build error

[dewan1988]

Dear MOOSE experts
I am trying to install moose for HPC. at first I created conda moose environment for LInux users by following commands of the link: https://mooseframework.inl.gov/getting_started/installation/conda.html then I followed the instructions are given for those operating on an HPC cluster: https://mooseframework.inl.gov/getting_started/installation/hpc_install_moose.html. but when I am trying to update and rebuild the libmesh.sh highlited here

it is showing following errors:

PETSc submodule will be used. PETSc submodule is our default solver.
IMPORTANT: If you did not run the update_and_rebuild_petsc.sh script yet, please run it before building libMesh
---------------------------------------------
----------- 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... /home/mdewan/projects/moose/scripts/../libmesh/build-aux/install-sh -C
checking whether build environment is sane... yes
checking for a race-free 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 '1108' is supported by ustar format... yes
checking whether GID '1047' 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...
trying prefix=/usr/lib64/compat-openmpi16
note: MPI library path not given...
trying prefix=/usr/lib64/compat-openmpi16
checking whether make supports the include directive... yes (GNU style)
checking whether the C compiler works... no
configure: error: in `/home/mdewan/projects/moose/libmesh/build':
configure: error: C compiler cannot create executables
See `config.log' for more details
Running make -j 6...
make: *** No targets specified and no makefile found.  Stop.

Could you please help me?

[GiudGiud]

Hello

Please run the diagnostics script in moose/scripts
Seems the compiler being found is not working:

checking whether the C compiler works... no

Guillaume

[milljm]

Don't mean to derail the thread... PETSc is usually the more finicky library, due to the myriad amount of contribs we are asking it to build. By any change can you attach the configure log for the PETSc build? It might help us better understand your cluster. The log file should reside at:

/home/mdewan/projects/moose/petsc/configure.log

[dewan1988]

There are lots of error. I just copied the last part:
Loop over declared dependencies of package and error if any are missing

                    Defined make rule "slepcbuild" with dependencies "" and code ['@echo "*** Building SLEPc ***"', '@${RM} /home/mdewan/projects/moose/petsc/arch-moose/lib/petsc/conf/slepc.errorflg', '+@(cd /home/mdewan/projects/moose/petsc/arch-moose/externalpackages/git.slepc && \\\n            SLEPC_DIR=/home/mdewan/projects/moose/petsc/arch-moose/externalpackages/git.slepc /home/mdewan/miniforge/bin/python3 ./configure --prefix=/home/mdewan/projects/moose/petsc/arch-moose  && \\\n            SLEPC_DIR=/home/mdewan/projects/moose/petsc/arch-moose/externalpackages/git.slepc ${OMAKE} SLEPC_DIR=/home/mdewan/projects/moose/petsc/arch-moose/externalpackages/git.slepc) || \\\n            (echo "**************************ERROR*************************************" && \\\n            echo "Error building SLEPc." && \\\n            echo "********************************************************************" && \\\n            touch /home/mdewan/projects/moose/petsc/arch-moose/lib/petsc/conf/slepc.errorflg && \\\n            exit 1)']
/tmp/petsc-w1_gvvnk/PETSc.Configure/conftest.c:4:15: error: ‘RTLD_DEFAULT’ undeclared here (not in a function)
/tmp/petsc-w1_gvvnk/PETSc.Configure/conftest.c:4:15: error: ‘RTLD_DEFAULT’ undeclared here (not in a function)
  -pass-exit-codes         Exit with highest error code from a phase.
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/* Override any gcc2 internal prototype to avoid an error. */
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/* Override any gcc2 internal prototype to avoid an error. */
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/* Override any gcc2 internal prototype to avoid an error. */
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/* Override any gcc2 internal prototype to avoid an error. */
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/* Override any gcc2 internal prototype to avoid an error. */
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/* Override any gcc2 internal prototype to avoid an error. */
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/* Override any gcc2 internal prototype to avoid an error. */
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/config.libraries/conftest.c:4:10: fatal error: windows.h: No such file or directory
/* Override any gcc2 internal prototype to avoid an error. */
/tmp/petsc-w1_gvvnk/PETSc.Configure/conftest.c:3:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/PETSc.Configure/conftest.c:3:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/PETSc.Configure/conftest.c:3:10: fatal error: windows.h: No such file or directory
/tmp/petsc-w1_gvvnk/PETSc.Configure/conftest.c:3:10: fatal error: windows.h: No such file or directory
  -pass-exit-codes         Exit with highest error code from a phase.
      Warning accessing  gives errors: [Errno 2] No such file or directory: ''
      Warning accessing  gives errors: [Errno 2] No such file or directory: ''
    If --with-strict-petscerrorcode = 1:
        @${RM} /home/mdewan/projects/moose/petsc/arch-moose/lib/petsc/conf/slepc.errorflg
            touch /home/mdewan/projects/moose/petsc/arch-moose/lib/petsc/conf/slepc.errorflg && \

[milljm]

There will naturally be lots of error looking lines. But what we really need is the attached log file. It can be several megabytes in size, so please do not even try to paste the text :).

If there actually was a failure in PETSc, then we need to stop there, and figure that out first, as libMesh will fail to build if PETSc isn't complete.

[dewan1988]

During PETSc rebuilding I didn't get error, that is why I have tried to update and rebuilding the libmesh.

[milljm]

Considering what has been posted, we are concerned at the current state of the build. That is why we wish to see the PETSc configure log. PETSc does a real good job at hunting for things all the contribs need. But sometimes it finds things it shouldn't. By attaching the PETSc configure log, we can better understand that environment, and possibly why libMesh is failing to build.

Can you attach your PETSc configure log? It should be located at:

home/mdewan/projects/moose/petsc/configure.log