From 5f3c3bbdb81965e203362a0c4e595a94a88182ea Mon Sep 17 00:00:00 2001
From: Evi Vanoost <vanooste@rcbi.rochester.edu>
Date: Mon, 26 Aug 2024 15:13:15 -0400
Subject: [PATCH] Add singularity_options to the native structure. This allows
 containers to specify additional options for Singularity such as --nv for
 nVIDIA GPU and --rocm for AMD GPU or --bind /etc/OpenCL for OpenCL (in
 combination with one of the prior).

---
 lib/ood_core/job/adapters/linux_host/launcher.rb         | 9 ++++++++-
 .../adapters/linux_host/templates/script_wrapper.erb.sh  | 2 +-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/lib/ood_core/job/adapters/linux_host/launcher.rb b/lib/ood_core/job/adapters/linux_host/launcher.rb
index ae3b10e12..0536f6513 100644
--- a/lib/ood_core/job/adapters/linux_host/launcher.rb
+++ b/lib/ood_core/job/adapters/linux_host/launcher.rb
@@ -170,6 +170,7 @@ def wrapped_script(script, session_name)
         'script_timeout' => script_timeout(script),
         'session_name' => session_name,
         'singularity_bin' => singularity_bin,
+        'singularity_options' => singularity_options(script.native),
         'singularity_image' => singularity_image(script.native),
         'ssh_hosts' => ssh_hosts,
         'tmux_bin' => tmux_bin,
@@ -205,6 +206,12 @@ def singularity_bindpath(native)
     native[:singularity_bindpath]
   end
 
+  def singularity_options(native)
+    return '' unless native && native[:singularity_options]
+
+    native[:singularity_options]
+  end
+
   def script_timeout(script)
     wall_time = script.wall_time.to_i
     return site_timeout if wall_time == 0
@@ -294,4 +301,4 @@ def parse_hostname(output)
     end.compact.last.to_s
   end
 
-end
+end
\ No newline at end of file
diff --git a/lib/ood_core/job/adapters/linux_host/templates/script_wrapper.erb.sh b/lib/ood_core/job/adapters/linux_host/templates/script_wrapper.erb.sh
index 945b75150..2d571960b 100644
--- a/lib/ood_core/job/adapters/linux_host/templates/script_wrapper.erb.sh
+++ b/lib/ood_core/job/adapters/linux_host/templates/script_wrapper.erb.sh
@@ -47,7 +47,7 @@ trap exit_script SIGINT SIGTERM
 OUTPUT_PATH=<%= output_path %>
 ERROR_PATH=<%= error_path %>
 ({
-timeout <%= script_timeout %>s <%= singularity_bin %> exec <%= contain %> --pid <%= singularity_image %> /bin/bash --login $singularity_tmp_file <%= arguments %>
+timeout <%= script_timeout %>s <%= singularity_bin %> exec <%= singularity_options %> <%= contain %> --pid <%= singularity_image %> /bin/bash --login $singularity_tmp_file <%= arguments %>
 } | tee "$OUTPUT_PATH") 3>&1 1>&2 2>&3 | tee "$ERROR_PATH"
 
 <%= email_on_terminated %>