Slurm cluster configuration test

perrymil · June 6, 2023, 9:00pm

Hi all,

Working off these instructions:

https://osc.github.io/ood-documentation/latest/installation/resource-manager/test.html

[perrymil@openondemanddev dashboard]$ sudo su perrymil -c 'source --trace /opt/ood/ondemand/enable; bin/rake test:jobs:exadev RAILS_ENV=production'
bash: line 0: source: --: invalid option
source: usage: source filename [arguments]
Could not find rails-6.1.7.3, jbuilder-2.11.5, byebug-11.1.3, capybara-3.39.0, dotenv-rails-2.8.1, redcarpet-3.6.0, bootstrap_form-4.5.0, local_time-1.0.3, jsbundling-rails-1.1.1, cssbundling-rails-1.1.2, ood_appkit-2.1.1, ood_core-0.23.5, pbs-2.2.1, rest-client-2.1.0, sinatra-contrib-3.0.6, actioncable-6.1.7.3, actionmailbox-6.1.7.3, actionmailer-6.1.7.3, actionpack-6.1.7.3, actiontext-6.1.7.3, actionview-6.1.7.3, activejob-6.1.7.3, activerecord-6.1.7.3, activestorage-6.1.7.3, railties-6.1.7.3, sprockets-rails-3.4.2, nokogiri-1.14.3, xpath-3.2.0, coffee-rails-5.0.0, lograge-0.12.0, ffi-1.15.5, http-cookie-1.0.5, nio4r-2.5.9, websocket-driver-0.7.5, mail-2.8.1, rails-dom-testing-2.0.3, rails-html-sanitizer-1.5.0, racc-1.6.2, domain_name-0.5.20190701, net-imap-0.3.4, loofah-2.20.0, unf-0.1.4, date-3.3.3, unf_ext-0.0.8.2 in any of the sources
Run `bundle install` to install missing gems.

I then tried the suggested bundle install:

$ sudo bundle install
Don't run Bundler as root. Bundler can ask for sudo if it is needed, and installing your bundle as root will break this application for all non-root
users on this machine.
Fetching gem metadata from https://rubygems.org/........
Using rake 13.0.6
Using zeitwerk 2.6.7
Using erubi 1.12.0
Using mini_portile2 2.8.1
Fetching racc 1.6.2
Using concurrent-ruby 1.2.2
Using crass 1.0.6
Using rack 2.2.6.4
Fetching nio4r 2.5.9
Using minitest 5.18.0
Using websocket-extensions 0.1.5
Using marcel 1.0.2
Using mini_mime 1.1.2
Fetching date 3.3.3
Using builder 3.2.4
Using timeout 0.3.2
Using public_suffix 5.0.1
Using execjs 2.8.1
Using browser 2.7.1
Using bundler 2.2.33
Fetching byebug 11.1.3
Installing racc 1.6.2 with native extensions
Installing date 3.3.3 with native extensions
Installing byebug 11.1.3 with native extensions
Installing nio4r 2.5.9 with native extensions
Using matrix 0.4.2
Using regexp_parser 2.7.0
Using childprocess 4.1.0
Using climate_control 0.2.0
Using coffee-script-source 1.12.2
Using method_source 1.0.0
Using thor 1.2.1
Using dalli 3.2.4
Fetching unf_ext 0.0.8.2
Installing unf_ext 0.0.8.2 with native extensions
Using dotenv 2.8.1
Fetching ffi 1.15.5
Using http-accept 1.7.0
Using mime-types-data 3.2023.0218.1
Using mocha 1.16.1
Using multi_json 1.15.0
Using ruby2_keywords 0.0.5
Using netrc 0.11.0
Using ood_support 0.0.5
Using rexml 3.2.5
Fetching redcarpet 3.6.0
Using rubyzip 2.3.2
Using websocket 1.2.9
Using tilt 2.1.0
Using timecop 0.9.6
Using webrick 1.8.1
Using zip_tricks 5.6.0
Using i18n 1.12.0
Using tzinfo 2.0.6
Using rack-test 2.1.0
Fetching websocket-driver 0.7.5
Installing websocket-driver 0.7.5 with native extensions
Installing redcarpet 3.6.0 with native extensions
Installing ffi 1.15.5 with native extensions
Using request_store 1.5.1
Using sprockets 4.2.0
Using rack-protection 3.0.6
Using net-protocol 0.2.1
Using addressable 2.8.4
Using coffee-script 2.4.1
Using autoprefixer-rails 10.2.5.1
Using mustermann 3.0.0
Using rss 0.2.9
Using selenium-webdriver 4.5.0
Using mime-types 3.4.1
Using net-pop 0.1.2
Using net-smtp 0.3.3
Using sinatra 3.0.6
Using activesupport 6.1.7.3
Fetching sinatra-contrib 3.0.6
Using globalid 1.1.0
Using activemodel 6.1.7.3
Using dotiw 5.3.3
Installing sinatra-contrib 3.0.6
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /usr/share/gems/gems/racc-1.6.2/ext/racc/cparse
/usr/bin/ruby -I /usr/share/rubygems -r ./siteconf20230606-36067-2cmepb.rb extconf.rb
checking for rb_block_call()... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
	--with-opt-dir
	--without-opt-dir
	--with-opt-include
	--without-opt-include=${opt-dir}/include
	--with-opt-lib
	--without-opt-lib=${opt-dir}/lib64
	--with-make-prog
	--without-make-prog
	--srcdir=.
	--curdir
	--ruby=/usr/bin/$(RUBY_BASE_NAME)
/usr/share/ruby/mkmf.rb:471:in `try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
	from /usr/share/ruby/mkmf.rb:564:in `try_link0'
	from /usr/share/ruby/mkmf.rb:582:in `try_link'
	from /usr/share/ruby/mkmf.rb:794:in `try_func'
	from /usr/share/ruby/mkmf.rb:1083:in `block in have_func'
	from /usr/share/ruby/mkmf.rb:971:in `block in checking_for'
	from /usr/share/ruby/mkmf.rb:361:in `block (2 levels) in postpone'
	from /usr/share/ruby/mkmf.rb:331:in `open'
	from /usr/share/ruby/mkmf.rb:361:in `block in postpone'
	from /usr/share/ruby/mkmf.rb:331:in `open'
	from /usr/share/ruby/mkmf.rb:357:in `postpone'
	from /usr/share/ruby/mkmf.rb:970:in `checking_for'
	from /usr/share/ruby/mkmf.rb:1082:in `have_func'
	from extconf.rb:6:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /usr/lib64/gems/ruby/racc-1.6.2/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /usr/share/gems/gems/racc-1.6.2 for inspection.
Results logged to /usr/lib64/gems/ruby/racc-1.6.2/gem_make.out

  /usr/share/rubygems/rubygems/ext/builder.rb:93:in `run'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:47:in `block in build'
  /usr/share/ruby/tempfile.rb:317:in `open'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:26:in `build'
  /usr/share/rubygems/rubygems/ext/builder.rb:159:in `build_extension'
  /usr/share/rubygems/rubygems/ext/builder.rb:193:in `block in build_extensions'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `each'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `build_extensions'
  /usr/share/rubygems/rubygems/installer.rb:837:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:71:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:28:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/source/rubygems.rb:204:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:54:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:16:in `install_from_spec'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:186:in `do_install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:177:in `block in worker_pool'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:62:in `apply_func'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:57:in `block in process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `loop'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:91:in `block (2 levels) in create_threads'

An error occurred while installing racc (1.6.2), and Bundler cannot continue.

In Gemfile:
  ood_appkit was resolved to 2.1.1, which depends on
    rails was resolved to 6.1.7.3, which depends on
      actioncable was resolved to 6.1.7.3, which depends on
        actionpack was resolved to 6.1.7.3, which depends on
          actionview was resolved to 6.1.7.3, which depends on
            rails-dom-testing was resolved to 2.0.3, which depends on
              nokogiri was resolved to 1.14.3, which depends on
                racc


Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /usr/share/gems/gems/nio4r-2.5.9/ext/nio4r
/usr/bin/ruby -I /usr/share/rubygems -r ./siteconf20230606-36067-o0a8yc.rb extconf.rb
checking for unistd.h... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
	--with-opt-dir
	--without-opt-dir
	--with-opt-include
	--without-opt-include=${opt-dir}/include
	--with-opt-lib
	--without-opt-lib=${opt-dir}/lib64
	--with-make-prog
	--without-make-prog
	--srcdir=.
	--curdir
	--ruby=/usr/bin/$(RUBY_BASE_NAME)
	--with-unistd-dir
	--without-unistd-dir
	--with-unistd-include
	--without-unistd-include=${unistd-dir}/include
	--with-unistd-lib
	--without-unistd-lib=${unistd-dir}/lib64
/usr/share/ruby/mkmf.rb:471:in `try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
	from /usr/share/ruby/mkmf.rb:613:in `try_cpp'
	from /usr/share/ruby/mkmf.rb:1124:in `block in have_header'
	from /usr/share/ruby/mkmf.rb:971:in `block in checking_for'
	from /usr/share/ruby/mkmf.rb:361:in `block (2 levels) in postpone'
	from /usr/share/ruby/mkmf.rb:331:in `open'
	from /usr/share/ruby/mkmf.rb:361:in `block in postpone'
	from /usr/share/ruby/mkmf.rb:331:in `open'
	from /usr/share/ruby/mkmf.rb:357:in `postpone'
	from /usr/share/ruby/mkmf.rb:970:in `checking_for'
	from /usr/share/ruby/mkmf.rb:1123:in `have_header'
	from extconf.rb:18:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /usr/lib64/gems/ruby/nio4r-2.5.9/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /usr/share/gems/gems/nio4r-2.5.9 for inspection.
Results logged to /usr/lib64/gems/ruby/nio4r-2.5.9/gem_make.out

  /usr/share/rubygems/rubygems/ext/builder.rb:93:in `run'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:47:in `block in build'
  /usr/share/ruby/tempfile.rb:317:in `open'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:26:in `build'
  /usr/share/rubygems/rubygems/ext/builder.rb:159:in `build_extension'
  /usr/share/rubygems/rubygems/ext/builder.rb:193:in `block in build_extensions'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `each'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `build_extensions'
  /usr/share/rubygems/rubygems/installer.rb:837:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:71:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:28:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/source/rubygems.rb:204:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:54:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:16:in `install_from_spec'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:186:in `do_install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:177:in `block in worker_pool'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:62:in `apply_func'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:57:in `block in process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `loop'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:91:in `block (2 levels) in create_threads'

An error occurred while installing nio4r (2.5.9), and Bundler cannot continue.

In Gemfile:
  ood_appkit was resolved to 2.1.1, which depends on
    rails was resolved to 6.1.7.3, which depends on
      actioncable was resolved to 6.1.7.3, which depends on
        nio4r


Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /usr/share/gems/gems/websocket-driver-0.7.5/ext/websocket-driver
/usr/bin/ruby -I /usr/share/rubygems -r ./siteconf20230606-36067-4p7jjx.rb extconf.rb
creating Makefile

current directory: /usr/share/gems/gems/websocket-driver-0.7.5/ext/websocket-driver
make DESTDIR\= clean
rm -f 
rm -f websocket_mask.so  *.o  *.bak mkmf.log .*.time

current directory: /usr/share/gems/gems/websocket-driver-0.7.5/ext/websocket-driver
make DESTDIR\=
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I.   -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2
-Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -m64 -o
websocket_mask.o -c websocket_mask.c
make: gcc: Command not found
make: *** [Makefile:245: websocket_mask.o] Error 127

make failed, exit code 2

Gem files will remain installed in /usr/share/gems/gems/websocket-driver-0.7.5 for inspection.
Results logged to /usr/lib64/gems/ruby/websocket-driver-0.7.5/gem_make.out

  /usr/share/rubygems/rubygems/ext/builder.rb:93:in `run'
  /usr/share/rubygems/rubygems/ext/builder.rb:44:in `block in make'
  /usr/share/rubygems/rubygems/ext/builder.rb:36:in `each'
  /usr/share/rubygems/rubygems/ext/builder.rb:36:in `make'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:63:in `block in build'
  /usr/share/ruby/tempfile.rb:317:in `open'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:26:in `build'
  /usr/share/rubygems/rubygems/ext/builder.rb:159:in `build_extension'
  /usr/share/rubygems/rubygems/ext/builder.rb:193:in `block in build_extensions'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `each'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `build_extensions'
  /usr/share/rubygems/rubygems/installer.rb:837:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:71:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:28:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/source/rubygems.rb:204:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:54:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:16:in `install_from_spec'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:186:in `do_install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:177:in `block in worker_pool'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:62:in `apply_func'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:57:in `block in process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `loop'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:91:in `block (2 levels) in create_threads'

An error occurred while installing websocket-driver (0.7.5), and Bundler cannot continue.

In Gemfile:
  ood_appkit was resolved to 2.1.1, which depends on
    rails was resolved to 6.1.7.3, which depends on
      actioncable was resolved to 6.1.7.3, which depends on
        websocket-driver


Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /usr/share/gems/gems/date-3.3.3/ext/date
/usr/bin/ruby -I /usr/share/rubygems -r ./siteconf20230606-36067-dfteq4.rb extconf.rb
checking for rb_category_warn()... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
	--with-opt-dir
	--without-opt-dir
	--with-opt-include
	--without-opt-include=${opt-dir}/include
	--with-opt-lib
	--without-opt-lib=${opt-dir}/lib64
	--with-make-prog
	--without-make-prog
	--srcdir=.
	--curdir
	--ruby=/usr/bin/$(RUBY_BASE_NAME)
/usr/share/ruby/mkmf.rb:471:in `try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
	from /usr/share/ruby/mkmf.rb:564:in `try_link0'
	from /usr/share/ruby/mkmf.rb:582:in `try_link'
	from /usr/share/ruby/mkmf.rb:794:in `try_func'
	from /usr/share/ruby/mkmf.rb:1083:in `block in have_func'
	from /usr/share/ruby/mkmf.rb:971:in `block in checking_for'
	from /usr/share/ruby/mkmf.rb:361:in `block (2 levels) in postpone'
	from /usr/share/ruby/mkmf.rb:331:in `open'
	from /usr/share/ruby/mkmf.rb:361:in `block in postpone'
	from /usr/share/ruby/mkmf.rb:331:in `open'
	from /usr/share/ruby/mkmf.rb:357:in `postpone'
	from /usr/share/ruby/mkmf.rb:970:in `checking_for'
	from /usr/share/ruby/mkmf.rb:1082:in `have_func'
	from extconf.rb:6:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /usr/lib64/gems/ruby/date-3.3.3/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /usr/share/gems/gems/date-3.3.3 for inspection.
Results logged to /usr/lib64/gems/ruby/date-3.3.3/gem_make.out

  /usr/share/rubygems/rubygems/ext/builder.rb:93:in `run'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:47:in `block in build'
  /usr/share/ruby/tempfile.rb:317:in `open'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:26:in `build'
  /usr/share/rubygems/rubygems/ext/builder.rb:159:in `build_extension'
  /usr/share/rubygems/rubygems/ext/builder.rb:193:in `block in build_extensions'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `each'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `build_extensions'
  /usr/share/rubygems/rubygems/installer.rb:837:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:71:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:28:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/source/rubygems.rb:204:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:54:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:16:in `install_from_spec'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:186:in `do_install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:177:in `block in worker_pool'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:62:in `apply_func'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:57:in `block in process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `loop'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:91:in `block (2 levels) in create_threads'

An error occurred while installing date (3.3.3), and Bundler cannot continue.

In Gemfile:
  ood_appkit was resolved to 2.1.1, which depends on
    rails was resolved to 6.1.7.3, which depends on
      actionmailbox was resolved to 6.1.7.3, which depends on
        mail was resolved to 2.8.1, which depends on
          net-imap was resolved to 0.3.4, which depends on
            date


Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /usr/share/gems/gems/byebug-11.1.3/ext/byebug
/usr/bin/ruby -I /usr/share/rubygems -r ./siteconf20230606-36067-8e9868.rb extconf.rb
creating Makefile

current directory: /usr/share/gems/gems/byebug-11.1.3/ext/byebug
make DESTDIR\= clean
rm -f 
rm -f byebug.so  *.o  *.bak mkmf.log .*.time

current directory: /usr/share/gems/gems/byebug-11.1.3/ext/byebug
make DESTDIR\=
gcc -I. -I/usr/include -I/usr/include/ruby/backward -I/usr/include -I.   -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2
-Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -m64 -o
breakpoint.o -c breakpoint.c
make: gcc: Command not found
make: *** [Makefile:245: breakpoint.o] Error 127

make failed, exit code 2

Gem files will remain installed in /usr/share/gems/gems/byebug-11.1.3 for inspection.
Results logged to /usr/lib64/gems/ruby/byebug-11.1.3/gem_make.out

  /usr/share/rubygems/rubygems/ext/builder.rb:93:in `run'
  /usr/share/rubygems/rubygems/ext/builder.rb:44:in `block in make'
  /usr/share/rubygems/rubygems/ext/builder.rb:36:in `each'
  /usr/share/rubygems/rubygems/ext/builder.rb:36:in `make'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:63:in `block in build'
  /usr/share/ruby/tempfile.rb:317:in `open'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:26:in `build'
  /usr/share/rubygems/rubygems/ext/builder.rb:159:in `build_extension'
  /usr/share/rubygems/rubygems/ext/builder.rb:193:in `block in build_extensions'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `each'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `build_extensions'
  /usr/share/rubygems/rubygems/installer.rb:837:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:71:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:28:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/source/rubygems.rb:204:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:54:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:16:in `install_from_spec'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:186:in `do_install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:177:in `block in worker_pool'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:62:in `apply_func'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:57:in `block in process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `loop'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:91:in `block (2 levels) in create_threads'

An error occurred while installing byebug (11.1.3), and Bundler cannot continue.

In Gemfile:
  byebug


Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /usr/share/gems/gems/unf_ext-0.0.8.2/ext/unf_ext
/usr/bin/ruby -I /usr/share/rubygems -r ./siteconf20230606-36067-cfwpkd.rb extconf.rb
checking for -lstdc++... *** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
	--with-opt-dir
	--without-opt-dir
	--with-opt-include
	--without-opt-include=${opt-dir}/include
	--with-opt-lib
	--without-opt-lib=${opt-dir}/lib64
	--with-make-prog
	--without-make-prog
	--srcdir=.
	--curdir
	--ruby=/usr/bin/$(RUBY_BASE_NAME)
	--with-static-libstdc++
	--without-static-libstdc++
	--with-stdc++-dir
	--without-stdc++-dir
	--with-stdc++-include
	--without-stdc++-include=${stdc++-dir}/include
	--with-stdc++-lib
	--without-stdc++-lib=${stdc++-dir}/lib64
	--with-stdc++lib
	--without-stdc++lib
/usr/share/ruby/mkmf.rb:471:in `try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
	from /usr/share/ruby/mkmf.rb:564:in `try_link0'
	from /usr/share/ruby/mkmf.rb:582:in `try_link'
	from /usr/share/ruby/mkmf.rb:801:in `try_func'
	from /usr/share/ruby/mkmf.rb:1029:in `block in have_library'
	from /usr/share/ruby/mkmf.rb:971:in `block in checking_for'
	from /usr/share/ruby/mkmf.rb:361:in `block (2 levels) in postpone'
	from /usr/share/ruby/mkmf.rb:331:in `open'
	from /usr/share/ruby/mkmf.rb:361:in `block in postpone'
	from /usr/share/ruby/mkmf.rb:331:in `open'
	from /usr/share/ruby/mkmf.rb:357:in `postpone'
	from /usr/share/ruby/mkmf.rb:970:in `checking_for'
	from /usr/share/ruby/mkmf.rb:1024:in `have_library'
	from extconf.rb:6:in `<main>'

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /usr/lib64/gems/ruby/unf_ext-0.0.8.2/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /usr/share/gems/gems/unf_ext-0.0.8.2 for inspection.
Results logged to /usr/lib64/gems/ruby/unf_ext-0.0.8.2/gem_make.out

  /usr/share/rubygems/rubygems/ext/builder.rb:93:in `run'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:47:in `block in build'
  /usr/share/ruby/tempfile.rb:317:in `open'
  /usr/share/rubygems/rubygems/ext/ext_conf_builder.rb:26:in `build'
  /usr/share/rubygems/rubygems/ext/builder.rb:159:in `build_extension'
  /usr/share/rubygems/rubygems/ext/builder.rb:193:in `block in build_extensions'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `each'
  /usr/share/rubygems/rubygems/ext/builder.rb:190:in `build_extensions'
  /usr/share/rubygems/rubygems/installer.rb:837:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:71:in `build_extensions'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/rubygems_gem_installer.rb:28:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/source/rubygems.rb:204:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:54:in `install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/gem_installer.rb:16:in `install_from_spec'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:186:in `do_install'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/installer/parallel_installer.rb:177:in `block in worker_pool'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:62:in `apply_func'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:57:in `block in process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `loop'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:54:in `process_queue'
  /usr/share/gems/gems/bundler-2.2.33/lib/bundler/worker.rb:91:in `block (2 levels) in create_threads'

An error occurred while installing unf_ext (0.0.8.2), and Bundler cannot continue.

In Gemfile:
  rest-client was resolved to 2.1.0, which depends on
    http-cookie was resolved to 1.0.5, which depends on
      domain_name was resolved to 0.5.20190701, which depends on
        unf was resolved to 0.1.4, which depends on
          unf_ext

perrymil · June 6, 2023, 9:00pm

This is on a newly provisioned RHEL 8.8 VM. It looks like I need to figure out how to install those missing ruby gems?

“You have to install development tools first.”

This seems to suggest installing ruby development tools?

dnf install ruby-devel

Appears to have reduced the amount of errors…

dnf install ruby-build

[perrymil@openondemanddev dashboard]$ bundle install
Ignoring byebug-11.1.3 because its extensions are not built. Try: gem pristine byebug --version 11.1.3
Ignoring date-3.3.3 because its extensions are not built. Try: gem pristine date --version 3.3.3
Ignoring ffi-1.15.5 because its extensions are not built. Try: gem pristine ffi --version 1.15.5
Ignoring nio4r-2.5.9 because its extensions are not built. Try: gem pristine nio4r --version 2.5.9
Ignoring racc-1.6.2 because its extensions are not built. Try: gem pristine racc --version 1.6.2
Ignoring redcarpet-3.6.0 because its extensions are not built. Try: gem pristine redcarpet --version 3.6.0
Ignoring unf_ext-0.0.8.2 because its extensions are not built. Try: gem pristine unf_ext --version 0.0.8.2
Ignoring websocket-driver-0.7.5 because its extensions are not built. Try: gem pristine websocket-driver --version 0.7.5
Fetching gem metadata from https://rubygems.org/........
Using rake 13.0.6
Following files may not be writable, so sudo is needed:
  /usr/bin
  /usr/share/gems
  /usr/share/gems/build_info
  /usr/share/gems/cache
  /usr/share/gems/doc
  /usr/share/gems/extensions
  /usr/share/gems/gems
  /usr/share/gems/plugins
  /usr/share/gems/specifications
Using minitest 5.18.0
Using zeitwerk 2.6.7
Using mini_portile2 2.8.1
Using concurrent-ruby 1.2.2
Using erubi 1.12.0
Using builder 3.2.4
Using crass 1.0.6
Using rack 2.2.6.4
Using websocket-extensions 0.1.5
Using marcel 1.0.2
Using mini_mime 1.1.2
Using timeout 0.3.2
Using public_suffix 5.0.1
Fetching racc 1.6.2
Using execjs 2.8.1
Fetching nio4r 2.5.9
Fetching date 3.3.3
Using browser 2.7.1
Using bundler 2.2.33
Fetching byebug 11.1.3
Installing racc 1.6.2 with native extensions
Installing date 3.3.3 with native extensions
Installing nio4r 2.5.9 with native extensions
Installing byebug 11.1.3 with native extensions
Using matrix 0.4.2
Using regexp_parser 2.7.0
Using childprocess 4.1.0
Using climate_control 0.2.0
Using coffee-script-source 1.12.2
Using method_source 1.0.0
Using thor 1.2.1
Using dalli 3.2.4
Fetching unf_ext 0.0.8.2
Installing unf_ext 0.0.8.2 with native extensions
Using dotenv 2.8.1
Fetching ffi 1.15.5
Installing ffi 1.15.5 with native extensions
Using http-accept 1.7.0
Using mime-types-data 3.2023.0218.1
Using mocha 1.16.1
Using multi_json 1.15.0
Using ruby2_keywords 0.0.5
Using netrc 0.11.0
Using ood_support 0.0.5
Using rexml 3.2.5
Fetching redcarpet 3.6.0
Installing redcarpet 3.6.0 with native extensions
Using rubyzip 2.3.2
Using websocket 1.2.9
Using tilt 2.1.0
Using timecop 0.9.6
Using webrick 1.8.1
Using zip_tricks 5.6.0
Using i18n 1.12.0
Using tzinfo 2.0.6
Using rack-test 2.1.0
Fetching websocket-driver 0.7.5
Installing websocket-driver 0.7.5 with native extensions
Using request_store 1.5.1
Using sprockets 4.2.0
Using rack-protection 3.0.6
Using net-protocol 0.2.1
Using addressable 2.8.4
Using autoprefixer-rails 10.2.5.1
Using nokogiri 1.14.3 (x86_64-linux)
Using coffee-script 2.4.1
Using mime-types 3.4.1
Using mustermann 3.0.0
Using rss 0.2.9
Using activesupport 6.1.7.3
Using unf 0.1.4
Using selenium-webdriver 4.5.0
Using rails-dom-testing 2.0.3
Using loofah 2.20.0
Using globalid 1.1.0
Using activemodel 6.1.7.3
Using net-pop 0.1.2
Using net-smtp 0.3.3
Using xpath 3.2.0
Using domain_name 0.5.20190701
Using dotiw 5.3.3
Using sinatra 3.0.6
Using rails-html-sanitizer 1.5.0
Using activejob 6.1.7.3
Using activerecord 6.1.7.3
Using capybara 3.39.0
Using http-cookie 1.0.5
Using sinatra-contrib 3.0.6
Using rest-client 2.1.0
Using actionview 6.1.7.3
Using actionpack 6.1.7.3
Using jbuilder 2.11.5
Using actioncable 6.1.7.3
Using activestorage 6.1.7.3
Using bootstrap_form 4.5.0
Using railties 6.1.7.3
Using sprockets-rails 3.4.2
Using actiontext 6.1.7.3
Using coffee-rails 5.0.0
Using cssbundling-rails 1.1.2
Using dotenv-rails 2.8.1
Using jsbundling-rails 1.1.1
Using lograge 0.12.0
Using local_time 1.0.3
Using net-imap 0.3.4
Using mail 2.8.1
Using actionmailbox 6.1.7.3
Using actionmailer 6.1.7.3
Using rails 6.1.7.3
Using ood_core 0.23.5
Using pbs 2.2.1
Using ood_appkit 2.1.1
Bundle complete! 31 Gemfile dependencies, 105 gems now installed.
Gems in the group 'doc' were not installed.
Use `bundle info [gemname]` to see where a bundled gem is installed.

Progress, but its currently failing to install:

byebug-11.1.3, redcarpet-3.6.0, ffi-1.15.5, nio4r-2.5.9, websocket-driver-0.7.5, racc-1.6.2, date-3.3.3, unf_ext-0.0.8.2

Ignoring byebug-11.1.3 because its extensions are not built. Try: gem pristine byebug --version 11.1.3
Ignoring date-3.3.3 because its extensions are not built. Try: gem pristine date --version 3.3.3
Ignoring ffi-1.15.5 because its extensions are not built. Try: gem pristine ffi --version 1.15.5
Ignoring nio4r-2.5.9 because its extensions are not built. Try: gem pristine nio4r --version 2.5.9
Ignoring racc-1.6.2 because its extensions are not built. Try: gem pristine racc --version 1.6.2
Ignoring redcarpet-3.6.0 because its extensions are not built. Try: gem pristine redcarpet --version 3.6.0
Ignoring unf_ext-0.0.8.2 because its extensions are not built. Try: gem pristine unf_ext --version 0.0.8.2
Ignoring websocket-driver-0.7.5 because its extensions are not built. Try: gem pristine websocket-driver --version 0.7.5

I reinstalled all of those gems? Now its no longer asking for those gems when I run:

[perrymil@openondemanddev dashboard]$ 'source /opt/ood/ondemand/enable; bin/rake --trace test:jobs:exadev RAILS_ENV=production'
-bash: source /opt/ood/ondemand/enable; bin/rake --trace test:jobs:exadev RAILS_ENV=production: No such file or directory
[perrymil@openondemanddev dashboard]$ sudo su perrymil -c 'source /opt/ood/ondemand/enable; bin/rake --trace test:jobs:exadev RAILS_ENV=production'
** Invoke test:jobs:exadev (first_time)
** Invoke environment (first_time)
** Execute environment
Rails Error: Unable to access log file. Please ensure that /var/www/ood/apps/sys/dashboard/log/production.log exists and is writable (ie, make it writable for user and group: chmod 0664 /var/www/ood/apps/sys/dashboard/log/production.log). The log level has been raised to WARN and the output directed to STDERR until the problem is fixed.
** Invoke /home/perrymil/test_jobs (first_time, not_needed)
** Execute test:jobs:exadev
Testing cluster 'exadev'...
Submitting job...
[2023-06-06 17:19:03 -0400 ]  INFO "execve = [{\"SLURM_CONF\"=>\"/etc/slurm/slurm.conf\"}, \"/usr/bin/sbatch\", \"-D\", \"/home/perrymil/test_jobs\", \"-J\", \"test_jobs_exadev\", \"-o\", \"/home/perrymil/test_jobs/output_exadev_2023_06_06t17_19_03_04_00_log\", \"-t\", \"00:01:00\", \"--export\", \"NONE\", \"--parsable\"]"
rake aborted!
Errno::ENOENT: No such file or directory - /usr/bin/sbatch
/usr/share/ruby/open3.rb:221:in `spawn'
/usr/share/ruby/open3.rb:221:in `popen_run'
/usr/share/ruby/open3.rb:102:in `popen3'
/usr/share/ruby/open3.rb:289:in `capture3'
/var/www/ood/apps/sys/dashboard/config/initializers/open3_extensions.rb:4:in `capture3'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/ood_core-0.23.5/lib/ood_core/job/adapters/slurm.rb:386:in `call'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/ood_core-0.23.5/lib/ood_core/job/adapters/slurm.rb:266:in `submit_string'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/ood_core-0.23.5/lib/ood_core/job/adapters/slurm.rb:527:in `submit'
/var/www/ood/apps/sys/dashboard/lib/tasks/test.rake:31:in `block (4 levels) in <top (required)>'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/task.rb:281:in `block in execute'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/task.rb:281:in `each'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/task.rb:281:in `execute'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/task.rb:219:in `block in invoke_with_call_chain'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/task.rb:199:in `synchronize'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/task.rb:199:in `invoke_with_call_chain'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/task.rb:188:in `invoke'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/application.rb:160:in `invoke_task'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/application.rb:116:in `block (2 levels) in top_level'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/application.rb:116:in `each'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/application.rb:116:in `block in top_level'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/application.rb:125:in `run_with_threads'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/application.rb:110:in `top_level'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/application.rb:83:in `block in run'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/application.rb:186:in `standard_exception_handling'
/opt/ood/ondemand/root/usr/share/gems/3.0/ondemand/3.0.1-1/gems/rake-13.0.6/lib/rake/application.rb:80:in `run'
bin/rake:10:in `<main>'
Tasks: TOP => test:jobs:exadev

But its still not working…

jeff.ohrstrom · June 7, 2023, 2:02pm

You shouldn’t have to install any new gems, only source that file so that the gems that we’ve installed are available to you. Your last comment seems to be working from our side.

This is happening because you’ve installed gems that are somehow incompatible with the ruby you’re currently running. They can be ignored.

Ignoring byebug-11.1.3 because its extensions are not built. Try: gem pristine byebug --version 11.1.3

We cannot submit the job because there is no sbatch binary installed on the machine.

[2023-06-06 17:19:03 -0400 ]  INFO "execve = [{\"SLURM_CONF\"=>\"/etc/slurm/slurm.conf\"}, \"/usr/bin/sbatch\", \"-D\", \"/home/perrymil/test_jobs\", \"-J\", \"test_jobs_exadev\", \"-o\", \"/home/perrymil/test_jobs/output_exadev_2023_06_06t17_19_03_04_00_log\", \"-t\", \"00:01:00\", \"--export\", \"NONE\", \"--parsable\"]"
rake aborted!
Errno::ENOENT: No such file or directory - /usr/bin/sbatch

The host you installed OnDemand on needs access to the binaries that launch jobs. Either directly (i.e., the binaries are on the same host) or through the submit_host configuration in the cluster.d cluster file (it’ll ssh into that host and issue commands).

perrymil · June 7, 2023, 8:08pm

Hi Jeff,

Thanks for the clarification.

The documentation at Slurm — Open OnDemand 3.0.3 documentation doesn’t quite make that clear.

If I were to have read something like, “If your slurm headnode is different than the host you are running on open ondemand on, then you will need to use the optional submit_host configuration option to submit jobs to the slurm scheduler via ssh”.

e.g. submit_host: headnodeHostname

But maybe that information is already present somewhere else in the docs? It would be helpful if there was some sort of expected setup diagram indicating that the docs assume the open ondemand service is running on the same host as the headnode.

Oh, and that error message doesn’t indicate to me that it is looking locally for the slurm commands. It would be nice to include something indicating that its looking for the command on the localhost machine, and doesn’t default to trying to ssh to the hostname specified in the login: hostname configuration? Maybe I am just trying a weird setup with the headnode and the ondemand node being different hosts?

I added:

  job:
    adapter: "slurm"
#    cluster: ""
    bin: "/usr/bin"
    conf: "/etc/slurm/slurm.conf"
    submit_host: "exadev.ohsu.edu"

And now its complaining about the host key verification failing. I have previously connected to the host in question using my user account on the ondemand host, do I need to specify that the key is acceptable somewhere in the cluster.yml file?

OodCore::JobAdapterError: No ECDSA host key is known for exadev.ohsu.edu and you have requested strict checking.

jeff.ohrstrom · June 7, 2023, 8:33pm

Yea sorry that’s not documented clearly (or at all).

The issue with the key is just that - the system is attempting to ssh to that submit_host and cannot use any key.

You have 2 options:

enabling host based authentication so that all the hosts knkow about each other
use the strict_host_checking: false in the same location as submit_host to disable host checking.

That said - without keys it may not work for all users. That is, if you have a key personally and are using it to ssh from the web node (where your OOD is installed) to your submit host, it may not work for other folks who do not have ssh keys.

Yea another thing that is not well documented. OnDemand issues commands to schedule and query for jobs, like sbatch and squeue. Either these commands need to be available on the same system that OnDemand is installed or you need seemless ssh from that host to another that can issue the same commands.

perrymil · June 7, 2023, 8:39pm

Ah, that makes sense.

I am going to give this a try, and will let you know if it works.

perrymil · June 20, 2023, 9:11pm

We ended up going with installing the slurm binaries on the VM, and copying the munge key over.

I am getting an error related to the dex service now.

 failed to initialize storage: failed to perform migrations: creating migration table: unable to open database file: no such file or directory

Which I think means that dex either doesn’t know which database to create the migration table in, or I don’t have a valid database installed?

https://dexidp.io/docs/storage/

Looks like I need to install a sql database. I went ahead and installed and configured mysql 8.0

I suppose I need to tell dex what database to use now?

There is a configuration item in /etc/ood/config/ood_portal.yml

storage_file: /etc/ood/dex/dex.db

Which doesn’t currently exist. I created the dex db user and database… I think?

[root@openondemanddev etc]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 8
Server version: 8.0.32 Source distribution

Copyright (c) 2000, 2023, Oracle and/or its affiliates.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> CREATE DATABASE dex_db;
Query OK, 1 row affected (0.00 sec)

mysql> CREATE USER dex IDENTIFIED BY 'REDACTED';
Query OK, 0 rows affected (0.00 sec)

mysql> GRANT ALL PRIVILEGES ON dex_db.* TO dex;
Query OK, 0 rows affected (0.00 sec)

But /var/lib/mysql/dex_db is empty…

perrymil · June 22, 2023, 12:02am

@jeff.ohrstrom Wasn’t sure if you saw my most recent message. When you get the chance can you advise on how best to configure ondemand-dex to make use of the dex_db mysql database?

jeff.ohrstrom · July 5, 2023, 4:45pm

Odd you seem to have the same issue as this topic. Look at it and do the same. the location you’re looking for is /etc/ood/config/dex I believe. I believe it’s either a straight permissions issue or an SELinux issue.

jeff.ohrstrom · July 5, 2023, 4:46pm

And sorry, I was in a summer camp for 2 weeks then on vacation for another so that’s why there was a delay.

system · January 1, 2024, 4:46pm

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