[aspect-devel] Fwd: Installation on cluster CentOS

Wed Sep 26 05:43:48 PDT 2018

Marine,

can you post your tmp/build/deal.II-v9.0.0/CMakeFiles/CMakeError.log
please? The errors at the end of the file should help us identify what
is going wrong.

On Wed, Sep 26, 2018 at 2:21 AM Marine Lasbleis <marine.lasbleis at elsi.jp> wrote:
>
> Hi John,
>
> For candi: I used the exact candi.cfg, with only add for BLAS and LAPACK directories
>
> BLAS_DIR=/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64
> LAPACK_DIR=/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64
>
> And the only additional info I gave candi was the install directory (so ./candi.sh -p __path__)
>
> I join the file candi_configure from the deal_ii folder
>
> At first, I tried to remove the installation of petsc and a couple of things, but I wasn't sure how to ask deal_ii not to use them, so I ended up installing them anyway. It's good to know only p4est and trilinos are required! I will see how to do that. And yes, it will definitely speedup the installation :-)
>
>
> I'll update you later if I manage to do something while removing the installation of petsc and others. And let me know if anyone has an idea to help :-)
>
> Best,
> Marine
>
> On 2018年09月25日 22:30, John Naliboff wrote:
>
> Hi Marine,
>
> A couple questions to help with debugging the installation issue:
>
>   1. Can you send over the candi.cfg file that you used and any additional specified options used when executing candi.sh?
>
>   2. In the specified candi install directory the following folder should be present: tmp/build/deal.II-v9.0.0. Within that directory should be a file called candi_configure.log, which contains detailed information about the configuration process (including errors). If present, can you send that file over as well?
>
> As a side note, I often configure candi to only install p4est and Trilinos with deal.II. Unless you are using PETSc instead of Trilinos, there is no need to include it, slepsc and parmetis. Likely completely unrelated to the issue you encountered, but not building these packages will help speedup the installation.
>
> Cheers,
> John
>
> On 09/25/2018 01:17 PM, Marine Lasbleis wrote:
>
> Yes, candi! I also found it quite easy... But I really don't understand the error (especially as there is none in the log file)
>
>
> On 2018年09月25日 20:31, Max Rudolph wrote:
>
> Are you using candi to install trilinos, p4est, and deal.ii? I found that this is much easier on our cluster than installing the packages manually.
>
> On Tue, Sep 25, 2018 at 1:29 AM Marine Lasbleis <marine.lasbleis at elsi.jp> wrote:
>>
>> Sorry, I sent the first message from the wrong email address. It would be better to use this one!
>>
>>
>>
>> -------- Forwarded Message --------
>> Subject: Installation on cluster CentOS
>> Date: Tue, 25 Sep 2018 10:17:18 +0200
>> From: Marine Lasbleis <marine.lasbleis at ens-lyon.fr>
>> To: aspect-devel at geodynamics.org
>>
>>
>> Hi all,
>>
>> I just moved to a new lab, and I am trying to install ASPECT on the cluster here. So far, it works on my new computer + the test computer, so I'm quite happy... But the installation on the cluster is more complicated.
>>
>> I am stucked with the installation of deal_ii.
>>
>> The cluster is on CentOS, and uses modules. So far, I asked the staff to provide most of the required librairies, and I think we got almost all of them.
>>
>> I am using candi to do the installation, and simply following the instructions.
>>
>> I am using gcc 8.1.0, and we have lapack compiled with gcc8.1.0. cmake is 3.9.6. I have tried to use hdf5 and petsc from the modules, but the system did not recognize the HDF5_DIR and PETSC_DIR, so I compiled them through candi.
>>
>> I got all installed (parmetis, p4est, slepc, hdf5, trilinos), but the compilation of deal_ii end up with an error (highlighted below). And I looked at the log file /home/LPGN/lasbleis-m/bin/tmp/build/deal.II-v9.0.0/CMakeFiles/CMakeOutput.log, but there is absolutely no error in the log file... So I'm a little bit puzzled.
>>
>> Any idea that could help me?
>>
>> (attached file: log file. And below, last lines I got while running candi.sh)
>>
>> Best,
>>
>> Marine
>>
>>
>> [more things here] ........
>>
>> -- Include /home/LPGN/lasbleis-m/bin/tmp/unpack/deal.II-v9.0.0/cmake/setup_cpack.cmake
>> --
>> -- Include /home/LPGN/lasbleis-m/bin/tmp/unpack/deal.II-v9.0.0/cmake/setup_custom_targets.cmake
>> --
>> -- Include /home/LPGN/lasbleis-m/bin/tmp/unpack/deal.II-v9.0.0/cmake/setup_finalize.cmake
>> CMake Error at cmake/setup_finalize.cmake:95 (MESSAGE):
>>
>>
>>     Configuration error: Cannot compile a test program with the final set of
>>     compiler and linker flags:
>>       CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Woverloaded-virtual -Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix -fopenmp-simd -std=c++17 -Wno-parentheses -Wno-unused-local-typedefs -Og -ggdb -Wa,--compress-debug-sections
>>       LD flags  (DEBUG): -Wl,--as-needed -rdynamic -fuse-ld=gold -ggdb
>>       LIBRARIES (DEBUG): /usr/lib64/libz.so;rt;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libmuelu-adapters.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libmuelu-interface.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libmuelu.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteko.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosbelos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosaztecoo.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosamesos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosml.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosifpack.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libifpack2-adapters.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libifpack2.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libanasazitpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libModeLaplace.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libanasaziepetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libanasazi.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libamesos2.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libbelostpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libbelosepetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libbelos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libml.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libifpack.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libzoltan2.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libpamgen_extras.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libpamgen.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libamesos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libgaleri-xpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libgaleri-epetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libaztecoo.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libisorropia.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libxpetra-sup.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libxpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libthyratpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libthyraepetraext.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libthyraepetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libthyracore.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libepetraext.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetraext.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetrainout.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libkokkostsqr.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetrakernels.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetraclassiclinalg.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetraclassicnodeapi.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetraclassic.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtriutils.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libzoltan.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libepetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libsacado.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/librtop.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchoskokkoscomm.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchoskokkoscompat.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchosremainder.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchosnumerics.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchoscomm.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchosparameterlist.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchoscore.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libkokkosalgorithms.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libkokkoscontainers.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libkokkoscore.so;/home/LPGN/lasbleis-m/bin/hdf5-1.10.1/lib/libhdf5_hl.so;/home/LPGN/lasbleis-m/bin/hdf5-1.10.1/lib/libhdf5.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKBO.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKBool.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKBRep.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKernel.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKFeat.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKFillet.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKG2d.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKG3d.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKGeomAlgo.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKGeomBase.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKHLR.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKIGES.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKMath.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKMesh.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKOffset.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKPrim.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKShHealing.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTEP.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTEPAttr.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTEPBase.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTEP209.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTL.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKTopAlgo.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKXSBase.so;mpi_usempif08;mpi_usempi_ignore_tkr;mpi_mpifh;mpi;c;gcc_s;gcc;/home/LPGN/lasbleis-m/bin/slepc-3.7.3/lib/libslepc.so;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libpetsc.so;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libcmumps.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libdmumps.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libsmumps.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libzmumps.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libmumps_common.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libpord.a;/home/LPGN/lasbleis-m/bin/parmetis-4.0.3/lib/libparmetis.so;/home/LPGN/lasbleis-m/bin/parmetis-4.0.3/lib/libmetis.so;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libHYPRE.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libscalapack.a;/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64/liblapack.a;/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64/libblas.a;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi_usempif08.so;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi_usempi_ignore_tkr.so;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi_mpifh.so;gfortran;quadmath;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi_cxx.so;m;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi.so;pthread;dl;/home/LPGN/lasbleis-m/bin/p4est-2.0/DEBUG/lib/libp4est.so;/home/LPGN/lasbleis-m/bin/p4est-2.0/DEBUG/lib/libsc.so
>>
>>
>>
>>
>> Call Stack (most recent call first):
>>   cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
>>   CMakeLists.txt:132 (VERBOSE_INCLUDE)
>>
>>
>> -- Configuring incomplete, errors occurred!
>> See also "/home/LPGN/lasbleis-m/bin/tmp/build/deal.II-v9.0.0/CMakeFiles/CMakeOutput.log".
>> Failure with exit status: 1
>> Exit message: There was a problem configuring dealii v9.0.0.
>>
>>
>>
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-- 
Timo Heister
http://www.math.clemson.edu/~heister/