Adds a patch to ATLAS for grep 3.8+

README.md

@@ -19,6 +19,13 @@ Currently supported OSes:
   - Ubuntu (20.04+)
   - Raspberry Pi OS (11+)
   - Debian (11+)
+  - Rocky Linux (9+)
+  - AlmaLinux (9+)
+  - CentOS Stream(9+)
+  - RHEL (9+)
+  - Fedora (38+)
+  - Arch Linux
+  - Manjaro
 
 Other OSes may need a few tweaks to work correctly. You can also run the playbook inside Docker (see the note under 'Benchmarking - Single Node'), but performance will be artificially limited.
 
@@ -33,6 +40,10 @@ Each host should be reachable via SSH using the username set in `ansible_user`.
 
 Tweak other settings inside `config.yml` as desired (the most important being `hpl_root`—this is where the compiled MPI, ATLAS, and HPL benchmarking code will live).
 
+> **Note**:
+> The names of the nodes inside `hosts.ini` must match the hostname of their corresponding node; otherwise, the benchmark will hang when you try to run it in a cluster. 
+> For example, if you have `node-01.local` in your `hosts.ini` your host's hostname should be `node-01` and not something else like `raspberry-pi`.
+
 Then run the benchmarking playbook inside this directory:
 
 ```

dependencies/arch-based.yml

@@ -0,0 +1,12 @@
+- name: Update pacman cache.
+  community.general.pacman:
+    update_cache: true
+  become: true
+
+- name: Install dependencies.
+  ansible.builtin.package:
+    name:
+      - base-devel
+      - gcc-fortran
+    state: present
+  become: true

dependencies/debian-based.yml

@@ -0,0 +1,14 @@
+- name: Update apt cache.
+  ansible.builtin.apt:
+    update_cache: true
+    cache_valid_time: 600
+  become: true
+
+- name: Install dependencies.
+  ansible.builtin.package:
+    name:
+      - build-essential
+      - gfortran
+      - automake
+    state: present
+  become: true

dependencies/rhel-based.yml

@@ -0,0 +1,15 @@
+- name: Update dnf cache.
+  ansible.builtin.dnf:
+    update_cache: true
+  become: true
+
+- name: Install dependencies.
+  ansible.builtin.package:
+    name:
+      - '@Development Tools'
+      - gcc-gfortran
+      # Fedora, at least Fedora Server, doesn't install this 
+      # with the Development Tools group for some reason
+      - gcc-g++
+    state: present
+  become: true

firewall/configure-firewall.yml

@@ -0,0 +1,30 @@
+- name: Creating new custom firewall zone.
+  ansible.posix.firewalld:
+    zone: top500
+    permanent: true
+    state: present
+  become: true
+
+- name: Setting custom firewall zone to accept connections.
+  ansible.posix.firewalld:
+    zone: top500
+    target: ACCEPT
+    state: enabled
+    permanent: true
+  become: true
+
+- name: Adding nodes as trusted sources in the firewall.
+  ansible.posix.firewalld:
+    source: "{{ item }}"
+    zone: top500
+    state: enabled
+    permanent: true
+  loop: "{{ host_ips }}"
+  when: item != ansible_default_ipv4.address
+  become: true
+
+- name: Restarting firewall for changes to take effect.
+  ansible.builtin.service:
+    name: firewalld
+    state: restarted
+  become: true

firewall/reset-firewall.yml

@@ -0,0 +1,20 @@
+# Remove our custom firewall zone since we don't need it anymore
+- name: Reverting firewall back to its original state.
+  ansible.posix.firewalld:
+    zone: top500
+    state: absent
+    permanent: true
+  become: true
+
+- name: Restarting firewall for changes to take effect.
+  ansible.builtin.service:
+    name: firewalld
+    state: restarted
+  become: true
+
+# When removing a custom firewall zone, a .xml.old file will sometimes remain
+- name: Cleaning up firewall rules.
+  ansible.builtin.file:
+    path: /etc/firewalld/zones/top500.xml.old
+    state: absent
+  become: true

main.yml

@@ -12,21 +12,14 @@
   vars_files: ['config.yml']
 
   tasks:
-    - name: Update apt cache.
-      ansible.builtin.apt:
-        update_cache: true
-        cache_valid_time: 600
+    - include_tasks: dependencies/rhel-based.yml
+      when: ansible_os_family == 'RedHat'
+
+    - include_tasks: dependencies/debian-based.yml
       when: ansible_os_family == 'Debian'
-      become: true
 
-    - name: Install dependencies.
-      ansible.builtin.package:
-        name:
-          - build-essential
-          - gfortran
-          - automake
-        state: present
-      become: true
+    - include_tasks: dependencies/arch-based.yml
+      when: ansible_os_family == 'Archlinux'
 
     - name: Create required temporary directories.
       ansible.builtin.file:
@@ -89,6 +82,24 @@
         remote_src: true
         creates: "{{ hpl_root }}/tmp/ATLAS/README"
 
+    # The source code for the configure script that ATLAS uses makes calls
+    # with fgrep to find information about the system from its various 
+    # outputs to set the configuration accordingly. However, 
+    # grep versions 3.8+ throw the following warning when calling fgrep:
+    # 'fgrep: warning: fgrep is obsolescent; using grep -F'
+    # This occurs as output from fgrep which causes the ATLAS configuration 
+    # to get invalid return values, causing the configuration to fail 
+    # due to it assuming the first value is the number it's looking for.
+    #
+    # If the version of grep is 3.8 or newer, we have to patch the ATLAS 
+    # source code to get rid of the warning produced by fgrep.
+    - name: Checking installed software.
+      package_facts:
+        manager: auto
+
+    - include_tasks: patch-atlas-src.yml
+      when: ansible_facts.packages['grep'][0].version is version("3.8", ">=")
+
     - name: Install ATLAS (takes a LONG time).
       ansible.builtin.command: "{{ item }}"
       args:
@@ -210,12 +221,20 @@
         dest: "{{ hpl_root }}/tmp/hpl-2.3/bin/rpi/HPL.dat"
         mode: 0644
 
+    # If this is not done, the nodes will fail to connect to each other
+    # causing the playbook to hang at 'Run the benchmark.'
+    - include_tasks: firewall/configure-firewall.yml
+      when: ansible_os_family == "RedHat"
+
     - name: Run the benchmark.
       ansible.builtin.command: mpirun -f cluster-hosts ./xhpl
       args:
         chdir: "{{ hpl_root }}/tmp/hpl-2.3/bin/rpi"
       register: mpirun_output
       run_once: true
 
+    - include_tasks: firewall/reset-firewall.yml
+      when: ansible_os_family == "RedHat"
+
     - name: Output the results.
       debug: var=mpirun_output.stdout

patch-atlas-src.yml

@@ -0,0 +1,40 @@
+- name: Checking to see if patches need to be applied.
+  ansible.builtin.stat:
+    path: "{{ hpl_root }}/tmp/ATLAS_PATCHING_COMPLETE"
+  register: no_patches_needed
+
+# Fixes fgrep warning being added to output and causing
+# the ATLAS configuration to fail to identify aspects of 
+# the given node
+- name: Patching ATLAS source code (Part 1).
+  ansible.builtin.replace:
+    path: "{{ hpl_root }}tmp/ATLAS/CONFIG/include/atlas_sys.h"
+    regexp: '2>&1'
+    replace: '2>/dev/null'
+  when: no_patches_needed.stat.exists == false
+
+# Fixes 'free(): invalid pointer' error during
+# ATLAS configuration
+- name: Patching ATLAS source code (Part 2).
+  ansible.builtin.lineinfile:
+    path: "{{ hpl_root }}tmp/ATLAS/CONFIG/src/probe_comp.c"
+    insertbefore: 'free\(cmnd\)'
+    line: '   printf("\n");'
+    firstmatch: true
+  when: no_patches_needed.stat.exists == false
+
+# Fixes 'corrupted size vs. prev_size' error during 
+# ATLAS configuration
+- name: Patching ATLAS source code (Part 3).
+  ansible.builtin.lineinfile:
+    path: "{{ hpl_root }}tmp/ATLAS/CONFIG/include/atlas_sys.h"
+    insertbefore: 'if \(fgets\(sout, len, fpin\)\)'
+    line: '   printf("\n");'
+    firstmatch: true
+  when: no_patches_needed.stat.exists == false
+
+- name: Create 'ATLAS_PATCHING_COMPLETE' file.
+  ansible.builtin.file:
+    path: "{{ hpl_root }}/tmp/ATLAS_PATCHING_COMPLETE"
+    state: touch
+    mode: 0644