Hi Timo,
I tried another compilation and installation of deal.ii without PETSC,
P4EST and LAPACK(by setting the corresponding
DEAL_II_WITH_PACKAGENAME=OFF). After successfully completing installation I
tried the examples step-1 and step-2 with *cmake . ; make ; make run*, and
both of them ran successfully. However, switching back to the build
directory and running *make test* resulted in failure of all quick tests.
Seems like there might then be some issue with the LAPACK, P4EST or PETSC
installation I am using. I will try the installation process with different
subsets of these packages and try to pinpoint the issue. What do you think?
Best,
Aaditya
On Saturday, October 24, 2020 at 5:43:50 PM UTC-4 Aaditya Lakshmanan wrote:
> Hi Timo,
> Thank you for your suggestion. I repeated the installation process and
> this time I didn't run the quick_tests. Rather I changed to examples/step-1
> directory in the deal.ii installation and executed the following :
>
> *cmake . *
> *make *
>
> which exited with the following error :
>
> *Scanning dependencies of target step-1*
> *[ 50%] Building CXX object CMakeFiles/step-1.dir/step-1.cc.o*
> *[100%] Linking CXX executable step-1*
> */usr/bin/ld:
> /global/project/projectdirs/m2360/packagesCPFE/dealii_install/lib/libdeal_II.g.so
>
> <http://libdeal_II.g.so>: file not recognized: file truncated*
> *make[2]: *** [CMakeFiles/step-1.dir/build.make:95: step-1] Error 1*
> *make[1]: *** [CMakeFiles/Makefile2:137: CMakeFiles/step-1.dir/all] Error
> 2*
> *make: *** [Makefile:84: all] Error 2*
>
>
> I am not sure why this is the case since installation completed without
> issues. I have attached the files *detailed.log* and *make_output.txt*(output
> from *make -j8 install* on the KNL compute node).
>
> Best,
> Aaditya
>
>
> On Saturday, October 24, 2020 at 10:38:49 AM UTC-4 Timo Heister wrote:
>
>> Running the tests seems to have triggered a rebuild of deal.iII. Can you
>> try running some of the tutorial steps instead?
>>
>> On Fri, Oct 23, 2020, 17:05 Aaditya Lakshmanan <aadit...@gmail.com>
>> wrote:
>>
>>> Hi Wolfgang,
>>> I tried compiling, installing and running the deal.ii tests
>>> interactively on a KNL compute node. Both compilation and installation were
>>> seemingly successful but all the tests failed. I have attached the output
>>> from make test in the file *test_output.txt*. An example error looks
>>> like the following :
>>> 2/11 Test #1: step.debug .......................***Failed 265.99 sec
>>> gmake[6]: *** write jobserver: Invalid argument. Stop.
>>> gmake[6]: *** Waiting for unfinished jobs....
>>> gmake[6]: *** write jobserver: Invalid argument. Stop.
>>> gmake[5]: *** [CMakeFiles/Makefile2:10829:
>>> tests/quick_tests/CMakeFiles/step.debug.run.dir/rule] Error 2
>>> gmake[4]: *** [Makefile:3700: step.debug.run] Error 2
>>> Test step.debug: BUILD
>>> =============================== OUTPUT BEGIN
>>> ===============================
>>> step.debug: BUILD failed. Output:
>>> [ 0%] Built target obj_sundials_inst
>>> [ 21%] Built target obj_physics_elasticity_inst
>>> [ 30%] Built target obj_dofs_inst
>>> [ 25%] Built target obj_matrix_free_inst
>>> [ 23%] Built target obj_amd_global_debug
>>> [ 34%] Built target obj_umfpack_DI_TRIPLET_MAP_NOX_debug
>>> [ 30%] Built target obj_differentiation_ad_inst
>>> [ 34%] Built target obj_multigrid_inst
>>> [ 59%] Built target obj_physics_inst
>>> [ 59%] Built target obj_non_matching_inst
>>> [ 59%] Built target obj_gmsh_inst
>>> [ 34%] Built target obj_distributed_inst
>>> [ 34%] Built target kill-step.debug-OK
>>> [ 34%] Built target obj_muparser_debug
>>> [ 34%] Built target obj_umfpack_DL_SOLVE_debug
>>> [ 59%] Built target obj_numerics_inst
>>> [ 59%] Built target obj_boost_system_debug
>>> [ 59%] Built target obj_umfpack_DL_STORE_debug
>>> [ 59%] Built target obj_umfpack_DL_TRIPLET_MAP_NOX_debug
>>> [ 59%] Built target obj_umfpack_DL_TRIPLET_MAP_X_debug
>>> [ 59%] Built target obj_umfpack_DI_TSOLVE_debug
>>> [ 78%] Built target obj_base_inst
>>> [ 78%] Built target obj_grid_inst
>>> [ 59%] Built target obj_umfpack_DI_SOLVE_debug
>>> [ 34%] Built target obj_amd_int_debug
>>> [ 59%] Built target obj_algorithms_inst
>>> [ 59%] Built target obj_meshworker_inst
>>> [ 59%] Built target obj_hp_inst
>>> [ 78%] Built target obj_particle_inst
>>> [ 59%] Built target obj_differentiation_sd_inst
>>> [ 59%] Built target obj_opencascade_inst
>>> [ 78%] Built target obj_lac_inst
>>> [ 59%] Built target obj_amd_long_debug
>>> [ 59%] Built target obj_umfpack_DL_TSOLVE_debug
>>> [ 59%] Built target obj_umfpack_DI_STORE_debug
>>> [ 59%] Built target obj_umfpack_DL_TRIPLET_NOMAP_X_debug
>>> [ 59%] Built target obj_umfpack_DI_TRIPLET_MAP_X_debug
>>> [ 59%] Built target obj_umfpack_DI_TRIPLET_NOMAP_X_debug
>>> [ 59%] Built target obj_umfpack_GENERIC_debug
>>> [ 78%] Built target obj_umfpack_DL_ASSEMBLE_debug
>>> [ 59%] Built target obj_umfpack_DI_ASSEMBLE_debug
>>> [ 84%] Built target obj_fe_inst
>>>
>>>
>>> step.debug: ****** BUILD failed *******
>>>
>>> =============================== OUTPUT END
>>> ===============================
>>> Expected stage PASSED - aborting
>>> CMake Error at
>>> /global/project/projectdirs/m2360/packagesCPFE/dealii/cmake/scripts/run_test.cmake:140
>>>
>>> (MESSAGE):
>>> *** abort
>>>
>>>
>>> Best,
>>> Aaditya
>>>
>>> On Friday, October 23, 2020 at 2:00:00 AM UTC-4 Aaditya Lakshmanan wrote:
>>>
>>>> Hi Wolfgang,
>>>> Thanks for your suggestion. I just checked that the Cori login nodes
>>>> are Haswell processors while the compute nodes on which I wish to run
>>>> simulations eventually are KNL processors(certain modules are also with
>>>> that intention). I will use idev to access the compute nodes interactively
>>>> and try the build, installation and testing phases again.
>>>>
>>>> Best,
>>>> Aaditya
>>>>
>>>> On Thursday, October 22, 2020 at 11:29:38 PM UTC-4 Wolfgang Bangerth
>>>> wrote:
>>>>
>>>>>
>>>>> Aaditya,
>>>>> is NERSC Cori a machine where the front-end node runs a different
>>>>> processor/system than the compute nodes? If so, you're building a
>>>>> library for
>>>>> the compute nodes, and the tests are also built for the compute nodes.
>>>>> But
>>>>> you're trying to run the test executables on the front-end node --
>>>>> which might
>>>>> help explain the error you see.
>>>>>
>>>>> Best
>>>>> W.
>>>>>
>>>>>
>>>>> On 10/22/20 7:52 PM, Aaditya Lakshmanan wrote:
>>>>> > Hi Everyone,
>>>>> > I have been trying to install deal.ii on the NERSC Cori System
>>>>> and after a
>>>>> > seemingly successful cmake and make install, make test yields
>>>>> failure for all
>>>>> > the tests setup. I briefly detail the procedure I followed and the
>>>>> outputs and
>>>>> > errors obtained.
>>>>> >
>>>>> > As a pre-requisite I installed p4est using the setup script(with
>>>>> some
>>>>> > modifications) and petsc manually with the configure.py script and
>>>>> appropriate
>>>>> > settings. The following modules were loaded :
>>>>> >
>>>>> > Currently Loaded Modulefiles:
>>>>> > 1) modules/3.2.11.4 5) craype-network-aries
>>>>> 9)
>>>>> > PrgEnv-intel/6.0.5 13) valgrind/3.15.0
>>>>> > 2) altd/2.0 6) craype/2.6.2
>>>>> 10)
>>>>> > craype-mic-knl 14) zlib/1.2.11
>>>>> > 3) darshan/3.1.7 7) pmi/5.0.14
>>>>> 11)
>>>>> > cray-mpich/7.7.14 15) cmake/3.14.4
>>>>> > 4) intel/19.0.3.199 8) atp/2.1.3
>>>>> 12)
>>>>> > craype-hugepages2M 16) cray-hdf5-parallel/1.10.5.2
>>>>> >
>>>>> >
>>>>> > After setting the environment variables P4EST_DIR, PETSC_DIR and
>>>>> PETSC_ARCH, I
>>>>> > compiled dealii-9.1.1 as follows :
>>>>> >
>>>>> > *cmake -DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment
>>>>> -DCMAKE_C_COMPILER=cc
>>>>> > -DCMAKE_CXX_COMPILER=CC -DCMAKE_Fortran_COMPILER=ftn
>>>>> -DDEAL_II_WITH_MPI=ON
>>>>> > -DDEAL_II_WITH_PETSC=ON -DDEAL_II_WITH_P4EST=ON
>>>>> -DDEAL_II_WITH_LAPACK=ON
>>>>> > -DCMAKE_INSTALL_PREFIX=$CPFE_PACKAGES/dealii_install ../dealii
>>>>> > *
>>>>> >
>>>>> > which ran successfully. I have attached the file *detailed.log*.
>>>>> Then
>>>>> > installing via
>>>>> >
>>>>> > *make -j8 install *
>>>>> >
>>>>> > ran without issues. I have attached the output from the above
>>>>> command in the
>>>>> > file *make_output.txt*. Then running the tests as
>>>>> >
>>>>> > *make -j4 test *
>>>>> > *
>>>>> > *
>>>>> > reports failure for all the tests. I have attached the entire output
>>>>> from the
>>>>> > above command in the file test_output.txt and an example error below
>>>>> :
>>>>> >
>>>>> > 2/11 Test #2: step.release .....................***Failed 0.69
>>>>> sec
>>>>> > gmake[6]: *** read jobs pipe: Bad file descriptor. Stop.
>>>>> > gmake[6]: *** Waiting for unfinished jobs....
>>>>> > gmake[5]: *** [CMakeFiles/Makefile2:10861:
>>>>> > tests/quick_tests/CMakeFiles/step.release.run.dir/rule] Error 2
>>>>> > gmake[4]: *** [Makefile:3713: step.release.run] Error 2
>>>>> > Test step.release: BUILD
>>>>> > =============================== OUTPUT BEGIN
>>>>> ===============================
>>>>> > step.release: BUILD failed. Output:
>>>>> > [ 1%] Built target obj_boost_iostreams_release
>>>>> >
>>>>> >
>>>>> > step.release: ****** BUILD failed *******
>>>>> >
>>>>> > =============================== OUTPUT END
>>>>> ===============================
>>>>> > Expected stage PASSED - aborting
>>>>> > CMake Error at
>>>>> >
>>>>> /global/project/projectdirs/m2360/packagesCPFE/dealii/cmake/scripts/run_test.cmake:140
>>>>>
>>>>>
>>>>> > (MESSAGE):
>>>>> > *** abort
>>>>> >
>>>>> > I am unable to understand what the issue might. Any insight on this
>>>>> will be
>>>>> > appreciated. Thank you.
>>>>> >
>>>>> > Best,
>>>>> > Aaditya
>>>>> >
>>>>> > --
>>>>> > The deal.II project is located at http://www.dealii.org/
>>>>> > <
>>>>> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.dealii.org%2F&data=04%7C01%7CWolfgang.Bangerth%40colostate.edu%7C67682f15035d469a23df08d876f649b8%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637390147477029066%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=snjl%2Fkw1PYq4xwYh0SGB03l6XvsgS8%2FfWr5sdHO4aI0%3D&reserved=0>
>>>>>
>>>>>
>>>>> > For mailing list/forum options, see
>>>>> > https://groups.google.com/d/forum/dealii?hl=en
>>>>> > <
>>>>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgroups.google.com%2Fd%2Fforum%2Fdealii%3Fhl%3Den&data=04%7C01%7CWolfgang.Bangerth%40colostate.edu%7C67682f15035d469a23df08d876f649b8%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637390147477039065%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=QD7qw6euanb6yVAY0KMhGpNc0%2B0APSrikkenzbG4wGU%3D&reserved=0>
>>>>>
>>>>>
>>>>> > ---
>>>>> > You received this message because you are subscribed to the Google
>>>>> Groups
>>>>> > "deal.II User Group" group.
>>>>> > To unsubscribe from this group and stop receiving emails from it,
>>>>> send an
>>>>> > email to dealii+un...@googlegroups.com
>>>>> > <mailto:dealii+un...@googlegroups.com>.
>>>>> > To view this discussion on the web visit
>>>>> >
>>>>> https://groups.google.com/d/msgid/dealii/ec2fe941-4ba0-498f-8a9f-009b48022977n%40googlegroups.com
>>>>>
>>>>> > <
>>>>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgroups.google.com%2Fd%2Fmsgid%2Fdealii%2Fec2fe941-4ba0-498f-8a9f-009b48022977n%2540googlegroups.com%3Futm_medium%3Demail%26utm_source%3Dfooter&data=04%7C01%7CWolfgang.Bangerth%40colostate.edu%7C67682f15035d469a23df08d876f649b8%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637390147477039065%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bEIaI%2BRLikBbmu8bt%2BL3QzA%2B%2Fs4nJLVFa%2BIfKLlVblE%3D&reserved=0>.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>> Wolfgang Bangerth email: bang...@colostate.edu
>>>>> www: http://www.math.colostate.edu/~bangerth/
>>>>>
>>>>> --
>>> The deal.II project is located at http://www.dealii.org/
>>> For mailing list/forum options, see
>>> https://groups.google.com/d/forum/dealii?hl=en
>>> ---
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>>> Groups "deal.II User Group" group.
>>>
>> To unsubscribe from this group and stop receiving emails from it, send an
>>> email to dealii+un...@googlegroups.com.
>>> To view this discussion on the web visit
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>>>
>>> <https://groups.google.com/d/msgid/dealii/b8878835-5d8a-4c18-92d8-dce463e0a4d8n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>>
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
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