Offline installation problem

[lucuo]

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Issue or question about MOOSE

An error is reported when running
./update_and_rebuild_petsc.sh --skip-submodule-update --with-packages-download-dir=~/projects/downloads
during offline installation. What is the reason？

=============================================================================================
=============================================================================================
               Configuring SCALAPACK with CMake; this may take several minutes
=============================================================================================
=============================================================================================
              Compiling and installing SCALAPACK; this may take several minutes
=============================================================================================
=============================================================================================
       Trying to download /home/Rookie01/projects/downloads/v7.1.4.tar.gz for STRUMPACK
=============================================================================================
=============================================================================================
               Configuring STRUMPACK with CMake; this may take several minutes
=============================================================================================
=============================================================================================
              Compiling and installing STRUMPACK; this may take several minutes
=============================================================================================

*********************************************************************************************
           UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
---------------------------------------------------------------------------------------------
                               Error running make on  STRUMPACK
*********************************************************************************************

There was an error. Exiting...

here is configure.log
configure.log

(Optional) code in question / simulation log / errors

No response

Encountering Errors? Please include diagnostic output

No response

[milljm]

I think your installation of Fortran might be too old:

-- The CXX compiler identification is GNU 9.3.1
-- The C compiler identification is GNU 9.3.1
-- The Fortran compiler identification is GNU 4.8.5

I might be wrong about fortran being too old though. I recall GCC and Fortran versions can differ. 🤷‍♂️

Can you run the following tool:

cd moose/scripts
./diagnostics.sh

If you can, please refrain from posting images of text.

[lucuo]

after ./diagnostics.sh
The output is as follows

##################################################################################################
Compiler(s) (CC CXX FC F77 F90):

CC=/mpich-3.4.2/bin/mpicc
CC -show:
gcc -I/mpich-3.4.2/include -L/mpich-3.4.2/lib -Wl,-rpath -Wl,/mpich-3.4.2/lib -Wl,--enable-new-dtags -lmpi
CC version:     gcc (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)

CXX=/mpich-3.4.2/bin/mpicxx
CXX -show:
g++ -I/mpich-3.4.2/include -L/mpich-3.4.2/lib -lmpicxx -Wl,-rpath -Wl,/mpich-3.4.2/lib -Wl,--enable-new-dtags -lmpi
CXX version:    g++ (GCC) 9.3.1 20200408 (Red Hat 9.3.1-2)

FC=/mpich-3.4.2/bin/mpif90
FC -show:
gfortran -I/mpich-3.4.2/include -I/mpich-3.4.2/include -L/mpich-3.4.2/lib -lmpifort -Wl,-rpath -Wl,/mpich-3.4.2/lib -Wl,--enable-new-dtags -lmpi
FC version:     GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

F77=/mpich-3.4.2/bin/mpif77
F77 -show:
gfortran -I/mpich-3.4.2/include -I/mpich-3.4.2/include -L/mpich-3.4.2/lib -lmpifort -Wl,-rpath -Wl,/mpich-3.4.2/lib -Wl,--enable-new-dtags -lmpi
F77 version:    GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

F90=/mpich-3.4.2/bin/mpif90
F90 -show:
gfortran -I/mpich-3.4.2/include -I/mpich-3.4.2/include -L/mpich-3.4.2/lib -lmpifort -Wl,-rpath -Wl,/mpich-3.4.2/lib -Wl,--enable-new-dtags -lmpi
F90 version:    GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

OK

##################################################################################################
Python Sanity Checks

Verify `/usr/bin/env python3 --version` (reporting as: Python 3.6.8),
matches versions for: `which python3 && which python`

Python 2.7.5
FAIL: Python 2.7.5
/usr/bin/python --version (reporting as ) != Python 3.6.8

This will likely result in the TestHarness failing. Or WASP/HIT parsing errors.

##################################################################################################
Python Modules (TestHarness, run-ability)

FAIL:    python module: `packaging` not available
WARNING: python module: `yaml` not available
WARNING: python module: `jinja2` not available

Failing Python packages will prevent you from building MOOSE.
Warning Python packages may cause miscellaneous runtime issues.

Either install the above packages, or perhaps you have yet to activate your
moose environment: `conda activate moose`.

[milljm]

My guess is that your version of Fortran is too old to build some of the PETSc contribs. It looks like these versions should match (as they do for me):

[~] which gcc
/opt/rh/gcc-toolset-12/root/usr/bin/gcc

[~] which gfortran
/opt/rh/gcc-toolset-12/root/usr/bin/gfortran

[~] gcc --version
gcc (GCC) 12.2.1 20221121 (Red Hat 12.2.1-7)
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[~] gfortran --version
GNU Fortran (GCC) 12.2.1 20221121 (Red Hat 12.2.1-7)
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

[~]

[milljm]

In our containers, we have to perform the following to install and make available GCC and gfortran 12.x for example:

    dnf install -y gcc-toolset-12 gcc-toolset-12-gcc gcc-toolset-12-gcc-gfortran \
        gcc-toolset-12-gcc-c++ gcc-toolset-12-gdb

    source /opt/rh/gcc-toolset-12/enable

As we can see, there is a separate package for gfortran. Perhaps all you need to do is install that one package:

dnf install gcc-toolset-9-gcc-gfortran

[lucuo]

I tried to skip the installation of STRUMPACK, but still got an error.

...
...
         CC arch-moose/obj/src/tao/bound/impls/blmvm/blmvm.o
         CC arch-moose/obj/src/tao/bound/impls/bqnk/bqnktl.o
         CC arch-moose/obj/src/tao/bound/impls/bqnk/bqnkls.o
         CC arch-moose/obj/src/tao/bound/impls/bqnk/bqnk.o
         CC arch-moose/obj/src/tao/bound/impls/bqnk/bqnktr.o
         CC arch-moose/obj/src/tao/bound/impls/bnk/bnls.o
         CC arch-moose/obj/src/tao/constrained/impls/ipm/pdipm.o
         CC arch-moose/obj/src/tao/bound/impls/bnk/bntr.o
         CC arch-moose/obj/src/tao/bound/impls/bnk/bntl.o
         CC arch-moose/obj/src/tao/bound/impls/bqnls/bqnls.o
         CC arch-moose/obj/src/tao/bound/impls/bnk/bnk.o
         CC arch-moose/obj/src/tao/bound/impls/tron/tron.o
         CC arch-moose/obj/src/tao/quadratic/impls/gpcg/gpcg.o
         CC arch-moose/obj/src/tao/bound/impls/bncg/bncg.o
         CC arch-moose/obj/src/tao/quadratic/impls/bqpip/bqpip.o
         CC arch-moose/obj/src/tao/util/tao_util.o
    CLINKER arch-moose/lib/libpetsc.so.3.20.3
make[3]: Leaving directory '/home/Rookie01/project2/moose/petsc'
*** Building SLEPc ***
Checking environment... done
Checking PETSc installation...
ERROR: Unable to link with PETSc
ERROR: See "arch-moose/lib/slepc/conf/configure.log" file for details
**************************ERROR*************************************
Error building SLEPc.
********************************************************************
make[2]: *** [/home/Rookie01/project2/moose/scripts/../petsc/arch-moose/lib/petsc/conf/petscrules:29: slepcbuild] Error 1
make[2]: Leaving directory '/home/Rookie01/project2/moose/petsc'
**************************ERROR*************************************
  Error during compile, check arch-moose/lib/petsc/conf/make.log
  Send it and arch-moose/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov
********************************************************************
make[1]: *** [all] Error 1
make: *** [all] Error 2
There was an error. Exiting...

Are these errors related?
configure.log
make.log

[milljm]

I was about to try and reproduce this in a container, but I cannot gain a version of Gfortran that old.

I really do think you need to install the same version of Fortran, that you have for GCC.

Rocky-8:

Apptainer> gfortran --version
GNU Fortran (GCC) 8.5.0 20210514 (Red Hat 8.5.0-22)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Yours:

Fortran compiler version: GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

I suspect your binaries are going to be in the following locations (as I was trying to duplicate your issue:

Apptainer> which gcc gfortran
/opt/rh/gcc-toolset-12/root/usr/bin/gcc
/usr/bin/gfortran

(latest GCC 12.x sitting in correct location, while gfortran is old-system version sitting in /usr/bin)

[GiudGiud]

Hello

Please include the diagnostics output from moose/scripts/diagnostics.sh