[aspect-devel] Fwd: Installation on cluster CentOS

Marine Lasbleis marine.lasbleis at elsi.jp
Wed Sep 26 01:21:20 PDT 2018


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./
>>>
>>>
>>>
>>>     _______________________________________________
>>>     Aspect-devel mailing list
>>>     Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org>
>>>     http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>>>
>>>
>>>
>>> _______________________________________________
>>> Aspect-devel mailing list
>>> Aspect-devel at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>>
>>
>>
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>
>
> _______________________________________________
> Aspect-devel mailing list
> Aspect-devel at geodynamics.org
> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/aspect-devel/attachments/20180926/14ab2a1d/attachment-0001.html>
-------------- next part --------------
#!/usr/bin/env bash
declare -x ARCH="x86_64"
declare -x BAD="\\033[1;31m"
declare -x BLAS_DIR="/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64"
declare -x BOLD="\\033[1m"
declare -x BUILDCHAIN="cmake"
declare -x BUILDDIR="/home/LPGN/lasbleis-m/bin//tmp/build/deal.II-v9.0.0"
declare -x BUILD_PATH="/home/LPGN/lasbleis-m/bin//tmp/build"
declare -x CC="mpicc"
declare -x CLEAN_BUILD="false"
declare -x CMAKE_DIR="/trinity/shared/apps/ccipl/machine-dependant/nazare-dc/soft/cmake/3.10.2"
declare -x CMD_PACKAGES=""
declare -x COL="\\033[1;32m"
declare -x CONFIGURATION_PATH="/home/LPGN/lasbleis-m/bin//configuration"
declare -x CONFOPTS="                                                         -D CMAKE_BUILD_TYPE=DebugRelease -D DEAL_II_WITH_MPI:BOOL=ON -D DEAL_II_WITH_THREADS:BOOL=ON -D DEAL_II_FORCE_BUNDLED_THREADS:BOOL=OFF -D DEAL_II_COMPONENT_DOCUMENTATION:BOOL=OFF -D DEAL_II_WITH_LAPACK:BOOL=ON -D DEAL_II_WITH_UMFPACK:BOOL=ON -D DEAL_II_FORCE_BUNDLED_UMFPACK:BOOL=OFF -D DEAL_II_WITH_BOOST:BOOL=ON -D DEAL_II_FORCE_BUNDLED_BOOST:BOOL=OFF -D DEAL_II_WITH_ZLIB:BOOL=ON          -D DEAL_II_WITH_METIS:BOOL=ON         -D METIS_DIR=/home/LPGN/lasbleis-m/bin//parmetis-4.0.3         -D DEAL_II_WITH_P4EST:BOOL=ON         -D P4EST_DIR=/home/LPGN/lasbleis-m/bin//p4est-2.0         -D DEAL_II_WITH_HDF5:BOOL=ON         -D HDF5_DIR=/home/LPGN/lasbleis-m/bin//hdf5-1.10.1         -D DEAL_II_WITH_TRILINOS:BOOL=ON         -D TRILINOS_DIR=/home/LPGN/lasbleis-m/bin//trilinos-release-12-10-1         -D DEAL_II_WITH_PETSC:BOOL=ON         -D PETSC_DIR=/home/LPGN/lasbleis-m/bin//petsc-3.7.6         -D DEAL_II_WITH_SLEPC:BOOL=ON         -D SLEPC_DIR=/home/LPGN/lasbleis-m/bin//slepc-3.7.3         -D DEAL_II_WITH_OPENCASCADE:BOOL=ON"
declare -x CPATH="/trinity/shared/apps/cv-standard/petsc/3.10.0/include:/trinity/shared/apps/cv-standard/netcdf/4.4.1.1/include:/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/include:/trinity/shared/apps/cv-standard/valgrind/3.13.0/include:/trinity/shared/apps/cv-standard/hdf5/openmpi/gcc81/1.10.2/include:/trinity/shared/apps/cv-standard/gcc/8.1.0/include:/trinity/shared/apps/cv-standard/gcc/7.2.0/include"
declare -x CVS_RSH="ssh"
declare -x CXX="mpicxx"
declare -x C_INCLUDE_PATH="/trinity/shared/apps/cv-standard/petsc/3.10.0/include:/trinity/shared/apps/cv-standard/netcdf/4.4.1.1/include:/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/include:/trinity/shared/apps/cv-standard/valgrind/3.13.0/include:/trinity/shared/apps/cv-standard/hdf5/openmpi/gcc81/1.10.2/include:/trinity/shared/apps/cv-standard/gcc/8.1.0/include:/trinity/shared/apps/cv-standard/gcc/8.1.0/lib/gcc/x86_64-pc-linux-gnu/8.1.0/include:/trinity/shared/apps/cv-standard/gcc/7.2.0/include"
declare -x DATE_CMD="/usr/bin/date"
declare -x DEAL_CONFOPTS=""
declare -x DEAL_II_VERSION="v9.0.0"
declare -x DEVELOPER_MODE="OFF"
declare -x DISPLAY="localhost:25.0"
declare -x DOWNLOADERS=" curl wget"
declare -x DOWNLOAD_PATH="/home/LPGN/lasbleis-m/bin//tmp/src"
declare -x EDITOR="vim"
declare -x EXTRACTSTO="deal.II-v9.0.0"
declare -x FC="mpif90"
declare -x FF="mpif77"
declare -x GOOD="\\033[1;32m"
declare -x HDF5_DIR="/home/LPGN/lasbleis-m/bin//hdf5-1.10.1"
declare -x HISTCONTROL="ignoredups"
declare -x HISTSIZE="1000"
declare -x HOME="/home/LPGN/lasbleis-m"
declare -x HOSTNAME="jaws.cluster"
declare -x HTTPS_PROXY="http://proxy-upgrade.univ-nantes.prive:3128"
declare -x HTTP_PROXY="http://proxy-upgrade.univ-nantes.prive:3128"
declare -x INCLUDE="/trinity/shared/apps/cv-standard/petsc/3.10.0/include:/trinity/shared/apps/cv-standard/netcdf/4.4.1.1/include:/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/include:/trinity/shared/apps/cv-standard/valgrind/3.13.0/include:/trinity/shared/apps/cv-standard/hdf5/openmpi/gcc81/1.10.2/include:/trinity/shared/apps/cv-standard/gcc/8.1.0/include:/trinity/shared/apps/cv-standard/gcc/8.1.0/lib/gcc/x86_64-pc-linux-gnu/8.1.0/include:/trinity/shared/apps/cv-standard/gcc/7.2.0/include"
declare -x INFO="\\033[1;34m"
declare -x INSTALL_PATH="/home/LPGN/lasbleis-m/bin//deal.II-v9.0.0"
declare -x KDEDIRS="/usr"
declare -x LANG="en_US.UTF-8"
declare -x LAPACK_DIR="/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64"
declare -x LC_ADDRESS="ja_JP.UTF-8"
declare -x LC_IDENTIFICATION="ja_JP.UTF-8"
declare -x LC_MEASUREMENT="ja_JP.UTF-8"
declare -x LC_MONETARY="ja_JP.UTF-8"
declare -x LC_NAME="ja_JP.UTF-8"
declare -x LC_NUMERIC="ja_JP.UTF-8"
declare -x LC_PAPER="ja_JP.UTF-8"
declare -x LC_TELEPHONE="ja_JP.UTF-8"
declare -x LC_TIME="ja_JP.UTF-8"
declare -x LDSUFFIX="so"
declare -x LD_LIBRARY_PATH="/trinity/shared/apps/cv-standard/petsc/3.10.0/lib:/trinity/shared/apps/cv-standard/netcdf/4.4.1.1/lib:/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib:/trinity/shared/apps/cv-standard/valgrind/3.13.0/lib:/trinity/shared/apps/cv-standard/hdf5/openmpi/gcc81/1.10.2/lib:/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64:/trinity/shared/apps/cv-standard/gcc/8.1.0/lib64:/trinity/shared/apps/cv-standard/gcc/8.1.0/lib:/trinity/shared/apps/cv-standard/gcc/7.2.0/lib64:/trinity/shared/apps/cv-standard/gcc/7.2.0/lib:/usr/mpi/gcc/openmpi-1.10.2/lib64"
declare -x LESSOPEN="||/usr/bin/lesspipe.sh %s"
declare -x LIBRARY_PATH="/trinity/shared/apps/cv-standard/petsc/3.10.0/lib:/trinity/shared/apps/cv-standard/netcdf/4.4.1.1/lib:/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib:/trinity/shared/apps/cv-standard/valgrind/3.13.0/lib:/trinity/shared/apps/cv-standard/hdf5/openmpi/gcc81/1.10.2/lib:/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64:/trinity/shared/apps/cv-standard/gcc/8.1.0/lib64:/trinity/shared/apps/cv-standard/gcc/8.1.0/lib:/trinity/shared/apps/cv-standard/gcc/7.2.0/lib64:/trinity/shared/apps/cv-standard/gcc/7.2.0/lib"
declare -x LOADEDMODULES="gcc/7.2.0:cmake/3.10.2:gcc/8.1.0:lapack/3.8.0_gcc81:hdf5/openmpi/gcc81/1.10.2:valgrind/3.13.0:openmpi/psm2/gcc81/3.1.0:netcdf/4.4.1.1:petsc/3.10.0"
declare -x LOGNAME="lasbleis-m"
declare -x LS_COLORS="rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:"
declare -x MAIL="/var/spool/mail/lasbleis-m"
declare -x MAJORVER="1.10"
declare -x MANPATH="/trinity/shared/apps/cv-standard/valgrind/3.13.0/share/man:/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/man:/trinity/shared/apps/cv-standard/gcc/8.1.0/share/man:/trinity/shared/apps/ccipl/machine-dependant/nazare-dc/soft/cmake/3.10.2/man:/trinity/shared/apps/cv-standard/gcc/7.2.0/share/man:/usr/mpi/gcc/openmpi-1.10.2/share/man:"
declare -x METIS_DIR="/home/LPGN/lasbleis-m/bin//parmetis-4.0.3"
declare -x MINORVER="1"
declare -x MIRROR="https://www.ces.clemson.edu/dealii/mirror/"
declare -x MKL="OFF"
declare -x MODULEPATH="/usr/share/Modules/modulefiles:/trinity/shared/modulefiles/ccipl:/trinity/shared/modulefiles/compilateurs_interpreteurs:/trinity/shared/modulefiles/calcul_parallele:/trinity/shared/modulefiles/profilage:/trinity/shared/modulefiles/bibliotheques_scientifiques:/trinity/shared/modulefiles/outils:/trinity/shared/modulefiles/arch-dependant/local-arch"
declare -x MODULESHOME="/usr/share/Modules"
declare -x MPI_HOME="/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0"
declare -x MPI_ROOT="/usr/mpi/gcc/openmpi-1.10.2"
declare -x MPI_RUN="/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/bin/mpirun"
declare -x NAME="dealii.git"
declare -x NetCDF_ROOT="/trinity/shared/apps/cv-standard/netcdf/4.4.1.1"
declare -x OLDPWD="/home/LPGN/lasbleis-m/bin/tmp/build/deal.II-v9.0.0"
declare -x OPA_JAVA="/opt/pgi/linux86-64/2016/java/jre1.8.0_45"
declare -x OPENCASCADE_DIR="/home/LPGN/lasbleis-m/bin//oce-OCE-0.18.2"
declare -x ORIG_CONFIGURATION_PATH="/home/LPGN/lasbleis-m/bin//configuration"
declare -x ORIG_DIR="/home/LPGN/lasbleis-m/Dev/candi"
declare -x ORIG_INSTALL_PATH="/home/LPGN/lasbleis-m/bin/"
declare -x ORIG_PROCS="1"
declare -x P4EST_DIR="/home/LPGN/lasbleis-m/bin//p4est-2.0"
declare -x PACKAGE="dealii"
declare -x PACKAGES="load:dealii-prepare once:opencascade once:parmetis once:hdf5 once:p4est once:trilinos once:petsc once:slepc dealii"
declare -x PACKAGES_OFF=""
declare -x PACKING="git"
declare -x PARMETIS_DIR="/home/LPGN/lasbleis-m/bin//parmetis-4.0.3"
declare -x PATH="/trinity/shared/apps/cv-standard/netcdf/4.4.1.1/bin:/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/bin:/trinity/shared/apps/cv-standard/valgrind/3.13.0/bin:/trinity/shared/apps/cv-standard/hdf5/openmpi/gcc81/1.10.2/bin:/trinity/shared/apps/cv-standard/gcc/8.1.0/bin:/trinity/shared/apps/ccipl/machine-dependant/nazare-dc/soft/cmake/3.10.2/bin:/trinity/shared/apps/cv-standard/gcc/7.2.0/bin:/usr/mpi/gcc/openmpi-1.10.2/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin"
declare -x PETSC_DIR="/home/LPGN/lasbleis-m/bin//petsc-3.7.6"
declare -x PLATFORM="deal.II-toolchain/platforms/supported/centos7.platform"
declare -x PLATFORM_OSTYPE="linux"
declare -x PREFIX="/home/LPGN/lasbleis-m/bin/"
declare -x PREFIX_PATH="/home/LPGN/lasbleis-m/bin/"
declare -x PROCS="1"
declare -x PROJECT="deal.II-toolchain"
declare -x PWD="/home/LPGN/lasbleis-m/bin/tmp/build/deal.II-v9.0.0"
declare -x PYTHONVER="2.7"
declare -x PYTHON_INTERPRETER="python2"
declare -x QT_GRAPHICSSYSTEM_CHECKED="1"
declare -x QT_PLUGIN_PATH="/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins"
declare -x RE="^[0-9]+\$"
declare -x REPLY=""
declare -x SCALAPACK_DIR="/home/LPGN/lasbleis-m/bin//petsc-3.7.6"
declare -x SHELL="/bin/bash"
declare -x SHLVL="2"
declare -x SKIP="false"
declare -x SLEPC_DIR="/home/LPGN/lasbleis-m/bin//slepc-3.7.3"
declare -x SOURCE="https://github.com/dealii/"
declare -x SSH_ASKPASS="/usr/libexec/openssh/gnome-ssh-askpass"
declare -x SSH_CLIENT="172.16.13.38 44452 22"
declare -x SSH_CONNECTION="172.16.13.38 44452 193.52.106.252 22"
declare -x SSH_TTY="/dev/pts/18"
declare -x STABLE_BUILD="true"
declare -x STATUS="0"
declare -x TERM="xterm-256color"
declare -x TIC="1537797985"
declare -x TIC_GLOBAL="1537797981"
declare -x TIMINGS="\\ndealii-prepare: 0 s\\nopencascade: 0 s\\nparmetis: 0 s\\nhdf5: 0 s\\np4est: 0 s\\ntrilinos: 0 s\\npetsc: 0 s\\nslepc: 0 s"
declare -x TOC="0"
declare -x TRILINOS_DIR="/home/LPGN/lasbleis-m/bin//trilinos-release-12-10-1"
declare -x TRILINOS_MAJOR_VERSION="AUTO"
declare -x TRILINOS_PARMETIS_CONFOPTS="         -D HAVE_PARMETIS_VERSION_4_0_3=ON"
declare -x UNPACK_PATH="/home/LPGN/lasbleis-m/bin//tmp/unpack"
declare -x USER="lasbleis-m"
declare -x VALGRIND_DIR="/trinity/shared/apps/cv-standard/valgrind/3.13.0"
declare -x VALUE="/home/LPGN/lasbleis-m/bin//tmp/build/dealii.git"
declare -x VAR="BUILDDIR"
declare -x VERSION="v9.0.0"
declare -x WARN="\\033[1;35m"
declare -x XDG_RUNTIME_DIR="/run/user/286207"
declare -x XDG_SESSION_ID="9859"
declare -x _LMFILES_="/trinity/shared/modulefiles/compilateurs_interpreteurs/gcc/7.2.0:/trinity/shared/modulefiles/compilateurs_interpreteurs/cmake/3.10.2:/trinity/shared/modulefiles/compilateurs_interpreteurs/gcc/8.1.0:/trinity/shared/modulefiles/bibliotheques_scientifiques/lapack/3.8.0_gcc81:/trinity/shared/modulefiles/bibliotheques_scientifiques/hdf5/openmpi/gcc81/1.10.2:/trinity/shared/modulefiles/profilage/valgrind/3.13.0:/trinity/shared/modulefiles/calcul_parallele/openmpi/psm2/gcc81/3.1.0:/trinity/shared/modulefiles/bibliotheques_scientifiques/netcdf/4.4.1.1:/trinity/shared/modulefiles/bibliotheques_scientifiques/petsc/3.10.0"
declare -x cmd_file="candi_configure"
declare -x external_pkg="mumps"
declare -x http_proxy="http://proxy-upgrade.univ-nantes.prive:3128"
declare -x https_proxy="http://proxy-upgrade.univ-nantes.prive:3128"
declare -x param="-p"
set -e
cmake -D CMAKE_BUILD_TYPE=DebugRelease -D DEAL_II_WITH_MPI:BOOL=ON -D DEAL_II_WITH_THREADS:BOOL=ON -D DEAL_II_FORCE_BUNDLED_THREADS:BOOL=OFF -D DEAL_II_COMPONENT_DOCUMENTATION:BOOL=OFF -D DEAL_II_WITH_LAPACK:BOOL=ON -D DEAL_II_WITH_UMFPACK:BOOL=ON -D DEAL_II_FORCE_BUNDLED_UMFPACK:BOOL=OFF -D DEAL_II_WITH_BOOST:BOOL=ON -D DEAL_II_FORCE_BUNDLED_BOOST:BOOL=OFF -D DEAL_II_WITH_ZLIB:BOOL=ON -D DEAL_II_WITH_METIS:BOOL=ON -D METIS_DIR=/home/LPGN/lasbleis-m/bin//parmetis-4.0.3 -D DEAL_II_WITH_P4EST:BOOL=ON -D P4EST_DIR=/home/LPGN/lasbleis-m/bin//p4est-2.0 -D DEAL_II_WITH_HDF5:BOOL=ON -D HDF5_DIR=/home/LPGN/lasbleis-m/bin//hdf5-1.10.1 -D DEAL_II_WITH_TRILINOS:BOOL=ON -D TRILINOS_DIR=/home/LPGN/lasbleis-m/bin//trilinos-release-12-10-1 -D DEAL_II_WITH_PETSC:BOOL=ON -D PETSC_DIR=/home/LPGN/lasbleis-m/bin//petsc-3.7.6 -D DEAL_II_WITH_SLEPC:BOOL=ON -D SLEPC_DIR=/home/LPGN/lasbleis-m/bin//slepc-3.7.3 -D DEAL_II_WITH_OPENCASCADE:BOOL=ON -DCMAKE_INSTALL_PREFIX=/home/LPGN/lasbleis-m/bin//deal.II-v9.0.0 /home/LPGN/lasbleis-m/bin//tmp/unpack/deal.II-v9.0.0


More information about the Aspect-devel mailing list