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testing removing double bind #489

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Merged
merged 1 commit into from
Feb 7, 2022
Merged

testing removing double bind #489

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
The versions coincide with releases on pip. Only major versions will be released as tags on Github.

## [0.0.x](https://github.scom/singularityhub/singularity-hpc/tree/master) (0.0.x)
- remove redundancy of manual bindpaths and SINGULARITY_BINDPATH (0.0.42)
- Do not unset container environment vars if they are already set (0.0.41)
- Central config should be read first (and updated with user config) (0.0.4)
- Add support for oras pull for singularity (0.0.39)
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6 changes: 3 additions & 3 deletions shpc/main/modules/templates/singularity.lua
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Expand Up @@ -51,9 +51,9 @@ 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 %} {% 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 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 inspectCmd = "singularity ${SINGULARITY_OPTS} inspect ${SINGULARITY_COMMAND_OPTS} "

-- set_shell_function takes bashStr and cshStr
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6 changes: 3 additions & 3 deletions shpc/main/modules/templates/singularity.tcl
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Expand Up @@ -70,9 +70,9 @@ conflict {{ name }}
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 %} {% 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 %} ${containerPath}"
set shellCmd "singularity \${SINGULARITY_OPTS} shell \${SINGULARITY_COMMAND_OPTS} -s {{ singularity_shell }} {% if features.gpu %}{{ features.gpu }} {% endif %}{% if features.home %}-B {{ features.home | replace("$", "\$") }} --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 inspectCmd "singularity \${SINGULARITY_OPTS} inspect \${SINGULARITY_COMMAND_OPTS} "

# set_shell_function takes bashStr and cshStr
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2 changes: 1 addition & 1 deletion shpc/version.py
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Expand Up @@ -2,7 +2,7 @@
__copyright__ = "Copyright 2021-2022, Vanessa Sochat"
__license__ = "MPL 2.0"

__version__ = "0.0.41"
__version__ = "0.0.42"
AUTHOR = "Vanessa Sochat"
NAME = "singularity-hpc"
PACKAGE_URL = "https://github.com/singularityhub/singularity-hpc"
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