Another installation issue

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Ylva Sjöberg

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Mar 30, 2022, 7:08:32 AM3/30/22
to ats-...@googlegroups.com

Dear ATS users,

 

I’m trying to install ATS on a mac (Monterey 12.3) but don’t manage to run the bootstrapping. I have previously installed ATS on the same computer, but have to re-install after IT-service changed systems on all computers. I have installed CMake and also MPI (through anaconda), and added both these directories to my path.).

The bootstrap fails with the message below, which I guess suggests that I’m either missing some compiler or paths, but I can’t figure out what I need to do. Does anyone have a clue?

 

Cheers,

Ylva

 

Running Amanzi Boostrap with:

  AMANZI_SRC_DIR: /Users/mbp317/ats/repos/amanzi

  AMANZI_BUILD_DIR: /Users/mbp317/ats/amanzi-build-master-Release

  AMANZI_INSTALL_DIR: /Users/mbp317/ats/amanzi-install-master-Release

  AMANZI_TPLS_BUILD_DIR: /Users/mbp317/ats/amanzi_tpls-build-master-Release

  AMANZI_TPLS_DIR: /Users/mbp317/ats/amanzi_tpls-install-master-Release

 with build type: Release

 

 

List of INPUT parameters

========================

opt:  --opt

opt:  --with-mpi=/Users/mbp317/opt/anaconda3/bin/mpicc

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=/Users/mbp317/ats/amanzi-install-master-Release

opt:  --amanzi-build-dir=/Users/mbp317/ats/amanzi-build-master-Release

opt:  --tpl-install-prefix=/Users/mbp317/ats/amanzi_tpls-install-master-Release

opt:  --tpl-build-dir=/Users/mbp317/ats/amanzi_tpls-build-master-Release

opt:  --tpl-download-dir=/Users/mbp317/ats/amanzi-tpls/Downloads

opt:  --tools-download-dir=/Users/mbp317/ats/amanzi-tpls/Downloads

opt:  --tools-build-dir=/Users/mbp317/ats/build

opt:  --tools-install-prefix=/Users/mbp317/ats/install

opt:  --with-cmake=/Applications/CMake.app/Contents/bin/cmake

opt:  --with-ctest=/Applications/CMake.app/Contents/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        = /Users/mbp317/opt/anaconda3/bin/mpicc

 

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

    kokkos       = 0 (Cuda=0, OpenMP=0)

    pflotran     = 0

    silo         = 1

    Spack        = 0

    xsdk         = 0

    external_downloads = 1

 

Tools and Tests:

    ccse_tools   = 0

    cmake_binary = /Applications/CMake.app/Contents/bin/cmake

    ctest_binary = /Applications/CMake.app/Contents/bin/ctest

    curl_binary  = /Users/mbp317/opt/anaconda3/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 = /Users/mbp317/ats/amanzi-install-master-Release

    amanzi_build_dir      = /Users/mbp317/ats/amanzi-build-master-Release

    tpl_install_prefix    = /Users/mbp317/ats/amanzi_tpls-install-master-Release

    tpl_build_dir         = /Users/mbp317/ats/amanzi_tpls-build-master-Release

    tpl_download_dir      = /Users/mbp317/ats/amanzi-tpls/Downloads

    tools_install_prefix  = /Users/mbp317/ats/install

    tools_build_dir       = /Users/mbp317/ats/build

    tools_download_dir    = /Users/mbp317/ats/amanzi-tpls/Downloads

    

 

[Wed Mar 30 11:51:38 CEST 2022] Amanzi installation: /Users/mbp317/ats/amanzi-install-master-Release

[Wed Mar 30 11:51:38 CEST 2022] TPL installation: /Users/mbp317/ats/amanzi_tpls-install-master-Release

[Wed Mar 30 11:51:38 CEST 2022] Build directories ready

[Wed Mar 30 11:51:38 CEST 2022] Searching for a C compiler

[Wed Mar 30 11:51:38 CEST 2022] Searching for /Users/mbp317/opt/anaconda3/bin/mpicc/bin/mpicc

[Wed Mar 30 11:51:38 CEST 2022] Searching for gcc

[Wed Mar 30 11:51:38 CEST 2022] Build with C compiler: /usr/bin/gcc

[Wed Mar 30 11:51:38 CEST 2022] Searching for a C++ compiler

[Wed Mar 30 11:51:38 CEST 2022] Searching for /Users/mbp317/opt/anaconda3/bin/mpicc/bin/mpicxx

[Wed Mar 30 11:51:38 CEST 2022] Searching for /Users/mbp317/opt/anaconda3/bin/mpicc/bin/mpiCC

[Wed Mar 30 11:51:38 CEST 2022] Searching for g++

[Wed Mar 30 11:51:38 CEST 2022] Build with C++ compiler: /usr/bin/g++

[Wed Mar 30 11:51:38 CEST 2022] Searching for a Fortran compiler

[Wed Mar 30 11:51:38 CEST 2022] Searching for /Users/mbp317/opt/anaconda3/bin/mpicc/bin/mpif90

[Wed Mar 30 11:51:38 CEST 2022] Searching for gfortran

[Wed Mar 30 11:51:38 CEST 2022] Build with Fortran compiler: /usr/local/bin/gfortran

[Wed Mar 30 11:51:38 CEST 2022] Compiler Check complete

[Wed Mar 30 11:51:38 CEST 2022] Git binary: /usr/bin/git

[Wed Mar 30 11:51:38 CEST 2022] CURL binary: /Users/mbp317/opt/anaconda3/bin/curl

[Wed Mar 30 11:51:38 CEST 2022] Found CMake version:  3.22.3

 

CMake suite maintained and supported by Kitware (kitware.com/cmake).

[Wed Mar 30 11:51:38 CEST 2022] CMake binary: /Applications/CMake.app/Contents/bin/cmake

[Wed Mar 30 11:51:38 CEST 2022] CTest binary: /Applications/CMake.app/Contents/bin/ctest

[Wed Mar 30 11:51:38 CEST 2022] Tools check complete

[Wed Mar 30 11:51:38 CEST 2022] Build with C compiler: /usr/bin/gcc

[Wed Mar 30 11:51:38 CEST 2022] Build with C++ compiler: /usr/bin/g++

[Wed Mar 30 11:51:38 CEST 2022] Build with Fortran compiler: /usr/local/bin/gfortran

[Wed Mar 30 11:51:38 CEST 2022] Compiler Check complete

-- 

------------------------------------------------

-- 

-- CMake: Configuring Amanzi TPLs build/install.

--

-- ---------------------------------------------

-- Identifying /usr/bin/gcc (AppleClang) version

-- Identifying /usr/bin/gcc (AppleClang) version -- Apple clang version 13.1.6 (clang-1316.0.21.2)

Target: x86_64-apple-darwin21.4.0

Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

-- Identifying /usr/bin/g++ (AppleClang) version

-- Identifying /usr/bin/g++ (AppleClang) version -- Apple clang version 13.1.6 (clang-1316.0.21.2)

Target: x86_64-apple-darwin21.4.0

Thread model: posix

InstalledDir: /Library/Developer/CommandLineTools/usr/bin

-- Identifying /usr/local/bin/gfortran (GNU) version

-- Identifying /usr/local/bin/gfortran (GNU) version -- 11.2.0

-- Checking whether C compiler can compile MPI program

-- Checking whether C compiler can compile MPI program - no

-- Checking whether C++ compiler can compile MPI program

-- Checking whether C++ compiler can compile MPI program - no

-- Checking whether Fortran compiler can compile MPI program

-- Performing Test MPI_Fortran

-- Performing Test MPI_Fortran - Failed

-- Checking whether Fortran compiler can compile MPI program - no

CMake Error at CMakeLists.txt:140 (message):

  Missing a compiler type for MPI applications -- exiting.

 

 

-- Configuring incomplete, errors occurred!

See also "/Users/mbp317/ats/amanzi_tpls-build-master-Release/CMakeFiles/CMakeOutput.log".

See also "/Users/mbp317/ats/amanzi_tpls-build-master-Release/CMakeFiles/CMakeError.log".

Amanzi Bootstrap ERROR: Failed to configure TPL build

 

Ethan Coon

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Mar 30, 2022, 7:25:58 AM3/30/22
to Ylva Sjöberg, ats-...@googlegroups.com
Your —with-mpi option should point to the directory containing the installation, not the executable itself.  Remove the bin/mpicc from that option and it should be good to go.

Ethan

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-------------------------------------------------------------------
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Ylva Sjöberg

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Mar 30, 2022, 7:33:43 AM3/30/22
to Ethan Coon, ats-...@googlegroups.com

Tack Ethan,

I seem to have more issues after fixing that:

 

 

Running Amanzi Boostrap with:

  AMANZI_SRC_DIR: /Users/mbp317/ats/repos/amanzi

  AMANZI_BUILD_DIR: /Users/mbp317/ats/amanzi-build-master-Release

  AMANZI_INSTALL_DIR: /Users/mbp317/ats/amanzi-install-master-Release

  AMANZI_TPLS_BUILD_DIR: /Users/mbp317/ats/amanzi_tpls-build-master-Release

  AMANZI_TPLS_DIR: /Users/mbp317/ats/amanzi_tpls-install-master-Release

 with build type: Release

 

 

List of INPUT parameters

========================

opt:  --opt

opt:  --with-mpi=/Users/mbp317/opt/anaconda3/

opt:  --enable-shared

Build configuration:

[Wed Mar 30 13:29:14 CEST 2022] Amanzi installation: /Users/mbp317/ats/amanzi-install-master-Release

[Wed Mar 30 13:29:14 CEST 2022] TPL installation: /Users/mbp317/ats/amanzi_tpls-install-master-Release

[Wed Mar 30 13:29:14 CEST 2022] Build directories ready

[Wed Mar 30 13:29:14 CEST 2022] Searching for a C compiler

[Wed Mar 30 13:29:14 CEST 2022] Searching for /Users/mbp317/opt/anaconda3//bin/mpicc

[Wed Mar 30 13:29:14 CEST 2022] Build with C compiler: /Users/mbp317/opt/anaconda3//bin/mpicc

[Wed Mar 30 13:29:14 CEST 2022] Searching for a C++ compiler

[Wed Mar 30 13:29:14 CEST 2022] Searching for /Users/mbp317/opt/anaconda3//bin/mpicxx

[Wed Mar 30 13:29:14 CEST 2022] Build with C++ compiler: /Users/mbp317/opt/anaconda3//bin/mpicxx

[Wed Mar 30 13:29:14 CEST 2022] Searching for a Fortran compiler

[Wed Mar 30 13:29:14 CEST 2022] Searching for /Users/mbp317/opt/anaconda3//bin/mpif90

[Wed Mar 30 13:29:14 CEST 2022] Build with Fortran compiler: /Users/mbp317/opt/anaconda3//bin/mpif90

[Wed Mar 30 13:29:14 CEST 2022] Compiler Check complete

[Wed Mar 30 13:29:14 CEST 2022] Git binary: /usr/bin/git

[Wed Mar 30 13:29:14 CEST 2022] CURL binary: /Users/mbp317/opt/anaconda3/bin/curl

[Wed Mar 30 13:29:14 CEST 2022] Found CMake version:  3.22.3

 

CMake suite maintained and supported by Kitware (kitware.com/cmake).

[Wed Mar 30 13:29:14 CEST 2022] CMake binary: /Applications/CMake.app/Contents/bin/cmake

[Wed Mar 30 13:29:14 CEST 2022] CTest binary: /Applications/CMake.app/Contents/bin/ctest

[Wed Mar 30 13:29:14 CEST 2022] Tools check complete

[Wed Mar 30 13:29:14 CEST 2022] Build with C compiler: /Users/mbp317/opt/anaconda3//bin/mpicc

[Wed Mar 30 13:29:14 CEST 2022] Build with C++ compiler: /Users/mbp317/opt/anaconda3//bin/mpicxx

[Wed Mar 30 13:29:14 CEST 2022] Build with Fortran compiler: /Users/mbp317/opt/anaconda3//bin/mpif90

[Wed Mar 30 13:29:14 CEST 2022] Compiler Check complete

-- 

------------------------------------------------

-- 

-- CMake: Configuring Amanzi TPLs build/install.

--

-- ---------------------------------------------

-- The C compiler identification is unknown

-- The CXX compiler identification is unknown

-- The Fortran compiler identification is unknown

/Users/mbp317/opt/anaconda3/bin/mpif90: line 392: x86_64-apple-darwin13.4.0-gfortran: command not found

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - failed

-- Check for working C compiler: /Users/mbp317/opt/anaconda3/bin/mpicc

-- Check for working C compiler: /Users/mbp317/opt/anaconda3/bin/mpicc - broken

CMake Error at /Applications/CMake.app/Contents/share/cmake-3.22/Modules/CMakeTestCCompiler.cmake:69 (message):

  The C compiler

 

    "/Users/mbp317/opt/anaconda3/bin/mpicc"

 

  is not able to compile a simple test program.

 

  It fails with the following output:

 

    Change Dir: /Users/mbp317/ats/amanzi_tpls-build-master-Release/CMakeFiles/CMakeTmp

    

    Run Build Command(s):/usr/bin/make -f Makefile cmTC_de728/fast && /Library/Developer/CommandLineTools/usr/bin/make  -f CMakeFiles/cmTC_de728.dir/build.make CMakeFiles/cmTC_de728.dir/build

    Building C object CMakeFiles/cmTC_de728.dir/testCCompiler.c.o

    /Users/mbp317/opt/anaconda3/bin/mpicc    -o CMakeFiles/cmTC_de728.dir/testCCompiler.c.o -c /Users/mbp317/ats/amanzi_tpls-build-master-Release/CMakeFiles/CMakeTmp/testCCompiler.c

    /Users/mbp317/opt/anaconda3/bin/mpicc: line 301: x86_64-apple-darwin13.4.0-clang: command not found

    make[1]: *** [CMakeFiles/cmTC_de728.dir/testCCompiler.c.o] Error 127

    make: *** [cmTC_de728/fast] Error 2

    

    

 

  

 

  CMake will not be able to correctly generate this project.

Call Stack (most recent call first):

  CMakeLists.txt:26 (project)

 

 

-- Configuring incomplete, errors occurred!

See also "/Users/mbp317/ats/amanzi_tpls-build-master-Release/CMakeFiles/CMakeOutput.log".

See also "/Users/mbp317/ats/amanzi_tpls-build-master-Release/CMakeFiles/CMakeError.log".

Amanzi Bootstrap ERROR: Failed to configure TPL build

(base) mbp317@SCI1002888 ats % 

Ethan Coon

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Mar 30, 2022, 7:57:51 AM3/30/22
to Ylva Sjöberg, ats-...@googlegroups.com
Hmm, that really does look like your compiler isn’t working.  Have you installed Xcode or command line tools?  Maybe check that those are working with the IT changes?  Then try running your mpicc on a small “hello world” problem?

You may have to reinstall Xcode/commandline_tools and/or anaconda.  Something isn’t working there, but the problem isn’t bootstrap.


Ethan

Lipnikov, Konstantin

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Mar 30, 2022, 12:08:25 PM3/30/22
to Ethan Coon, Ylva Sjöberg, ats-...@googlegroups.com

/Users/mbp317/opt/anaconda3/bin/mpicc: line 301: x86_64-apple-darwin13.4.0-clang: command not found


Sounds like the local configuration issue of MPI. It does not see the installation of clang. What is output of "mpicc --show" ? 


Konstantin

From: ats-...@googlegroups.com <ats-...@googlegroups.com> on behalf of Ethan Coon <etc...@gmail.com>
Sent: Wednesday, March 30, 2022 5:57:39 AM
To: Ylva Sjöberg
Cc: ats-...@googlegroups.com
Subject: [EXTERNAL] Re: Another installation issue
 

Ylva Sjöberg

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Mar 30, 2022, 12:11:02 PM3/30/22
to Lipnikov, Konstantin, Ethan Coon, ats-...@googlegroups.com

mpicc --show

clang -I/usr/local/Cellar/open-mpi/4.1.2/include -L/usr/local/Cellar/open-mpi/4.1.2/lib -L/usr/local/opt/libevent/lib -lmpi

 

Ylva

 

From: "Lipnikov, Konstantin" <lipn...@lanl.gov>


Date: Wednesday, 30 March 2022 at 18.08
To: Ethan Coon <etc...@gmail.com>, Ylva Sjöberg <y...@ign.ku.dk>
Cc: "ats-...@googlegroups.com" <ats-...@googlegroups.com>

Subject: Re: [EXTERNAL] Re: Another installation issue

 

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