[aspect-devel] Fwd: Installation on cluster CentOS
John Naliboff
jbnaliboff at ucdavis.edu
Wed Sep 26 10:58:31 PDT 2018
Hi Marine,
You can exclude certain packages by commenting out the associated lines
in candi.cfg . The following wiki page shows how to do this in addition
to other relevant steps:
https://github.com/geodynamics/aspect/wiki/Compiling-and-Running-ASPECT-on-TACC-Stampede2
When executing the candi installer, are you specifying the install
directory? For example, on the link above the following command is used
to specify the number of processors available for the installation and
the install directory:
./candi.sh -j 48 --prefix="$WORK"/stampede2/software/candi/install/
If the install directory is not specified, candi places it in some
default location. Perhaps this is part of the issue?
My suggestion is to delete the old install directory and then specify a
directory where you would like the packages to be installed.
tmp/build/deal.II-v9.0.0/candi_configure.log will be located in the
install directory. Unfortunately hard to debug what is going wrong
without more info.
Cheers,
John
On 09/26/2018 01:21 AM, Marine Lasbleis 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 <mailto: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>
>>>> <mailto:marine.lasbleis at ens-lyon.fr>
>>>> To: aspect-devel at geodynamics.org
>>>> <mailto: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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>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>>>>
>>>>
>>>>
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>>>
>>>
>>>
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>>
>>
>>
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