TPL Build Error- Trilinos
Dannielle Pratt
Coon, Ethan
Please send the full output of bootstrap, not just what is in your image, but the whole thing.
Then also send the files referenced at the end of the error message, e.g. these two files:
Ethan
--
-------------------------------------------------------------------------
Ethan Coon
Senior Research Scientist
Oak Ridge National Laboratory
https://www.ornl.gov/staff-profile/ethan-t-coon
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Dannielle Pratt
Running Amanzi Boostrap with:
AMANZI_SRC_DIR: /home/depratt/ATS-master/amanzi
AMANZI_BUILD_DIR: /home/depratt/ATS-master/amanzi-build-master-Release
AMANZI_INSTALL_DIR: /home/depratt/ATS-master/amanzi-install-master-Release
AMANZI_TPLS_BUILD_DIR: /home/depratt/ATS-master/amanzi_tpls-build-master-Release
AMANZI_TPLS_DIR: /home/depratt/ATS-master/amanzi_tpls-install-master-Release
with build type: Release
List of INPUT parameters
========================
opt: --opt
opt: --with-mpi=/usr
opt: --enable-shared
opt: --enable-clm
opt: --disable-structured
opt: --enable-unstructured
opt: --enable-mesh_mstk
opt: --disable-mesh_moab
opt: --enable-hypre
opt: --enable-silo
opt: --disable-petsc
opt: --disable-amanzi_physics
opt: --enable-ats_physics
opt: --disable-ats_dev
opt: --disable-geochemistry
opt: --amanzi-install-prefix=/home/depratt/ATS-master/amanzi-install-master-Release
opt: --amanzi-build-dir=/home/depratt/ATS-master/amanzi-build-master-Release
opt: --tpl-install-prefix=/home/depratt/ATS-master/amanzi_tpls-install-master-Release
opt: --tpl-build-dir=/home/depratt/ATS-master/amanzi_tpls-build-master-Release
opt: --tpl-download-dir=/home/depratt/ATS-master/amanzi-tpls/Downloads
opt: --tools-download-dir=/home/depratt/ATS-master/amanzi-tpls/Downloads
opt: --tools-build-dir=/home/depratt/ATS-master/build
opt: --tools-install-prefix=/home/depratt/ATS-master/install
opt: --with-cmake=/usr/bin/cmake
opt: --with-ctest=/usr/bin/ctest
opt: --branch_ats=master
opt: --parallel=6
List of computed and ADJUSTED parameters
========================================
Compilers and Flags:
build_c_compiler =
build_cxx_compiler =
build_fort_compiler =
build_c_flags =
build_cxx_flags =
build_fort_flags =
build_link_flags =
mpi_root_dir = /usr
Build configuration:
build_type = Release
dbc = 1
build_stage_1 = 0
build_stage_2 = 0
parallel = 6
shared = 1
static_libs_prefer = 1
static_executables = 0
trilinos_build_type = Release
tpls_build_type = Release
tpl_config_file =
blas_dir =
lapack_dir =
blas_vendor =
debug_find_blas = 0
amanzi_arch =
Amanzi Components:
structured = 0
spacedim = 2
unstructured = 1
amanzi_physics = 0
ats_physics = 1
clm = 1
geochemistry = 0
Amanzi TPLs:
alquimia = 0
crunchtope = 0
mesh_mstk = 1
mesh_moab = 0
netcdf4 = 1
hypre = 1
superlu = 1
petsc = 0
epetra = 1
tpetra = 0
cuda = 0
openmp = 0
pflotran = 0
silo = 1
Spack = 0
xsdk = 0
external_downloads = 1
Tools and Tests:
ccse_tools = 0
cmake_binary = /usr/bin/cmake
ctest_binary = /usr/bin/ctest
curl_binary = /usr/bin/curl
git_binary = /usr/bin/git
Spack_binary =
reg_tests = 0
test_suite = 0
tools_mpi = openmpi
python_exec =
Directories:
prefix =
amanzi_install_prefix = /home/depratt/ATS-master/amanzi-install-master-Release
amanzi_build_dir = /home/depratt/ATS-master/amanzi-build-master-Release
tpl_install_prefix = /home/depratt/ATS-master/amanzi_tpls-install-master-Release
tpl_build_dir = /home/depratt/ATS-master/amanzi_tpls-build-master-Release
tpl_download_dir = /home/depratt/ATS-master/amanzi-tpls/Downloads
tools_install_prefix = /home/depratt/ATS-master/install
tools_build_dir = /home/depratt/ATS-master/build
tools_download_dir = /home/depratt/ATS-master/amanzi-tpls/Downloads
[Sun Jul 31 08:33:41 EDT 2022] Amanzi installation: /home/depratt/ATS-master/amanzi-install-master-Release
[Sun Jul 31 08:33:41 EDT 2022] TPL installation: /home/depratt/ATS-master/amanzi_tpls-install-master-Release
[Sun Jul 31 08:33:41 EDT 2022] Build directories ready
[Sun Jul 31 08:33:41 EDT 2022] Searching for a C compiler
[Sun Jul 31 08:33:41 EDT 2022] Searching for /usr/bin/mpicc
[Sun Jul 31 08:33:41 EDT 2022] Build with C compiler: /usr/bin/mpicc
[Sun Jul 31 08:33:41 EDT 2022] Searching for a C++ compiler
[Sun Jul 31 08:33:41 EDT 2022] Searching for /usr/bin/mpicxx
[Sun Jul 31 08:33:41 EDT 2022] Build with C++ compiler: /usr/bin/mpicxx
[Sun Jul 31 08:33:41 EDT 2022] Searching for a Fortran compiler
[Sun Jul 31 08:33:41 EDT 2022] Searching for /usr/bin/mpif90
[Sun Jul 31 08:33:41 EDT 2022] Build with Fortran compiler: /usr/bin/mpif90
[Sun Jul 31 08:33:41 EDT 2022] Compiler Check complete
[Sun Jul 31 08:33:41 EDT 2022] Git binary: /usr/bin/git
[Sun Jul 31 08:33:41 EDT 2022] CURL binary: /usr/bin/curl
[Sun Jul 31 08:33:41 EDT 2022] Found CMake version: 3.16.3
CMake suite maintained and supported by Kitware (kitware.com/cmake).
[Sun Jul 31 08:33:41 EDT 2022] CMake binary: /usr/bin/cmake
[Sun Jul 31 08:33:41 EDT 2022] CTest binary: /usr/bin/ctest
[Sun Jul 31 08:33:41 EDT 2022] Tools check complete
[Sun Jul 31 08:33:41 EDT 2022] Build with C compiler: /usr/bin/mpicc
[Sun Jul 31 08:33:41 EDT 2022] Build with C++ compiler: /usr/bin/mpicxx
[Sun Jul 31 08:33:41 EDT 2022] Build with Fortran compiler: /usr/bin/mpif90
[Sun Jul 31 08:33:41 EDT 2022] Compiler Check complete
--
------------------------------------------------
--
-- CMake: Configuring Amanzi TPLs build/install.
--
-- ---------------------------------------------
-- Compilers ...
-- CMAKE_C_COMPILER = /usr/bin/mpicc
-- CMAKE_CXX_COMPILER = /usr/bin/mpicxx
-- CMAKE_Fortran_COMPILER) = /usr/bin/mpif90
-- Identifying /usr/bin/mpicc (GNU) version
-- Identifying /usr/bin/mpicc (GNU) version -- 9.4.0
-- Identifying /usr/bin/mpicxx (GNU) version
-- Identifying /usr/bin/mpicxx (GNU) version -- 9.4.0
-- Identifying /usr/bin/mpif90 (GNU) version
-- Identifying /usr/bin/mpif90 (GNU) version -- 9.4.0
-- Checking whether C compiler can compile MPI program
-- Checking whether C compiler can compile MPI program - yes
-- Checking whether C++ compiler can compile MPI program
-- Checking whether C++ compiler can compile MPI program - yes
-- Checking whether Fortran compiler can compile MPI program
-- Performing Test MPI_Fortran
-- Performing Test MPI_Fortran - Success
-- Checking whether Fortran compiler can compile MPI program - yes
-- Setting build type -- Release
-- Download TPL files in /home/depratt/ATS-master/amanzi-tpls/Downloads
-- Checking external downloads (https://raw.githubusercontent.com/amanzi/amanzi-tpls/master/src/MD5SUMS)
-- Checking external downloads (https://raw.githubusercontent.com/amanzi/amanzi-tpls/master/src/MD5SUMS) -- works
-- Install TPLs in /home/depratt/ATS-master/amanzi_tpls-install-master-Release
-- Pre-FindMPI-DEBUGGING: MPIEXEC =
-- FindMPI-DEBUGGING: Languages --------------------------
-- FindMPI-DEBUGGING: MPI_C_FOUND = TRUE
-- FindMPI-DEBUGGING: MPI_CXX_FOUND = TRUE
-- FindMPI-DEBUGGING: MPI_Fortran_FOUND = TRUE
-- FindMPI-DEBUGGING: Compilers --------------------------
-- FindMPI-DEBUGGING: MPI_Fortran_HAVE_F90_MODULE = TRUE
-- FindMPI-DEBUGGING: MPI_MPICXX_FOUND = TRUE
-- FindMPI-DEBUGGING: ----------
-- FindMPI-DEBUGGING: MPI_C_COMPILER = /usr/bin/mpicc
-- FindMPI-DEBUGGING: MPI_CXX_COMPILER = /usr/bin/mpicxx
-- FindMPI-DEBUGGING: MPI_Fortran_COMPILER = /usr/bin/mpif90
-- FindMPI-DEBUGGING: Runtime Environment --------------------
-- FindMPI-DEBUGGING: MPIEXEC_EXECUTABLE = /usr/bin/mpiexec
-- FindMPI-DEBUGGING: MPIEXEC = /usr/bin/mpiexec - is defined for compatability
-- Found MPI: MPIEXEC=/usr/bin/mpiexec
-- Detected 8 processors and will set maximum to 16
-- Amanzi Arch:
-- >>> Amanzi: Starting Search for BLAS
-- >>> Amanzi: BLAS_LIBRARIES = /usr/lib/x86_64-linux-gnu/libopenblas.so
-- >>> Amanzi: Starting Search for LAPACK
-- >>> Amanzi: LAPACK_LIBRARIES = /usr/lib/x86_64-linux-gnu/libopenblas.so;/usr/lib/x86_64-linux-gnu/libopenblas.so
-- Common compile flags for build type Release
-- common C flags -fPIC -O3 -DNDEBUG -fPIC
-- common C++ flags -fPIC -O3 -DNDEBUG -fPIC
-- common Fortran flags -fPIC -O3 -DNDEBUG -O3 -fPIC
-- common Linker flags
-- common arguments -DCMAKE_INSTALL_RPATH:PATH=/home/depratt/ATS-master/amanzi_tpls-install-master-Release/lib;-DCMAKE_INSTALL_NAME_DIR:PATH=/home/depratt/ATS-master/amanzi_tpls-install-master-Release/lib;-DCMAKE_PREFIX_PATH:PATH=/home/depratt/ATS-master/amanzi_tpls-install-master-Release
-- BOOST: CMAKE_CXX_COMPILER = /usr/bin/mpicxx
-- BOOST: Boost_bjam_args (ini): cxxflags=\ -fPIC\ -O3\ -DNDEBUG\ -fPIC
-- BOOST: CMAKE_SYSTEM = Linux-5.10.102.1-microsoft-standard-WSL2
-- BOOST: CMAKE_SYSTEM_VERSION = 5.10.102.1-microsoft-standard-WSL2
-- BOOST: compiler_id_lc = gnu
-- BOOST: Boost_bjam_args (fin): cxxflags=\ -fPIC\ -O3\ -DNDEBUG\ -fPIC
-- BOOST: Boost_toolset = gcc
-- HDF5: HDF5_HL_LIBRARY = /home/depratt/ATS-master/amanzi_tpls-install-master-Release/lib/libhdf5_hl.so
-- HDF5_C_LIBRARY = /home/depratt/ATS-master/amanzi_tpls-install-master-Release/lib/libhdf5.so
-- ZLIB_LIBRARIES = /home/depratt/ATS-master/amanzi_tpls-install-master-Release/lib/libz.so
-- HYPRE git repository = https://github.com/hypre-space/hypre
-- Applying SEACAS patches
-- Trilinos Packages Required: Teuchos;Epetra;EpetraExt;Basker;Amesos;Amesos2;Ifpack;NOX;Belos;ML;AztecOO;Zoltan
-- Trilinos BLAS libraries: /usr/lib/x86_64-linux-gnu/libopenblas.so
-- Trilinos LAPACK libraries: /usr/lib/x86_64-linux-gnu/libopenblas.so;/usr/lib/x86_64-linux-gnu/libopenblas.so
-- Enabling support for Hypre in Trilinos
-- Trilinos_CXX_COMPILER /usr/bin/mpicxx
-- Trilinos_CMAKE_CXX_FLAGS -fPIC
-- Applying trilinos patches
-- Trilinos git repository = https://github.com/trilinos/Trilinos
-- Configuring done
-- Generating done
-- Build files have been written to: /home/depratt/ATS-master/amanzi_tpls-build-master-Release
[Sun Jul 31 08:33:46 EDT 2022] TPL configure complete
[ 5%] Built target nanoflann
[ 10%] Built target zlib
[ 15%] Built target hdf5
[ 20%] Built target silo
[ 25%] Built target metis
[ 30%] Built target netcdf
[ 35%] Built target seacas
[ 40%] Built target superlu
[ 45%] Built target parmetis
[ 50%] Built target superlu_dist
[ 55%] Built target boost
[ 60%] Built target hypre
[ 65%] Performing configure step for 'trilinos'
CMake Error at /home/depratt/ATS-master/amanzi_tpls-build-master-Release/trilinos/trilinos-timestamps/trilinos-configure-Release.cmake:49 (message):
Command failed: 1
'/usr/bin/cmake' '-GUnix Makefiles' '-C/home/depratt/ATS-master/amanzi_tpls-build-master-Release/trilinos/tmp/trilinos-cache-Release.cmake' '/home/depratt/ATS-master/amanzi_tpls-build-master-Release/trilinos/trilinos-13-0-afc4e525-source'
See also
/home/depratt/ATS-master/amanzi_tpls-build-master-Release/trilinos/trilinos-timestamps/trilinos-configure-*.log
make[2]: *** [CMakeFiles/trilinos.dir/build.make:114: trilinos/trilinos-timestamps/trilinos-configure] Error 1
make[1]: *** [CMakeFiles/Makefile2:1989: CMakeFiles/trilinos.dir/all] Error 2
make: *** [Makefile:130: all] Error 2
Amanzi Bootstrap ERROR: Failed to build TPLs
Joe Beisman
Coon, Ethan
Yes, I hope Joe is right. This error is becoming more common as more operating systems update to python3 and drop python2 support. There is work going in to fix this problem (and it may already be on master), and we’ll backport those changes onto the release versions soon. But for now I think Joe’s fix will work.
-- Checking external downloads (hxxps://raw.githubusercontent.com/amanzi/amanzi-tpls/master/src/MD5SUMS)
-- Checking external downloads (hxxps://raw.githubusercontent.com/amanzi/amanzi-tpls/master/src/MD5SUMS) -- works
-- HYPRE git repository = hxxps://github.com/hypre-space/hypre
-- Applying SEACAS patches
-- Trilinos Packages Required: Teuchos;Epetra;EpetraExt;Basker;Amesos;Amesos2;Ifpack;NOX;Belos;ML;AztecOO;Zoltan
-- Trilinos BLAS libraries: /usr/lib/x86_64-linux-gnu/libopenblas.so
-- Trilinos LAPACK libraries: /usr/lib/x86_64-linux-gnu/libopenblas.so;/usr/lib/x86_64-linux-gnu/libopenblas.so
-- Enabling support for Hypre in Trilinos
-- Trilinos_CXX_COMPILER /usr/bin/mpicxx
-- Trilinos_CMAKE_CXX_FLAGS -fPIC
-- Applying trilinos patches
-- Trilinos git repository = hxxps://github.com/trilinos/Trilinos
Ethan
--
hxxps://www.ornl.gov/staff-profile/ethan-t-coon
-------------------------------------------------------------------------
From: ats-...@googlegroups.com <ats-...@googlegroups.com> on behalf of Dannielle Pratt <dep...@udel.edu>
Date: Friday, July 29, 2022 at 4:55 PM
To: Amanzi-ATS Users <ats-...@googlegroups.com>
Subject: [EXTERNAL] TPL Build Error- TrilinosHello,
I'm trying to build ATS using Ubuntu and I'm getting stuck at 65% when trying to build TPLs. I downloaded the recent version of Trilinos and that did not fix the issue. Any suggestions?
Thanks!
Dannielle Pratt
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Dannielle Pratt
Dannielle