There is a problem with installing MOOSE offline and configuring petsc

[shin-chan-cpu]

Check these boxes if you have followed the posting rules.

• I have consulted the Posting Guidelines.
• I have searched the Discussions Forum and MOOSE Framework Troubleshooting and have not found what I was looking for
• Q&A Getting Started is the most appropriate category for my question (trouble installing, beginner user, ...)

Issue or question about MOOSE

When I refer to the offline installation tutorial on the official website:https://mooseframework.inl.gov/releases/moose/2021-05-18/getting_started/installation/offline_installation.html
After the prerequisites were installed, I downloaded all the files I said, and when I ran the petsc configuration script, I got the following error

---------------------------------------------------------------------------------------------
  Error during download/extract/detection of HDF5:
  file could not be opened successfully
  Downloaded package HDF5 from: /root/offline/downloads/hdf5-1.14.3-p1.tar.bz2 is not a
  tarball.
  [or installed python cannot process compressed files]
  * If you are behind a firewall - please fix your proxy and rerun ./configure
  For example at LANL you may need to set the environmental variable http_proxy (or
  HTTP_PROXY?) to  http://proxyout.lanl.gov
  * You can run with --with-packages-download-dir=/adirectory and ./configure will instruct
  you what packages to download manually
  * or you can download the above URL manually, to
  /yourselectedlocation/hdf5-1.14.3-p1.tar.bz2
  and use the configure option:
  --download-hdf5=/yourselectedlocation/hdf5-1.14.3-p1.tar.bz2

But when I checked again, my file was already in the downloads folder he said, and I tried to add the configuration again and still got this error after adding --download-hdf5, I want to ask why?

(Optional) code in question / simulation log / errors

No response

Encountering Errors? Please include diagnostic output

#!/bin/bash
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html

SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

function ecolor_support()
{
    ECOLOR_SUPPORT="${ECOLOR_SUPPORT:-$(tput colors)}"
    echo "${ECOLOR_SUPPORT}"
}

function get_value()
{
    grep "^$1: " "${SCRIPT_DIR}"/../framework/doc/packages_config.yml | awk '{print $2}'
}

function print_failure_and_exit()
{
    if [[ -n "${CANCELED}" ]]; then exit 1; fi
    print_red "ERROR: "
    printf "Printing report.\n"
    env_test
    printf '

There was an error while %s

Please report the entirety of the output of diagnostics on
this terminal to either YOUR existing post OR a new post on
https://github.com/idaholab/moose/discussions\n' "$(print_red "$@")"
    exit_on_failure 1
}

function print_reset()
{
    if [[ "${NO_COLOR:-0}" == 0 ]]; then
        printf "\033[0m"
    fi
}

function print_sep()
{
    max_len=$(tput cols)
    if [[ $max_len -gt 100 ]]; then max_len=100; fi
    printf -v foo "%${max_len}s" '' && echo "${foo//?/#}"
}

function print_bold()
{
    if [[ "${NO_COLOR}" == 1 ]]; then
        printf '%b' "$@"
    elif [[ "$(ecolor_support)" -ge 256 ]]; then
        printf '\033[1;37m%b' "$@"
    else
        printf '\033[1m%b' "$@"
    fi
    print_reset
}
function print_red()
{
    if [[ "${NO_COLOR}" == 1 ]]; then
        printf '%b' "$@"
    else
        printf '\033[1;91m%b' "$@"
    fi
    print_reset
}

function print_orange()
{
    if [[ "${NO_COLOR}" == 1 ]]; then
        printf '%b' "$@"
    elif [[ "$(ecolor_support)" -ge 256 ]]; then
        printf "\033[38;5;202m%b" "$@"
    else
        printf "\033[0;33m%b" "$@"
    fi
    print_reset
}

function print_green()
{
    if [[ "${NO_COLOR}" == 1 ]]; then
        printf '%b' "$@"
    else
        printf "\033[1;92m%b" "$@"
    fi
    print_reset
}

function run_command()
{
    if [[ "${NO_COLOR}" == 1 ]]; then
        true
    elif [[ "$(ecolor_support)" -ge 256 ]]; then
        printf "\033[38;5;236m"
    else
        printf "\033[1;30m"
    fi
    # shellcheck disable=SC2068
    $@
    exit_code=$?
    print_reset
    return $exit_code
}

function create_tmp()
{
    if [[ -n "$CTMP_DIR" ]]; then echo "${CTMP_DIR}"; return; fi
    if [[ "$(uname)" == 'Darwin' ]]; then
        local TMP_DIR="${TMP_DIR:-"$(mktemp -d -t MOOSE)"}"
    else
        local TMP_DIR="${TMP_DIR:-"$(mktemp -d -t MOOSE.XXXXXXXX)"}"
    fi
    echo "${TMP_DIR}"
}

function exit_on_failure()
{
    if [[ "${NO_FAILURE}" == '1' ]]; then
        printf '\n--continue-on-fail enabled. Not exiting.\n\n'
        return
    fi
    exit "${1}"
}

function print_help()
{
    # shellcheck disable=SC2034
    args=("-h|--help"\
          "-f|--full-build"\
          "-r|--run-checks"\
          "-c|--conda-channel"\
          "--continue-on-fail"\
          "-v|--verbose"\
          "--no-colors")

    # shellcheck disable=SC2034
    args_about=("Print this message and exit."\
                "Build PETSc, libMesh, WASP, MOOSE, and then run entire test suite."\
                "Build MOOSE and then run aggregated tests."\
                "Prioritize MOOSE packages with this channel (default is public)."\
                "Do not stop on failure. If this option works, you have intermittent network issues."\
                "Print additional output from commands being executed."\
                "Do not print color.")

    printf '\nSyntax:\n\t./%s\n\nOptions:\n\n' "$(basename "$0")"
    print_args args args_about
    printf '\nInfluencial Environment Variables:\n
\tMETHODS             libMesh build type \"opt dbg devel oprof\" (default: opt)
\tMETHOD              MOOSE build type (default: \"opt\")
\tMOOSE_JOBS          Cores available during make

Proxies/Certificate Authority environmet variables:
(corporate work machines may require that these be set)

\tREQUESTS_CA_BUNDLE=%s
\tSSL_CERT_FILE=%s
\tCURL_CA_BUNDLE=%s
\thttp_proxy=%s
\thttps_proxy=%s

Supplying no arguments prints useful environment information.\n\n' \
 "${REQUESTS_CA_BUNDLE:-'not set'}" \
 "${SSL_CERT_FILE:-'not set'}" \
 "${CURL_CA_BUNDLE:-'not set'}" \
 "${HTTP_PROXY:-${http_proxy:-'not set'}}" \
 "${HTTPS_PROXY:-${https_proxy:-'not set'}}"
}

function ctl_c()
{
    printf "\033[0m\n\nYou canceled diagnostics. Running clean-up routines.
Please do not ctl-c again, and allow the temp directory to be deleted.\n"
    export CANCELED=true
    exit 1
}

# Check Arguments. If PRISTINE is already set, break out of argument checking
if [[ -z "$PRISTINE_ENVIRONMENT" ]]; then
    # shellcheck disable=SC1091
    source "${SCRIPT_DIR}"/functions/help_system
    while [[ "$#" -gt 0 ]]; do
        case "${1}" in
            -h|--help)
                print_help; exit 0;;
            -f|--full-build)
                export FULL_BUILD=1; shift ;;
            -r|--run-checks)
                export RUN_CHECKS=1; shift ;;
            -c|--conda-channel)
                if ! [[ "${2}" =~ ^http|^file ]]; then
                    print_red '\ninvalid -c|--conda-channel value\n'
                    print_help; exit 1
                fi
                export CONDA_CHANNEL="${2}"; shift 2;;
            --continue-on-fail)
                export NO_FAILURE=1; shift ;;
            -v|--verbose)
                export VERBOSITY=1; shift ;;
            --no-colors)
                export NO_COLOR=1; shift ;;
            *)
                printf 'Unknown argument: %s\n' "${1}"; exit 1;;
        esac
    done
    # default to printing active environment, otherwise do not print active environment
    # (basically I want the default behavior to behave like the previous diagnostic.sh script)
    if [[ -n "${FULL_BUILD}" ]] || [[ -n "${RUN_CHECKS}" ]]; then
        NO_ENVIRONMENT=1
    fi
    # FULL_BUILD or RUN_CHECKS is set, but not PRISTINE_ENVIRONMENT
    if [[ "${PRISTINE_ENVIRONMENT}" != 0 ]] && [[ "${NO_ENVIRONMENT}" == 1 ]]; then
        # Obtain a temp directory
        export CTMP_DIR
        CTMP_DIR=$(create_tmp)
        # Delete temporary directory at any time this script exits
        trap 'printf "\033[0m\n\nDeleting temporary directory\n\n\t${CTMP_DIR}\n"; rm -rf "$CTMP_DIR";' EXIT
        printf "Beginning in a pristine environment\n"
        env -i bash --rcfile <(echo "CLEAN_ENV='True' \
          TERM=${TERM:-'xterm'} \
          PRISTINE_ENVIRONMENT=1 \
          METHODS=${METHODS:-opt} \
          METHOD=${METHOD:-opt} \
          MOOSE_JOBS=${MOOSE_JOBS:-6} \
          FULL_BUILD=${FULL_BUILD:-0} \
          RUN_CHECKS=${RUN_CHECKS:-0} \
          NO_FAILURE=${NO_FAILURE:-0} \
          VERBOSITY=${VERBOSITY:-0} \
          NO_COLOR=${NO_COLOR:-0} \
          CONDA_CHANNEL=${CONDA_CHANNEL:-'https://conda.software.inl.gov/public'} \
          REQUESTS_CA_BUNDLE=${REQUESTS_CA_BUNDLE:-''} \
          SSL_CERT_FILE=${SSL_CERT_FILE:-''} \
          CURL_CA_BUNDLE=${CURL_CA_BUNDLE:-''} \
          CTMP_DIR=${CTMP_DIR} \
          NO_ENVIRONMENT=1 \
          ${SCRIPT_DIR}/${BASH_SOURCE[0]}; exit")
        exit $?
    else
        # Set defaults
        export PRISTINE_ENVIRONMENT=${PRISTINE_ENVIRONMENT:-0}
        export FULL_BUILD=${FULL_BUILD:-0}
        export METHOD=${METHOD:-opt}
        export METHODS=${METHODS:-opt}
        export MOOSE_JOBS=${MOOSE_JOBS:-6}
        export RUN_CHECKS=${RUN_CHECKS:-0}
        export NO_FAILURE=${NO_FAILURE:-0}
        export VERBOSITY=${VERBOSITY:-0}
        export NO_COLOR=${NO_COLOR:-0}
        export CONDA_CHANNEL=${CONDA_CHANNEL:-'https://conda.software.inl.gov/public'}
        export REQUESTS_CA_BUNDLE=${REQUESTS_CA_BUNDLE:-''}
        export SSL_CERT_FILE=${SSL_CERT_FILE:-''}
        export CURL_CA_BUNDLE=${CURL_CA_BUNDLE:-''}
        export NO_ENVIRONMENT=${NO_ENVIRONMENT:-0}
    fi
fi

# Augment additional pristine environment variables
if [[ "${PRISTINE_ENVIRONMENT}" == "1" ]]; then
    trap 'ctl_c' INT
    # Further sandbox our environment
    export HOME=${CTMP_DIR}
    # Make our environment more sane
    export PATH=/bin:/usr/bin:/sbin
    if [[ "$(ecolor_support)" -ge 256 ]]; then
        export TERM=xterm-256color
    else
        export TERM=xterm
    fi
    # Make our environment safe
    umask 027
    # It's not enough to set these with --rcfile.
    # They must be exported to be inherited by child processes
    export CTMP_DIR REQUESTS_CA_BUNDLE SSL_CERT_FILE CURL_CA_BUNDLE
    print_sep
    printf 'Temporary Directory:\n%s\n' "${CTMP_DIR}"
fi

# Make print_environment available in any step
# shellcheck disable=SC1091
source "${SCRIPT_DIR}"/functions/diagnostic_environment.sh

# Do only the one thing if default behavior
if [[ "${NO_ENVIRONMENT}" == 0 ]]; then print_environment; exit; fi
# Do all the things
printf '
Note: The following steps will be performed in a temporary directory,
      and will be deleted when finished or upon encountering an error.

      The purpose of this tool is to determine if external factors
      are preventing you from building or running MOOSE.

      Errors encountered will usually mean network or hardware related
      causes (VPN, Network Proxies, Corporate SSL Certificates, etc).

      If diagnostics runs to completion without errors then likely the
      issue will be something in your environment as to the cause. If
      this is case, run %s again without any arguments, and
      carefully scrutinize the output.\n' "$(basename "$0")"
print_sep
# shellcheck disable=SC1091
source "${SCRIPT_DIR}"/functions/diagnostic_conda.sh
# shellcheck disable=SC1091
source "${SCRIPT_DIR}"/functions/diagnostic_application.sh
# shellcheck disable=SC1091
source "${SCRIPT_DIR}"/functions/diagnostic_tests.sh

# Get individual packages for now, until moose-mpi becomes available
export MOOSE_PACKAGES
MOOSE_PACKAGES="moose-mpi moose-libmesh-vtk moose-tools $(get_value 'default_mpi') \
 zlib python packaging pyaml jinja2"

install_conda
create_env
build_application
test_application

[milljm]

My guess is you ran curl (an example):

cd ~/offline/downloads
curl -L -O https://bitbucket.org/petsc/pkg-fblaslapack/get/v3.4.2-p3.tar.gz

while on the machine with no access to the internet?

This will produce the files, with nothing but HTML web content in them (explaining that the file could not be downloaded).

Can we verify that these files are indeed tarballs?

file /root/offline/downloads/hdf5-1.14.3-p1.tar.bz

Should report what kind of file it is.

[shin-chan-cpu]

My guess is you ran curl (an example):

Actually, I do use it on a computer with an internet connection

Should report what kind of file it is.

The results for me are shown below

./hdf5-1.14.3-p1.tar.bz:bzip2 compressed data, block size = 900k