In continuation to the previous mail, I am sending the tasks done while
configuring libmesh 1.6.2. The error is mentioned in this file. Please find
the attached file and do the needful.
Thanks and Regards
Srinivas
On Wed, Aug 30, 2023 at 1:47 PM INTURU SRINIVAS 20PHD0548 <
inturu.srinivas2...@vitstudent.ac.in> wrote:
> Hello,
>
> I am building IBAMR open software as given in the link
> https://ibamr.github.io/. When I configured libmesh, I got the error
> mentioning "petsc was not found". I am sharing the config.log file. Please
> find the attachment and do the needful.
>
>
> Thanks and Regards
> Srinivas
>
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[hpcsmec15767@hpcvisualization 3.17.5]$ cd ..
[hpcsmec15767@hpcvisualization petsc]$ cd ..
[hpcsmec15767@hpcvisualization sfw]$ cd linux/libmesh/1.6.2/objs-debug/
[hpcsmec15767@hpcvisualization objs-debug]$ ls
config.log
[hpcsmec15767@hpcvisualization objs-debug]$ rm -fr config.log
[hpcsmec15767@hpcvisualization objs-debug]$ ../LIBMESH/configure
--prefix=/home/hpcsmec15767/sfw/li
nux/libmesh/1.6.2/1.6.2-debug --with-methods=dbg
PETSC_DIR=/home/hpcsmec15767/sfw/petsc/3.17.5/linu
x-debug PETSC_ARCH=linux-debug
CC=/home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc CXX=/home/apps/lib/ope
nmpi/4.1.0/gnu/bin/mpicxx
FC=/home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 F77=/home/apps/lib/openmpi
/4.1.0/gnu/bin/mpif90
--enable-exodus --enable-triangle --enable-petsc-required --disable-boost --d
isable-eigen
--disable-hdf5 --disable-openmp --disable-perflog --disable-pthreads
--disable-tbb --d
isable-timestamps --disable-reference-counting --disable-strict-lgpl
--disable-glibcxx-debugging --
disable-vtk --with-thread-model=none
LDFLAGS="-L/home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/lib
"
CPPFLAGS="-I/home/hpcsmec15767/sfw/petsc/3.17.5/linux-debug/include"
---------------------------------------------
----------- Configuring libMesh -------------
---------------------------------------------
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '1030' is supported by ustar format... yes
checking whether GID '1030' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for src/base/libmesh.C... no
<<< Configuring build directory for VPATH build >>>
checking for perl... /usr/bin/perl
note: MPI library path not given...
<<< Could not find a viable PETSc Makefile to determine PETSC_CC_INCLUDES, etc.
>>>
checking whether make supports the include directive... yes (GNU style)
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc accepts -g... yes
checking for /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc option to accept ISO
C89... none needed
checking whether /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc understands -c and
-o together... yes
checking dependency style of /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc... gcc3
checking whether we are using the GNU Fortran compiler... yes
checking whether /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 accepts -g... yes
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx accepts -g... yes
checking dependency style of /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx... gcc3
<<< C++ compiler is gcc-7.x >>>
checking for a sed that does not truncate output... /usr/bin/sed
checking for C++ compiler vendor... gnu
checking whether /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx supports C++11
features by default...
yes
<<< Configuring libMesh with methods "dbg" >>>
<<< Compiler warnings are just warnings >>>
<<< Disabling extra paranoid compiler warnings >>>
checking for C++11 auto keyword support... yes
checking for C++11 range-based for loop support... yes
checking for C++11 initializer list support... yes
checking for C++11 std::unique_ptr support... yes
checking for C++11 std::make_unique workaround support... yes
checking for C++11 std::tuple support... yes
checking for C++11 lambda support... yes
checking for C++11 fixed type enumeration support... yes
checking for C++11 fixed type enumeration forward declaration support... yes
checking for C++11 override keyword support... yes
checking for C++11 move constructor support... yes
checking for C++11 deleted functions support... yes
checking for C++11 defaulted functions support... yes
checking for C++11 nullptr support... yes
checking for C++11 'final' keyword support... yes
checking for C++11 decltype support... yes
checking for C++11 std::begin/end support for arrays... yes
checking for C++11 std container erase() functions returning iterators... yes
checking for C++11 std container emplace() functions... yes
checking for C++11 std::iota algorithm... yes
checking for C++11 std::vector::data() API... yes
checking for C++11 std::shared_ptr support... yes
checking for C++11 rvalue references support... yes
checking for C++11 std::to_string() support... yes
checking for C++11 constexpr support... yes
checking for C++11 variadic template support... yes
checking for C++11 alias declarations support... yes
checking for C++11 std::array... yes
checking for C++11 std::isnan... yes
checking for C++11 std::isinf... yes
checking for C++14 std::make_unique support... yes
checking for C++11 std::regex support... yes
checking for C++11 <thread> support... yes
checking for C++11 <condition_variable> support... yes
checking for C++11 <type_traits> support... yes
checking for C++11 std::asinh support in <cmath>... yes
checking for C++11 std::acosh support in <cmath>... yes
checking for C++11 std::atanh support in <cmath>... yes
checking for C++11 std::asinh(complex) support in <complex>... yes
checking for C++11 std::acosh(complex) support in <complex>... yes
checking for C++11 std::atanh(complex) support in <complex>... yes
checking for C++11 std::erf support in <cmath>... yes
checking for C++17 fallthrough attribute support... yes
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc...
/opt/rh/devtoolset-7/root/usr
/libexec/gcc/x86_64-redhat-linux/7/ld
checking if the linker
(/opt/rh/devtoolset-7/root/usr/libexec/gcc/x86_64-redhat-linux/7/ld) is GNU
ld... yes
checking for BSD- or MS-compatible name lister (nm)...
/opt/rh/devtoolset-7/root/usr/bin/nm -B
checking the name lister (/opt/rh/devtoolset-7/root/usr/bin/nm -B) interface...
BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3458764513820540925
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu
format... func_conver
t_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format...
func_convert_file_noo
p
checking for /opt/rh/devtoolset-7/root/usr/libexec/gcc/x86_64-redhat-linux/7/ld
option to reload ob
ject files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /opt/rh/devtoolset-7/root/usr/bin/nm -B output from
/home/apps/lib/openmp
i/4.1.0/gnu/bin/mpicc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor...
/home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc supports -fno-rtti
-fno-exceptions... no
checking for /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc option to produce
PIC... -fPIC -DPIC
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc PIC flag -fPIC -DPIC
works... yes
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc static flag -static
works... no
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc supports -c -o file.o...
yes
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc supports -c -o file.o...
(cached) yes
checking whether the /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicc linker
(/opt/rh/devtoolset-7/root/u
sr/libexec/gcc/x86_64-redhat-linux/7/ld -m elf_x86_64) supports shared
libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor...
/home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx -E
checking for ld used by /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx...
/opt/rh/devtoolset-7/root/us
r/libexec/gcc/x86_64-redhat-linux/7/ld -m elf_x86_64
checking if the linker
(/opt/rh/devtoolset-7/root/usr/libexec/gcc/x86_64-redhat-linux/7/ld -m elf_x
86_64) is GNU ld... yes
checking whether the /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx linker
(/opt/rh/devtoolset-7/root/
usr/libexec/gcc/x86_64-redhat-linux/7/ld -m elf_x86_64) supports shared
libraries... yes
checking for /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx option to produce
PIC... -fPIC -DPIC
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx PIC flag -fPIC -DPIC
works... yes
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx static flag -static
works... no
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx supports -c -o
file.o... yes
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx supports -c -o
file.o... (cached) yes
checking whether the /home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx linker
(/opt/rh/devtoolset-7/root/
usr/libexec/gcc/x86_64-redhat-linux/7/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 option to produce
PIC... -fPIC
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 PIC flag -fPIC works...
yes
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 static flag -static
works... no
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 supports -c -o
file.o... yes
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 supports -c -o
file.o... (cached) yes
checking whether the /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 linker
(/opt/rh/devtoolset-7/root/
usr/libexec/gcc/x86_64-redhat-linux/7/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 option to produce
PIC... -fPIC
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 PIC flag -fPIC works...
yes
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 static flag -static
works... no
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 supports -c -o
file.o... yes
checking if /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 supports -c -o
file.o... (cached) yes
checking whether the /home/apps/lib/openmpi/4.1.0/gnu/bin/mpif90 linker
(/opt/rh/devtoolset-7/root/
usr/libexec/gcc/x86_64-redhat-linux/7/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking Major version... 1
checking Minor version... 6
checking Point version... 2
checking whether ln -s works... yes
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking whether the compiler implements namespaces... yes
---------------------------------------------
------- Configuring compiler features -------
---------------------------------------------
<<< Default floating point is double precision (double) >>>
checking for C/C++ restrict keyword... __restrict
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
<<< Configuring library with getpwuid >>>
<<< Configuring library with exception throwing support >>>
checking size of short int... 2
checking size of int... 4
checking size of unsigned int... 4
checking size of size_t... 8
checking size of long int... 8
checking size of float... 4
checking size of double... 8
checking size of void *... 8
checking size of function_pointer... 8
checking whether the compiler supports Run-Time Type Identification... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking csignal usability... yes
checking csignal presence... yes
checking for csignal... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking whether the compiler has locale... yes
checking whether the compiler has stringstream... yes
checking fenv.h usability... yes
checking fenv.h presence... yes
checking for fenv.h... yes
checking xmmintrin.h usability... yes
checking xmmintrin.h presence... yes
checking for xmmintrin.h... yes
checking whether sigaction is declared... yes
checking for mkdir with two arguments... yes
checking direct.h usability... no
checking direct.h presence... no
checking for direct.h... no
checking whether _mkdir is declared... no
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking whether the compiler supports std::unordered_multimap... yes
checking whether the compiler supports std::unordered_map... yes
checking whether the compiler supports std::unordered_multiset... yes
checking whether the compiler supports std::unordered_set... yes
checking whether the compiler supports std::hash... yes
checking for library containing dlopen... -ldl
checking whether the c++ compiler supports dlopen/dlsym/dlclose... yes
checking whether the compiler supports GCC C++ ABI name demangling... yes
checking whether the c++ compiler supports glibc backtrace... yes
checking if errno.h can be wrapped in namespace... yes
---------------------------------------------
----- Done configuring compiler features ----
---------------------------------------------
---------------------------------------------
----- Configuring core library features -----
---------------------------------------------
configuring gdb command... "no"
<<< Configuring library with warnings >>>
<<< Configuring library with deprecated code support >>>
<<< Configuring library with forward declared enumerations >>>
<<< Configuring library to require ``include "libmesh/etc.h"'' style >>>
<<< Configuring library to keep names in libMesh namespace >>>
configuring size of boundary_id... 2
configuring size of dof_id... 4
configuring size of processor_id... 4
configuring size of subdomain_id... 2
<<< Configuring library with AMR support >>>
<<< Configuring library with variational smoother support >>>
<<< Configuring library with periodic BC support >>>
<<< Configuring library with Dirichlet constraint support >>>
<<< Configuring library to use ghosted local vectors >>>
<<< Configuring library to store node valence >>>
<<< Configuring library with higher order p-FEM shapes >>>
<<< Configuring library with second derivatives >>>
<<< Configuring library with real number support >>>
<<< No RTTI: disabling reference counting support >>>
<<< Configuring library example suite support >>>
---------------------------------------------
-- Done configuring core library features ---
---------------------------------------------
---------------------------------------------
----- Configuring for optional packages -----
---------------------------------------------
checking for built-in XDR support... yes
/home/apps/lib/openmpi/4.1.0/gnu/bin/mpicxx Compiler Supports MPI
configure: error: *** PETSc was not found, but --enable-petsc-required was
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