Cmake does not find PETSC

[gtheler]

Hi @lcpt . I use PETSc all the time and I have PETSC_DIR and PETSC_ARCH:

gtheler@tom:~/codigos/3ros/build/xc/build$ echo $PETSC_DIR
/home/gtheler/libs/petsc-3.15.0
gtheler@tom:~/codigos/3ros/build/xc/build$ echo $PETSC_ARCH
arch-linux2-c-debug
gtheler@tom:~/codigos/3ros/build/xc/build$ 

But CMake cannot find PETSc:

gtheler@tom:~/codigos/3ros/build/xc/build$ cmake ../src/
CMake version is greater than 2.8.4
-- xc project dir: /home/gtheler/codigos/3ros/build/xc/
-- xc include dir: /home/gtheler/codigos/3ros/build/xc/src/
-- xc lib dir: /home/gtheler/codigos/3ros/build/xc/lib
-- ************* find packages begins ****************
-- Found GTK2_GTK: /usr/lib/x86_64-linux-gnu/libgtk-x11-2.0.so  
-- Using header-only CGAL
-- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so
-- Found MPFR: /usr/include (Required is at least version "1.0.0") 
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.48")  
-- Boost include dirs: /usr/include
-- Boost libraries:    
-- Using gcc version 4 or later. Adding -frounding-math
-- GNUGTS include dir: /usr/include
-- GNUGTS libraries: /usr/lib/x86_64-linux-gnu/libgts.so
-- Found CImg: 
CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message):
  The package name passed to `find_package_handle_standard_args` (PkgConfig)
  does not match the name of the calling package (GLIB2).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  /usr/share/cmake-3.18/Modules/FindPkgConfig.cmake:59 (find_package_handle_standard_args)
  /home/gtheler/codigos/3ros/build/xc/CMake/FindGLIB2.cmake:29 (INCLUDE)
  /home/gtheler/codigos/3ros/build/xc/CMake/find_packages.cmake:10 (find_package)
  CMakeLists.txt:75 (INCLUDE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2") 
-- Checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found Python: /usr/bin/python3.9 (found version "3.9.2") found components: Interpreter Development Development.Module Development.Embed 
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.62")  
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: python 
-- Found PythonInterp: /usr/bin/python (found version "3.9.2") 
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.9.so (found version "3.9.2") 
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system regex filesystem thread math_c99 math_c99f math_c99l math_tr1 math_tr1f math_tr1l 
-- PYTHON_LIBRARIES = /usr/lib/x86_64-linux-gnu/libpython3.9.so
-- PYTHON_EXECUTABLE = /usr/bin/python
-- PYTHON_INCLUDE_DIRS = /usr/include/python3.9
-- Found F2C: /usr/lib/x86_64-linux-gnu/libf2c.so  
-- Looking for execinfo
-- Looking for execinfo headers - found
-- Found plotter.h: /usr/include
-- Found plotter lib: /usr/lib/x86_64-linux-gnu/libplotter.so
-- Found Gnuplot: /usr/bin/gnuplot (found version "5.4.1") 
-- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so
-- SQLite3 library found.
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") 
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") 
-- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/libmpi_usempif08.so (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- Found Arpack: /usr/lib/x86_64-linux-gnu/libarpack.so
-- Found Arpack++: /usr/include/arpack++
-- Found Arpack++ lib: /usr/lib/x86_64-linux-gnu/libarpack++.so
CMake Error at /home/gtheler/codigos/3ros/build/xc/CMake/FindPetsc.cmake:32 (MESSAGE):
  petsc.h not found.
Call Stack (most recent call first):
  /home/gtheler/codigos/3ros/build/xc/CMake/find_packages.cmake:47 (find_package)
  CMakeLists.txt:75 (INCLUDE)


-- Configuring incomplete, errors occurred!
See also "/home/gtheler/codigos/3ros/build/xc/build/CMakeFiles/CMakeOutput.log".
See also "/home/gtheler/codigos/3ros/build/xc/build/CMakeFiles/CMakeError.log".
gtheler@tom:~/codigos/3ros/build/xc/build$

This is Debian\ 11. Any ideas?

[lcpt]

Hi, @gtheler!

The file that tells CMake where to search for PETSC is here. It doesn't use $PETSC_DIR nor $PETSC_ARCH :(. Maybe you can help me to figure out how to use those variables inside the script (I always use the PETSc libraries shipped with Ubuntu, so I have no experience using a "custom folder" for PETSc). Where are your "petsc.h" and "petscconf.h" files?

Sorry for the inconvenience.

[gtheler]

Honestly I am not a CMake fan, I'm more an autotools guy. This is how I look for PETSc in FeenoX: https://github.com/seamplex/feenox/blob/main/configure.ac#L144

My petsc.h is in $PETSC_DIR/include and petscconf.h is in $PETSC_DIR/$PETSC_ARCH/include. Note that this is how one can have different PETSc configurations (one with debugging symbols, one for release, one with 64-bit indices, etc).
So far, I fallback to setting PETSC_DIR=/usr/lib/petsc and PETSC_ARCH= that seems to work in Debian/Ubuntu for the apt-installed packages (but not for Fedora, see seamplex/feenox#4 and seamplex/feenox#5).

[lcpt]

Hi, @gtheler. I've modified FindPetsc.cmake to take into account the environment variables if they exist. Could you test if the modification works on your machine?

Regarding Fedora, when I have a bit more time to spend, I'll try to create a virtual machine with Fedora installed to test the installation process.

Thanks!

[gtheler]

Yes, it does work. Thanks.

I now face something similar regarding Gmsh: I don't like to have system-wide headers and libraries because I keep changing versions from stable to develop. Can I provide the location of the Gmsh headers and libraries as a CMake variable?

[lcpt]

Inspecting the related file FindGMSH.cmake it seems you can set the `GMSH_ROOT_DIR' similarly as you did with PETSC_DIR. Could you try that?

[gtheler]

Oh, I missed that. But still does not work. This is what I have

gtheler@tom:~/gmsh-4.8.4-Linux64-sdk$ pwd
/home/gtheler/gmsh-4.8.4-Linux64-sdk
gtheler@tom:~/gmsh-4.8.4-Linux64-sdk$ ls
bin  include  lib  README.txt  share
gtheler@tom:~/gmsh-4.8.4-Linux64-sdk$ ls include/
gmshc.h  gmsh.h  gmsh.h_cwrap
gtheler@tom:~/gmsh-4.8.4-Linux64-sdk$ ls lib/
gmsh.jl  gmsh.py  libgmsh.so  libgmsh.so.4.8  libgmsh.so.4.8.4
gtheler@tom:~/gmsh-4.8.4-Linux64-sdk$ 

Now,

gtheler@tom:~/codigos/3ros/build/xc/build$ export GMSH_ROOT_DIR=/home/gtheler/gmsh-4.8.4-Linux64-sdk
gtheler@tom:~/codigos/3ros/build/xc/build$ cmake ../src
CMake version is greater than 2.8.4
-- xc project dir: /home/gtheler/codigos/3ros/build/xc/
-- xc include dir: /home/gtheler/codigos/3ros/build/xc/src/
-- xc lib dir: /home/gtheler/codigos/3ros/build/xc/lib
-- ************* find packages begins ****************
-- Using header-only CGAL
-- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.48")  
-- Boost include dirs: /usr/include
-- Boost libraries:    
-- Using gcc version 4 or later. Adding -frounding-math
-- GNUGTS include dir: /usr/include
-- GNUGTS libraries: /usr/lib/x86_64-linux-gnu/libgts.so
-- Found CImg: 
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.62")  
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: python 
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system regex filesystem thread math_c99 math_c99f math_c99l math_tr1 math_tr1f math_tr1l 
-- PYTHON_LIBRARIES = /usr/lib/x86_64-linux-gnu/libpython3.9.so
-- PYTHON_EXECUTABLE = /usr/bin/python
-- PYTHON_INCLUDE_DIRS = /usr/include/python3.9
-- Looking for execinfo
-- Looking for execinfo headers - found
-- Found plotter.h: /usr/include
-- Found plotter lib: /usr/lib/x86_64-linux-gnu/libplotter.so
-- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so
-- SQLite3 library found.
-- Found Arpack: /usr/lib/x86_64-linux-gnu/libarpack.so
-- Found Arpack++: /usr/include/arpack++
-- Found Arpack++ lib: /usr/lib/x86_64-linux-gnu/libarpack++.so
-- Found PETSC: /home/gtheler/libs/petsc-3.15.0/include
-- A library with LAPACK API found.
-- Found SuperLU: /usr/include/superlu
-- Berkeley DB 5.3.28: (September  9, 2013)
-- Found METIS: /usr/include
-- found sqlplus version: /bin/sh: 1: /bin/sqlplus: not found
-- Guessed ORACLE_OCI_VERSION value: 10G_R2
-- Oracle not found.
-- Oracle: You can specify includes: -DORACLE_PATH_INCLUDES=/usr/include/oracle/10.2.0.3/client
--    currently found includes: ORACLE_INCLUDES-NOTFOUND
-- Oracle: You can specify libs: -DORACLE_PATH_LIB=/usr/lib/oracle/10.2.0.3/client/lib
--    currently found libs: ORACLE_LIBRARY_OCCI-NOTFOUND;ORACLE_LIBRARY_CLNTSH-NOTFOUND;ORACLE_LIBRARY_LNNZ-NOTFOUND
CMake Error at /home/gtheler/codigos/3ros/build/xc/CMake/FindGMSH.cmake:65 (MESSAGE):
  Could not find GMSH
Call Stack (most recent call first):
  /home/gtheler/codigos/3ros/build/xc/CMake/find_packages.cmake:56 (find_package)
  CMakeLists.txt:75 (INCLUDE)


-- Configuring incomplete, errors occurred!
See also "/home/gtheler/codigos/3ros/build/xc/build/CMakeFiles/CMakeOutput.log".
See also "/home/gtheler/codigos/3ros/build/xc/build/CMakeFiles/CMakeError.log".
gtheler@tom:~/codigos/3ros/build/xc/build$ 

[lcpt]

I'll try to figure out how to modify FindGMSH.cmake.

[lcpt]

Problem solved, I think. Could you give it a try?

[gtheler]

The Gmsh part worked (although it says it found v4.8.0 instead of the actual v4.8.4).
Yet we're back to a detail in PETSc now:

gtheler@tom:~/codigos/3ros/build/xc/build$ cmake ../src/
CMake version is greater than 2.8.4
-- xc project dir: /home/gtheler/codigos/3ros/build/xc/
-- xc include dir: /home/gtheler/codigos/3ros/build/xc/src/
-- xc lib dir: /home/gtheler/codigos/3ros/build/xc/lib
-- ************* find packages begins ****************
-- Using header-only CGAL
-- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.48")  
-- Boost include dirs: /usr/include
-- Boost libraries:    
-- Using gcc version 4 or later. Adding -frounding-math
-- GNUGTS include dir: /usr/include
-- GNUGTS libraries: /usr/lib/x86_64-linux-gnu/libgts.so
-- Found CImg: 
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.62")  
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: python 
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system regex filesystem thread math_c99 math_c99f math_c99l math_tr1 math_tr1f math_tr1l 
-- PYTHON_LIBRARIES = /usr/lib/x86_64-linux-gnu/libpython3.9.so
-- PYTHON_EXECUTABLE = /usr/bin/python
-- PYTHON_INCLUDE_DIRS = /usr/include/python3.9
-- Looking for execinfo
-- Looking for execinfo headers - found
-- Found plotter.h: /usr/include
-- Found plotter lib: /usr/lib/x86_64-linux-gnu/libplotter.so
-- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so
-- SQLite3 library found.
-- Found Arpack: /usr/lib/x86_64-linux-gnu/libarpack.so
-- Found Arpack++: /usr/include/arpack++
-- Found Arpack++ lib: /usr/lib/x86_64-linux-gnu/libarpack++.so
-- Found PETSC: /home/gtheler/libs/petsc-3.15.0/include
-- A library with LAPACK API found.
-- Found SuperLU: /usr/include/superlu
-- Berkeley DB 5.3.28: (September  9, 2013)
-- Found METIS: /usr/include
-- found sqlplus version: /bin/sh: 1: /bin/sqlplus: not found
-- Guessed ORACLE_OCI_VERSION value: 10G_R2
-- Oracle not found.
-- Oracle: You can specify includes: -DORACLE_PATH_INCLUDES=/usr/include/oracle/10.2.0.3/client
--    currently found includes: ORACLE_INCLUDES-NOTFOUND
-- Oracle: You can specify libs: -DORACLE_PATH_LIB=/usr/lib/oracle/10.2.0.3/client/lib
--    currently found libs: ORACLE_LIBRARY_OCCI-NOTFOUND;ORACLE_LIBRARY_CLNTSH-NOTFOUND;ORACLE_LIBRARY_LNNZ-NOTFOUND
-- GMSH_ROOT_DIR: /home/gtheler/gmsh-4.8.4-Linux64-sdk
-- cmake_prefix_path: /home/gtheler/gmsh-4.8.4-Linux64-sdk
-- Gmsh headers: /home/gtheler/gmsh-4.8.4-Linux64-sdk/include
-- Gmsh libraries: /home/gtheler/gmsh-4.8.4-Linux64-sdk/lib/libgmsh.so
-- Found GMSH:  version: 4.8.0
-- Found GMSH: /home/gtheler/gmsh-4.8.4-Linux64-sdk/include (Required is at least version "4.8") 
-- Found AMD headers in: /usr/include/suitesparse
-- Found AMD library: /usr/lib/x86_64-linux-gnu/libamd.so
-- Found CAMD headers in: /usr/include/suitesparse
-- Found CAMD library: /usr/lib/x86_64-linux-gnu/libcamd.so
-- Found COLAMD headers in: /usr/include/suitesparse
-- Found COLAMD library: /usr/lib/x86_64-linux-gnu/libcolamd.so
-- Found CCOLAMD headers in: /usr/include/suitesparse
-- Found CCOLAMD library: /usr/lib/x86_64-linux-gnu/libccolamd.so
-- Found CHOLMOD headers in: /usr/include/suitesparse
-- Found CHOLMOD library: /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found SUITESPARSEQR headers in: /usr/include/suitesparse
-- Found SUITESPARSEQR library: /usr/lib/x86_64-linux-gnu/libspqr.so
-- Found Intel Thread Building Blocks (TBB) library (2020.3 / 11103) include location: /usr/include. Assuming SuiteSparseQR was compiled with TBB.
-- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse
-- Found SUITESPARSE_CONFIG library: /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so
-- Found LIBRT library: /usr/lib/x86_64-linux-gnu/librt.so
-- Adding librt: /usr/lib/x86_64-linux-gnu/librt.so to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing).
-- Found METIS library: /usr/lib/x86_64-linux-gnu/libmetis.so
-- Found SuiteSparse: TRUE (found version "5.8.1") 
-- ************* find packages ends ****************
-- MySQL libraries: /usr/lib/x86_64-linux-gnu/libmysqlclient.so
-- Found PETSC: /home/gtheler/libs/petsc-3.15.0/include
-- **** compiler fortran flags  -fPIC
-- **** compiler c flags  -fopenmp
-- **** compiler cxx flags  -std=gnu++17 -O3 -DNDEBUG -Wall -march=native -pedantic -fPIC -Wno-unused-but-set-variable -fopenmp
-- **** linker flags  
-- Configuring done
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
PETSC_LIB_PETSC
    linked by target "XcBib" in directory /home/gtheler/codigos/3ros/build/xc/src

-- Generating done
CMake Generate step failed.  Build files cannot be regenerated correctly.
gtheler@tom:~/codigos/3ros/build/xc/build$ 

[lcpt]

Are the PETSc libraries in $PETSC_DIR/$PETSC_ARCH/lib?

[gtheler]

Yes:

gtheler@tom:~$ ls $PETSC_DIR/$PETSC_ARCH/lib
libcmumps.a             libhdf5_fortran.so.200.0.0  libhdf5hl_fortran.so.200      libhdf5.settings    libmumps_common.a   libscalapack.a
libdmumps.a             libhdf5_hl.a                libhdf5hl_fortran.so.200.0.0  libhdf5.so          libparmetis.so      libsmumps.a
libhdf5.a               libhdf5_hl_fortran.a        libhdf5_hl.la                 libhdf5.so.200      libpetsc.so         libzmumps.a
libhdf5_fortran.a       libhdf5hl_fortran.a         libhdf5_hl.so                 libhdf5.so.200.0.0  libpetsc.so.3.15    petsc
libhdf5_fortran.la      libhdf5hl_fortran.la        libhdf5_hl.so.200             libHYPRE-2.20.0.so  libpetsc.so.3.15.0  pkgconfig
libhdf5_fortran.so      libhdf5_hl_fortran.so       libhdf5_hl.so.200.0.0         libHYPRE.so         libpord.a
libhdf5_fortran.so.200  libhdf5hl_fortran.so        libhdf5.la                    libmetis.so         libpragmatic.so
gtheler@tom:~$ 

Note that CMake first says

-- Found PETSC: /home/gtheler/libs/petsc-3.15.0/include

but then it complains about PETSC_LIB_PETSC.

[lcpt]

Yeah, I've told FindPetsc.cmaketo be more precise about its findings :)

I think it's fixed now. Could you give it a try?

[gtheler]

Cmake works now, but the code fails to compile. I'm using Debian 11 that comes with gcc10 which is very picky and does not like dirty tricks:

gtheler@tom:~/codigos/3ros/build/xc/build$ cmake ../src/
CMake version is greater than 2.8.4
-- xc project dir: /home/gtheler/codigos/3ros/build/xc/
-- xc include dir: /home/gtheler/codigos/3ros/build/xc/src/
-- xc lib dir: /home/gtheler/codigos/3ros/build/xc/lib
-- ************* find packages begins ****************
-- Using header-only CGAL
-- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.48")  
-- Boost include dirs: /usr/include
-- Boost libraries:    
-- Using gcc version 4 or later. Adding -frounding-math
-- GNUGTS include dir: /usr/include
-- GNUGTS libraries: /usr/lib/x86_64-linux-gnu/libgts.so
-- Found CImg: 
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.62")  
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: python 
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system regex filesystem thread math_c99 math_c99f math_c99l math_tr1 math_tr1f math_tr1l 
-- PYTHON_LIBRARIES = /usr/lib/x86_64-linux-gnu/libpython3.9.so
-- PYTHON_EXECUTABLE = /usr/bin/python
-- PYTHON_INCLUDE_DIRS = /usr/include/python3.9
-- Looking for execinfo
-- Looking for execinfo headers - found
-- Found plotter.h: /usr/include
-- Found plotter lib: /usr/lib/x86_64-linux-gnu/libplotter.so
-- Found GMP: /usr/lib/x86_64-linux-gnu/libgmp.so
-- SQLite3 library found.
-- Found Arpack: /usr/lib/x86_64-linux-gnu/libarpack.so
-- Found Arpack++: /usr/include/arpack++
-- Found Arpack++ lib: /usr/lib/x86_64-linux-gnu/libarpack++.so
-- Found PETSC include dir: /home/gtheler/libs/petsc-3.15.0/include
-- Found PETSC library: /home/gtheler/libs/petsc-3.15.0/arch-linux2-c-debug/lib/libpetsc.so
-- A library with LAPACK API found.
-- Found SuperLU: /usr/include/superlu
-- Berkeley DB 5.3.28: (September  9, 2013)
-- Found METIS: /usr/include
-- found sqlplus version: /bin/sh: 1: /bin/sqlplus: not found
-- Guessed ORACLE_OCI_VERSION value: 10G_R2
-- Oracle not found.
-- Oracle: You can specify includes: -DORACLE_PATH_INCLUDES=/usr/include/oracle/10.2.0.3/client
--    currently found includes: ORACLE_INCLUDES-NOTFOUND
-- Oracle: You can specify libs: -DORACLE_PATH_LIB=/usr/lib/oracle/10.2.0.3/client/lib
--    currently found libs: ORACLE_LIBRARY_OCCI-NOTFOUND;ORACLE_LIBRARY_CLNTSH-NOTFOUND;ORACLE_LIBRARY_LNNZ-NOTFOUND
-- Gmsh headers: /home/gtheler/gmsh-4.8.4-Linux64-sdk/include
-- Gmsh libraries: /home/gtheler/gmsh-4.8.4-Linux64-sdk/lib/libgmsh.so
-- Found GMSH:  version: 4.8.0
-- Found AMD headers in: /usr/include/suitesparse
-- Found AMD library: /usr/lib/x86_64-linux-gnu/libamd.so
-- Found CAMD headers in: /usr/include/suitesparse
-- Found CAMD library: /usr/lib/x86_64-linux-gnu/libcamd.so
-- Found COLAMD headers in: /usr/include/suitesparse
-- Found COLAMD library: /usr/lib/x86_64-linux-gnu/libcolamd.so
-- Found CCOLAMD headers in: /usr/include/suitesparse
-- Found CCOLAMD library: /usr/lib/x86_64-linux-gnu/libccolamd.so
-- Found CHOLMOD headers in: /usr/include/suitesparse
-- Found CHOLMOD library: /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found SUITESPARSEQR headers in: /usr/include/suitesparse
-- Found SUITESPARSEQR library: /usr/lib/x86_64-linux-gnu/libspqr.so
-- Found Intel Thread Building Blocks (TBB) library (2020.3 / 11103) include location: /usr/include. Assuming SuiteSparseQR was compiled with TBB.
-- Found SUITESPARSE_CONFIG headers in: /usr/include/suitesparse
-- Found SUITESPARSE_CONFIG library: /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so
-- Found LIBRT library: /usr/lib/x86_64-linux-gnu/librt.so
-- Adding librt: /usr/lib/x86_64-linux-gnu/librt.so to SuiteSparse_config libraries (required on Linux & Unix [not OSX] if SuiteSparse is compiled with timing).
-- Found METIS library: /usr/lib/x86_64-linux-gnu/libmetis.so
-- ************* find packages ends ****************
-- MySQL libraries: /usr/lib/x86_64-linux-gnu/libmysqlclient.so
-- Found PETSC include dir: /home/gtheler/libs/petsc-3.15.0/include
-- Found PETSC library: /home/gtheler/libs/petsc-3.15.0/arch-linux2-c-debug/lib/libpetsc.so
-- **** compiler fortran flags  -fPIC
-- **** compiler c flags  -fopenmp
-- **** compiler cxx flags  -std=gnu++17 -O3 -DNDEBUG -Wall -march=native -pedantic -fPIC -Wno-unused-but-set-variable -fopenmp
-- **** linker flags  
-- Configuring done
-- Generating done
-- Build files have been written to: /home/gtheler/codigos/3ros/build/xc/build
gtheler@tom:~/codigos/3ros/build/xc/build$ make
Scanning dependencies of target xc_basic_utils
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/home/gtheler/codigos/3ros/build/xc/src/utility/utils/sqlitepp/Database.cpp: In constructor ‘Database::Database(const string&, IError*)’:
/home/gtheler/codigos/3ros/build/xc/src/utility/utils/sqlitepp/Database.cpp:46:1: warning: ‘Database::m_mutex’ is initialized with itself [-Winit-self]
   46 | Database::Database(const std::string& d,IError *e)
      | ^~~~~~~~
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/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:484:72:

  484 |       IF (INCX.EQ.INCY) IF (INCX-1) 10 , 30 , 70
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:534:72:

  534 |       IF (INCX.EQ.INCY) IF (INCX-1) 10 , 30 , 70
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:588:72:

  588 |       IF (INCX.EQ.INCY) IF (INCX-1) 10 , 30 , 70
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3871:72:

 3871 |          DO 20 JJ = IBGN,IEND
      |                                                                        1
Warning: Fortran 2018 deleted feature: Shared DO termination label 20 at (1)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:1060:23:

 1059 |       DO 10 I = 2,N
      |                                                                        2
 1060 |          D(I) = -TRI(1,I)
      |                       1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:1061:28:

 1059 |       DO 10 I = 2,N
      |                                                                        2
 1060 |          D(I) = -TRI(1,I)
 1061 |          E2(I) = DABS(TRI(2,I))
      |                            1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2030:19:

 2027 |       DO 70 K = 2,NM1
      |                                                                        2
......
 2030 |          IBGN = IA(K)
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2031:19:

 2027 |       DO 70 K = 2,NM1
      |                                                                        2
......
 2031 |          IEND = IA(K+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (3 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2061:19:

 2059 |   110 DO 130 II = 1,N
      |                                                                        2
 2060 |          IBGN = IA(II)
 2061 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2139:19:

 2136 |    40 DO 60 II = 1,N
      |                                                                        2
......
 2139 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2241:19:

 2238 |       DO 30 I = 1,N
      |                                                                        2
......
 2241 |          IEND = IA(I+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2313:12:

 2312 |       DO 80 I = 1,N
      |                                                                        2
 2313 |          IA(I+1) = NEWIA(I)
      |            1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2314:16:

 2312 |       DO 80 I = 1,N
      |                                                                        2
 2313 |          IA(I+1) = NEWIA(I)
 2314 |          K = IA(I+1)-IA(I)
      |                1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2797:19:

 2795 |       DO 30 II = 1,N
      |                                                                        2
 2796 |          IBGN = IA(II)
 2797 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2813:19:

 2811 |       DO 70 II = 1,N
      |                                                                        2
 2812 |          IBGN = IA(II)
 2813 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2549:19:

 2547 |       DO 30 II = 1,N
      |                                                                        2
 2548 |          IBGN = IA(II)
 2549 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2565:19:

 2563 |    40 DO 80 II = 1,N
      |                                                                        2
 2564 |          IBGN = IA(II)
 2565 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2633:19:

 2631 |       DO 30 II = 1,N
      |                                                                        2
 2632 |          IBGN = IA(II)
 2633 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2651:19:

 2649 |    40 DO 80 II = 1,N
      |                                                                        2
 2650 |          IBGN = IA(II)
 2651 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2721:19:

 2719 |       DO 20 II = 1,N
      |                                                                        2
 2720 |          IBGN = IA(II)
 2721 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:2736:19:

 2734 |    30 DO 50 II = 1,N
      |                                                                        2
 2735 |          IBGN = IA(II)
 2736 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3135:19:

 3133 |    30 DO 50 I = 1,NR
      |                                                                        2
 3134 |          IBGN = IA(I)
 3135 |          IEND = IA(I+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3173:19:

 3171 |       DO 20 II = 1,NR
      |                                                                        2
 3172 |          IBGN = IA(II)
 3173 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3240:19:

 3237 |       DO 30 II = 1,N
      |                                                                        2
......
 3240 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3260:19:

 3257 |    40 DO 80 II = 1,N
      |                                                                        2
......
 3260 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3426:19:

 3424 |       DO 20 II = 1,N
      |                                                                        2
 3425 |          IBGN = IA(II)
 3426 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3782:16:

 3781 |       DO 80 I = 1,N
      |                                                                        2
 3782 |          J = IA(I+1)-1
      |                1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3869:19:

 3867 |       DO 20 II = 1,N
      |                                                                        2
 3868 |          IBGN = IA(II)
 3869 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3883:19:

 3881 |       DO 80 II = 1,N
      |                                                                        2
 3882 |          IBGN = IA(II)
 3883 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:3943:19:

 3941 |       DO 120 II = 1,N
      |                                                                        2
 3942 |          IBGN = IA(II)
 3943 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:4163:19:

 4162 |       DO 100 I = 1,N
      |                                                                        2
 4163 |          IDEG = IA(I+1)
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:4164:12:

 4162 |       DO 100 I = 1,N
      |                                                                        2
 4163 |          IDEG = IA(I+1)
 4164 |          IA(I+1) = L
      |            1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:4434:19:

 4432 |       DO 80 II = 1,N
      |                                                                        2
 4433 |          IBGN = IA(II)
 4434 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:4493:19:

 4491 |       DO 140 II = 1,N
      |                                                                        2
 4492 |          IBGN = IA(II)
 4493 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:4712:19:

 4710 |       DO 30 II = 1,N
      |                                                                        2
 4711 |          IBGN = IA(II)
 4712 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
/home/gtheler/codigos/3ros/build/xc/src/utility/itpack/dsrc2c.f:4725:19:

 4723 |       DO 60 II = 1,N
      |                                                                        2
 4724 |          IBGN = IA(II)
 4725 |          IEND = IA(II+1)-1
      |                   1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
[  4%] Building Fortran object CMakeFiles/xc_basic_utils.dir/utility/itpack/jcg.f.o
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/home/gtheler/codigos/3ros/build/xc/src/utility/umfpack/umd2f0.f:618:23:

  613 |      $          ICNTL, AP, AI, AX, AN, ANZ, PRESRV, NBLKS, II (BLKPP),
      |                       2
......
  618 |      $          ICNTL, 0, II, XX, 0, MNZ, PRESRV, 0, 0,
      |                       1
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
make[2]: *** [CMakeFiles/xc_basic_utils.dir/build.make:1018: CMakeFiles/xc_basic_utils.dir/utility/umfpack/umd2f0.f.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:166: CMakeFiles/xc_basic_utils.dir/all] Error 2
make: *** [Makefile:149: all] Error 2
gtheler@tom:~/codigos/3ros/build/xc/build$ 

[lcpt]

Yeah, he's complaining about the FORTRAN code in ITPACK which is quite old. We'll need to search for a flag to instruct the FORTRAN compiler to be more tolerant ...

[lcpt]

Hi, @gtheler
I've updated the offending file. Now I don't get any warnings when compiling. Could you try again?

[lcpt]

I was wrong. I didn't fix anything. For some reason, I did not see the warning messages when using the new file.

Nevertheless, I've specified FORTRAN 95 as the standard for those files and updated some lines of code. If that solves the problem, please let me know.

[gtheler]

Thanks. Commit 06a3436 did the Fortran trick. I am now facing some issues with MPI. I'll need some time to figure out what's going on because it is mixing openmpi and mpic:

In file included from /usr/include/x86_64-linux-gnu/mpich/mpi.h:2241,
                 from /usr/include/x86_64-linux-gnu/mpi/openmpi/ompi/mpi/cxx/mpicxx.h:39,
                 from /usr/include/x86_64-linux-gnu/mpi/mpi.h:2887,
                 from /home/gtheler/codigos/3ros/build/xc/src/utility/actor/address/MPI_ChannelAddress.h:66,
                 from /home/gtheler/codigos/3ros/build/xc/src/utility/actor/address/MPI_ChannelAddress.cpp:62:
/usr/include/x86_64-linux-gnu/mpich/mpicxx.h:1955:18: note: ‘virtual MPI::Aint MPI::File::Get_type_extent(const MPI::Datatype&) const’ previously defined here
 1955 |     virtual Aint Get_type_extent( const Datatype &v2 ) const
      |                  ^~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/mpi/openmpi/ompi/mpi/cxx/mpicxx.h:282,
                 from /usr/include/x86_64-linux-gnu/mpi/mpi.h:2887,
                 from /home/gtheler/codigos/3ros/build/xc/src/utility/actor/address/MPI_ChannelAddress.h:66,
                 from /home/gtheler/codigos/3ros/build/xc/src/utility/actor/address/MPI_ChannelAddress.cpp:62:
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/file_inln.h:111:1: error: redefinition of ‘void MPI::File::Get_view(MPI::Offset&, MPI::Datatype&, MPI::Datatype&, char*) const’
  111 | MPI::File::Get_view(MPI::Offset& disp,
      | ^~~
In file included from /usr/include/x86_64-linux-gnu/mpich/mpi.h:2241,
                 from /usr/include/x86_64-linux-gnu/mpi/openmpi/ompi/mpi/cxx/mpicxx.h:39,
                 from /usr/include/x86_64-linux-gnu/mpi/mpi.h:2887,
                 from /home/gtheler/codigos/3ros/build/xc/src/utility/actor/address/MPI_ChannelAddress.h:66,
                 from /home/gtheler/codigos/3ros/build/xc/src/utility/actor/address/MPI_ChannelAddress.cpp:62:
/usr/include/x86_64-linux-gnu/mpich/mpicxx.h:2085:18: note: ‘virtual void MPI::File::Get_view(MPI::Offset&, MPI::Datatype&, MPI::Datatype&, char*) const’ previously defined here
 2085 |     virtual void Get_view( Offset & v2, Datatype &v3, Datatype &v4, char * v5 ) const
      |                  ^~~~~~~~

[lcpt]

I've only openmpi installed. I think XC will work also with mpich so, if this can help, you can remove openmpi.

[lcpt]

Hi @gtheler.
I've removed some errors and I've compiled the code against https://petsc.org/release/download/ and it works.
I'll test with https://gitlab.com/petsc/petsc.git also.

[lcpt]

It works.

[gtheler]

Sorry for the delay, but I have to uninstall MPICH (which is the one I use for everyday work) and switch to OpenMPI to test this, so I had to wait until Saturday.

I now have problems finding the Gmsh header even though the GMSH_ROOT_DIR is set:

gtheler@tom:~/codigos/3ros/build/xc/build$ export GMSH_ROOT_DIR=/home/gtheler/gmsh-4.8.4-Linux64-sdk
gtheler@tom:~/codigos/3ros/build/xc/build$ make
[  7%] Built target xc_basic_utils
[ 18%] Built target xc_utils
[ 18%] Built target xcGnuGts
[ 18%] Building CXX object CMakeFiles/XcBib.dir/preprocessor/multi_block_topology/entities/1d/Line.cc.o
/home/gtheler/codigos/3ros/build/xc/src/preprocessor/multi_block_topology/entities/1d/Line.cc:41:10: fatal error: gmsh.h: No such file or directory
   41 | #include <gmsh.h>
      |          ^~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/XcBib.dir/build.make:15994: CMakeFiles/XcBib.dir/preprocessor/multi_block_topology/entities/1d/Line.cc.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:221: CMakeFiles/XcBib.dir/all] Error 2
make: *** [Makefile:149: all] Error 2
gtheler@tom:~/codigos/3ros/build/xc/build$ 

[lcpt]

No worries :). I'll take a look a soon as possible.

[lcpt]

If you want CMake to modify the paths where make will search the headers and/or the libraries, you need to remove the file CMakeCache.txt and rerun cmake; otherwise, makewill use the last setup.

Nevertheless, I've added the string obtained from GMSH_ROOT_DIR to the list of paths where CMake must search for this library (for some reason, this was missing in FindGMSH.cmake).

I think this will fix the problem.

[lcpt]

It worked?

[gtheler]

It says

-- GMSH_ROOT_DIR: /home/gtheler/gmsh-4.8.4-Linux64-sdk
-- cmake_prefix_path: /home/gtheler/gmsh-4.8.4-Linux64-sdk
-- Gmsh headers: /home/gtheler/gmsh-4.8.4-Linux64-sdk/include
-- Gmsh libraries: /home/gtheler/gmsh-4.8.4-Linux64-sdk/lib/libgmsh.so
-- Found GMSH:  version: 4.8.0

I removed the build directory and built from scratch to make sure there were no problematic caches. But the appropriate -I option does not get included.

[lcpt]

You are right. The line that instructs CMake to include the GMSH_INCLUDE_DIRS was missing. I've fixed the error. I hope it works now.

[lcpt]

Did this solve the problem?

[jeremyonscale]

Sorry I still did not find time to try. I cannot make it work with mpich and I need to do a full switch to openmpi to test this and that breaks my whole dev environment.

[lcpt]

OK, no worries. If I can help you, let me know.