXX=/usr/local/bin/mpic++ FC=/usr/local/bin/mpif90
>> F77=/usr/local/bin/mpif77 <OTHER_CONFIGURE_OPTIONS>
>>
>> Vijay
>>
>> On Fri, May 13, 2016 at 10:52 AM, Vijay S. Mahadevan <vijay.m at gmail.com>
>> wrote:
>>
>> Please use --with-mpi=/usr/local as the configure option. If you have
>> MPI pre-installed, either through PETSc or natively in your system,
>> always try to re-use that to maintain consistency. This will help
>> avoid mix-up of MPI implementations when you try to launch a parallel
>> job later.
>>
>> Let us know if the new configuration works.
>>
>> Vijay
>>
>> On Thu, May 12, 2016 at 6:32 PM, Jie Wu <jie.voo at gmail.com> wrote:
>>
>> Thank you very much for your reply. I search in my src/moab/MOABConfig.h
>> file, and I did not find the MOAB_HAVE_MPI. So I think the MOAB on my laptop
>> cannot run in parallel yet.
>>
>> I have this from my terminal.
>>
>> dyn-160-39-10-173:moab jiewu$ which mpic++
>> /usr/local/bin/mpic++
>>
>> But I cannot get anything by inputing which mpi. So I don’t know where the
>> mpi is in my laptop.
>>
>> dyn-160-39-10-173:moab jiewu$ which mpi
>>
>> I have petsc installed which has mpich, and linking that directory to the
>> MOAB configure option also did not work.
>>
>> Should I install mpi solely? I am afraid it might conflict with the one
>> installed in petsc.
>>
>> Is there any method that the mpi could be installed with MOAB automatically,
>> or maybe other proper manner? Thanks a lot!
>>
>> Best,
>> Jie
>>
>>
>> On May 12, 2016, at 6:11 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
>>
>> Can you send the config.log. Looks like MPI is not getting enabled
>> (possibly), even with --dowload-mpich. Or you can check
>> src/moab/MOABConfig.h in your build directory and grep for
>> MOAB_HAVE_MPI.
>>
>> Vijay
>>
>> On Thu, May 12, 2016 at 4:46 PM, Jie Wu <jie.voo at gmail.com> wrote:
>>
>> Hi Iulian,
>>
>> Thanks for your reply. I think my configure is with mpi. Here is my
>> configure command
>>
>> dyn-160-39-10-173:moab jiewu$ ./configure --download-metis
>> --download-hdf5 --download-netcdf --download-mpich --enable-docs
>> --with-doxygen=/Applications/Doxygen.app/Contents/Resources/
>>
>> Best,
>> Jie
>>
>> On May 12, 2016, at 5:43 PM, Grindeanu, Iulian R. <iulian at mcs.anl.gov>
>> wrote:
>>
>> Hi Jie,
>> Did you configure with mpi? What is your configure command?
>>
>> Iulian
>> ________________________________
>> From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf
>> of Jie Wu [jie.voo at gmail.com]
>> Sent: Thursday, May 12, 2016 4:23 PM
>> To: moab-dev at mcs.anl.gov
>> Subject: [MOAB-dev] Error message when compiling the mbcoupler_test.cpp
>>
>> Hi all,
>>
>> My name is Jie and I am part of computational mechanics group at civil
>> engineering dept. of Columbia university.
>>
>> I am working on large deformation problems which may lead mesh distortions
>> and a re-meshing become necessary.
>>
>> I would like to compile mbcoupler_test.cpp to learn how it transfer the
>> variables from old to the new mesh.
>>
>> Now I can successfully compile the codes in build/examples and they works
>> good! But I cannot compile the codes in folder build/tools/mbcoupler by
>> following the instructions in build/tools/readme.tools, which shows error
>> message like following.
>>
>> Do you have any idea for this problem? Thanks a lot!
>>
>> Best,
>> Jie
>>
>> DataCoupler.cpp:136:25: error: member access into incomplete
>> type 'moab::ParallelComm'
>> if (myPcomm && myPcomm->size() > 1) {
>> ^
>> ./DataCoupler.hpp:34:7: note: forward declaration of
>> 'moab::ParallelComm'
>> class ParallelComm;
>> ^
>> DataCoupler.cpp:161:12: error: member access into incomplete
>> type 'moab::ParallelComm'
>> myPcomm->proc_config().crystal_router()->gs_tran...
>> ^
>> ./DataCoupler.hpp:34:7: note: forward declaration of
>> 'moab::ParallelComm'
>> class ParallelComm;
>> ^
>> DataCoupler.cpp:187:12: error: member access into incomplete
>> type 'moab::ParallelComm'
>> myPcomm->proc_config().crystal_router()->gs_tran...
>> ^
>> ./DataCoupler.hpp:34:7: note: forward declaration of
>> 'moab::ParallelComm'
>> class ParallelComm;
>> ^
>> 3 errors generated.
>> make[2]: *** [DataCoupler.lo] Error 1
>> make[2]: *** Waiting for unfinished jobs....
>> Coupler.cpp:344:45: error: no member named 'gs_transfer' in
>> 'moab::gs_data::crystal_data'
>> (myPc->proc_config().crystal_router())->gs_trans...
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> Coupler.cpp:388:45: error: no member named 'gs_transfer' in
>> 'moab::gs_data::crystal_data'
>> (myPc->proc_config().crystal_router())->gs_trans...
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> Coupler.cpp:611:45: error: no member named 'gs_transfer' in
>> 'moab::gs_data::crystal_data'
>> (myPc->proc_config().crystal_router())->gs_trans...
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> Coupler.cpp:638:43: error: no member named 'gs_transfer' in
>> 'moab::gs_data::crystal_data'
>> myPc->proc_config().crystal_router()->gs_transfe...
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> 4 errors generated.
>> make[2]: *** [Coupler.lo] Error 1
>> make[1]: *** [all-recursive] Error 1
>> make: *** [all-recursive] Error 1
>>
>>
>>
>>
>>
>>
>>
>>
>>
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