Merge pull request #494 from marcodelapierre/update/bindpath-strategy

avoid double bindpath: use -B, ditch SINGULARITY_BINDPATH

Author: vsoch

shpc/main/modules/templates/singularity.lua

@@ -41,8 +41,7 @@ For each of the above, you can export:
 -- we probably don't need this
 local MODULEPATH="{{ module_dir }}"
 
--- singularity environment variables to bind the paths and set shell
-{% if bindpaths %}setenv("SINGULARITY_BINDPATH", "{{ bindpaths }}"){% endif %}
+-- singularity environment variable to set shell
 setenv("SINGULARITY_SHELL", "{{ singularity_shell }}")
 
 -- Environment: only set options and command options if not already set
@@ -51,9 +50,9 @@ if not os.getenv("SINGULARITY_COMMAND_OPTS") then setenv ("SINGULARITY_COMMAND_O
 
 -- interactive shell to any container, plus exec for aliases
 local containerPath = '{{ container_sif }}'
-local shellCmd = "singularity ${SINGULARITY_OPTS} shell ${SINGULARITY_COMMAND_OPTS} -s {{ singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} " .. containerPath
-local execCmd = "singularity ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} "
-local runCmd = "singularity ${SINGULARITY_OPTS} run ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} " .. containerPath
+local shellCmd = "singularity ${SINGULARITY_OPTS} shell ${SINGULARITY_COMMAND_OPTS} -s {{ singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} {% if bindpaths %}-B {{ bindpaths }}{% endif %} " .. containerPath
+local execCmd = "singularity ${SINGULARITY_OPTS} exec ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} {% if bindpaths %}-B {{ bindpaths }}{% endif %} "
+local runCmd = "singularity ${SINGULARITY_OPTS} run ${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home }} --home {{ features.home }} {% endif %}{% if features.x11 %}-B {{ features.x11 }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} {% if bindpaths %}-B {{ bindpaths }}{% endif %} " .. containerPath
 local inspectCmd = "singularity ${SINGULARITY_OPTS} inspect ${SINGULARITY_COMMAND_OPTS} " 
 
 -- set_shell_function takes bashStr and cshStr

shpc/main/modules/templates/singularity.tcl

@@ -65,14 +65,13 @@ conflict {{ name }}
 {% if aliases %}{% for alias in aliases %}{% if alias != name %}conflict {{ alias.name }}{% endif %}
 {% endfor %}{% endif %}
 
-# singularity environment variables to bind the paths and set shell
-{% if bindpaths %}setenv SINGULARITY_BINDPATH {{ bindpaths }}{% endif %}
+# singularity environment variable to set shell
 setenv SINGULARITY_SHELL {{ singularity_shell }}
 
 # interactive shell to any container, plus exec for aliases
-set shellCmd "singularity \${SINGULARITY_OPTS} shell \${SINGULARITY_COMMAND_OPTS} -s {{ singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} ${containerPath}" 
-set execCmd "singularity \${SINGULARITY_OPTS} exec \${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} "
-set runCmd "singularity \${SINGULARITY_OPTS} run \${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} ${containerPath}"
+set shellCmd "singularity \${SINGULARITY_OPTS} shell \${SINGULARITY_COMMAND_OPTS} -s {{ singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} {% if bindpaths %}-B {{ bindpaths }}{% endif %} ${containerPath}"
+set execCmd "singularity \${SINGULARITY_OPTS} exec \${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} {% if bindpaths %}-B {{ bindpaths }}{% endif %} "
+set runCmd "singularity \${SINGULARITY_OPTS} run \${SINGULARITY_COMMAND_OPTS} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --home {{ features.home | replace("$", "\$") }} {% endif %}{% if features.x11 %}-B {{ features.x11 | replace("$", "\$") }} {% endif %}{% if envfile %}-B {{ module_dir }}/{{ envfile }}:/.singularity.d/env/{{ envfile }}{% endif %} {% if bindpaths %}-B {{ bindpaths }}{% endif %} ${containerPath}"
 set inspectCmd "singularity \${SINGULARITY_OPTS} inspect \${SINGULARITY_COMMAND_OPTS} " 
 
 # set_shell_function takes bashStr and cshStr