containerized code: setting and running containerized code (docker, sarus, singularity, conda)

.github/config/add-docker.yaml

@@ -0,0 +1,12 @@
+---
+label: add-docker
+description: add docker
+default_calc_job_plugin: core.arithmetic.add
+on_computer: true
+computer: localhost
+filepath_executable: /bin/bash
+image: ubuntu
+engine_command: docker run -v $PWD:/workdir:rw -w /workdir {image} sh -c
+escape_exec_line: true
+prepend_text: ' '
+append_text: ' '

.github/config/add.yaml

@@ -1,9 +1,9 @@
 ---
 label: add
 description: add
-default_calc_job_plugin: core.arithmetic.add
+input_plugin: core.arithmetic.add
 on_computer: true
 computer: localhost
-filepath_executable: /bin/bash
+remote_abs_path: /bin/bash
 prepend_text: ' '
 append_text: ' '

.github/config/doubler.yaml

@@ -1,9 +1,9 @@
 ---
 label: doubler
 description: doubler
-default_calc_job_plugin: core.templatereplacer
+input_plugin: core.templatereplacer
 on_computer: true
 computer: localhost
-filepath_executable: PLACEHOLDER_REMOTE_ABS_PATH_DOUBLER
+remote_abs_path: PLACEHOLDER_REMOTE_ABS_PATH_DOUBLER
 prepend_text: ' '
 append_text: ' '

.github/config/localhost.yaml

@@ -6,6 +6,7 @@ transport: core.local
 scheduler: core.direct
 shebang: '#!/usr/bin/env bash'
 work_dir: PLACEHOLDER_WORK_DIR
+use_double_quotes: true
 mpirun_command: ' '
 mpiprocs_per_machine: 1
 prepend_text: ' '

.github/system_tests/test_containerized_code.py

@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved.                     #
+# This file is part of the AiiDA code.                                    #
+#                                                                         #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file        #
+# For further information please visit http://www.aiida.net               #
+###########################################################################
+"""Test run on containrized code."""
+from aiida import orm
+from aiida.engine import run_get_node
+from aiida.plugins import CalculationFactory
+
+ArithmeticAddCalculation = CalculationFactory('core.arithmetic.add')
+
+inputs = {
+    'code': orm.load_code('add-docker@localhost'),
+    'x': orm.Int(4),
+    'y': orm.Int(6),
+    'metadata': {
+        'options': {
+            'resources': {
+                'num_machines': 1,
+                'num_mpiprocs_per_machine': 1
+            }
+        }
+    }
+}
+
+res, node = run_get_node(ArithmeticAddCalculation, **inputs)
+assert 'sum' in res
+assert 'remote_folder' in res
+assert 'retrieved' in res
+assert res['sum'].value == 10

.github/workflows/nightly.yml

@@ -1,6 +1,7 @@
 name: nightly
 
 on:
+    workflow_dispatch:  # To manually trigger nightly
     schedule:
     -   cron: '0 0 * * *'  # Run every day at midnight
     pull_request:

.github/workflows/setup.sh

@@ -21,8 +21,9 @@ verdi setup --non-interactive --config "${CONFIG}/profile.yaml"
 verdi computer setup --non-interactive --config "${CONFIG}/localhost.yaml"
 verdi computer configure core.local localhost --config "${CONFIG}/localhost-config.yaml"
 verdi computer test localhost
-verdi code create core.code.installed --non-interactive --config "${CONFIG}/doubler.yaml"
-verdi code create core.code.installed --non-interactive --config "${CONFIG}/add.yaml"
+verdi code setup --non-interactive --config "${CONFIG}/doubler.yaml"
+verdi code setup --non-interactive --config "${CONFIG}/add.yaml"
+verdi code create core.code.installed.containerized --non-interactive --config "${CONFIG}/add-docker.yaml"
 
 # set up slurm-ssh computer
 verdi computer setup --non-interactive --config "${CONFIG}/slurm-ssh.yaml"

.github/workflows/tests_nightly.sh

@@ -9,6 +9,7 @@ export PYTHONPATH="${PYTHONPATH}:${SYSTEM_TESTS}:${MODULE_POLISH}"
 
 verdi daemon start 4
 verdi -p test_aiida run ${SYSTEM_TESTS}/test_daemon.py
+verdi -p test_aiida run ${SYSTEM_TESTS}/test_containerized_code.py
 bash ${SYSTEM_TESTS}/test_polish_workchains.sh
 verdi daemon stop
 

aiida/engine/processes/calcjobs/calcjob.py

@@ -24,6 +24,7 @@
 from aiida.common.folders import Folder
 from aiida.common.lang import classproperty, override
 from aiida.common.links import LinkType
+from aiida.orm.nodes.data.code.containerized import Containerized
 
 from ..exit_code import ExitCode
 from ..ports import PortNamespace
@@ -615,7 +616,7 @@ def presubmit(self, folder: Folder) -> CalcInfo:
         from aiida.common.datastructures import CodeInfo, CodeRunMode
         from aiida.common.exceptions import InputValidationError, InvalidOperation, PluginInternalError, ValidationError
         from aiida.common.utils import validate_list_of_string_tuples
-        from aiida.orm import AbstractCode, Code, Computer, InstalledCode, PortableCode, load_node
+        from aiida.orm import AbstractCode, Computer, PortableCode, load_code
         from aiida.schedulers.datastructures import JobTemplate, JobTemplateCodeInfo
 
         inputs = self.node.base.links.get_incoming(link_type=LinkType.INPUT_CALC)
@@ -719,7 +720,7 @@ def presubmit(self, folder: Folder) -> CalcInfo:
 
             if code_info.code_uuid is None:
                 raise PluginInternalError('CalcInfo should have the information of the code to be launched')
-            this_code = load_node(code_info.code_uuid, sub_classes=(Code, InstalledCode, PortableCode))
+            this_code = load_code(code_info.code_uuid)
 
             # To determine whether this code should be run with MPI enabled, we get the value that was set in the inputs
             # of the entire process, which can then be overwritten by the value from the `CodeInfo`. This allows plugins
@@ -740,8 +741,32 @@ def presubmit(self, folder: Folder) -> CalcInfo:
 
             cmdline_params = [str(this_code.get_executable())] + (code_info.cmdline_params or [])
 
+            escape_exec_line = False
+            if isinstance(this_code, Containerized):
+                prepend_cmdline_params += this_code.get_engine_command()
+                # escape exec line will put the all parameters after `prepend_cmdline_params`
+                # into the single quotes.
+                # It is only needed for docker type containerized code,
+                # therefore default set to False.
+                escape_exec_line = this_code.escape_exec_line
+
+                inner_mpi = this_code.inner_mpi
+                if inner_mpi:
+                    # First always serials outside
+                    prepend_cmdline_params = this_code.get_engine_command()
+
+                    # Set mpi args for code if not exist use the computer one as default
+                    if this_code.get_mpirun_command():
+                        code_mpi_args = this_code.get_mpirun_command()
+                    else:
+                        code_mpi_args = mpi_args
+
+                    # import ipdb; ipdb.set_trace()
+                    cmdline_params = [arg.format(**subst_dict) for arg in code_mpi_args] + cmdline_params
+
             tmpl_code_info = JobTemplateCodeInfo()
             tmpl_code_info.prepend_cmdline_params = prepend_cmdline_params
+            tmpl_code_info.escape_exec_line = escape_exec_line
             tmpl_code_info.cmdline_params = cmdline_params
             tmpl_code_info.use_double_quotes = [computer.get_use_double_quotes(), this_code.use_double_quotes]
             tmpl_code_info.stdin_name = code_info.stdin_name

aiida/orm/__init__.py

@@ -62,6 +62,7 @@
     'GroupEntityLoader',
     'ImportGroup',
     'InstalledCode',
+    'InstalledContainerizedCode',
     'Int',
     'JsonableData',
     'Kind',
@@ -81,6 +82,7 @@
     'OrderSpecifier',
     'OrmEntityLoader',
     'PortableCode',
+    'PortableContainerizedCode',
     'ProcessNode',
     'ProjectionData',
     'QueryBuilder',

aiida/orm/nodes/__init__.py

@@ -37,6 +37,7 @@
     'Float',
     'FolderData',
     'InstalledCode',
+    'InstalledContainerizedCode',
     'Int',
     'JsonableData',
     'Kind',
@@ -48,6 +49,7 @@
     'NumericType',
     'OrbitalData',
     'PortableCode',
+    'PortableContainerizedCode',
     'ProcessNode',
     'ProjectionData',
     'RemoteData',

aiida/orm/nodes/data/__init__.py

@@ -49,6 +49,7 @@
     'Float',
     'FolderData',
     'InstalledCode',
+    'InstalledContainerizedCode',
     'Int',
     'JsonableData',
     'Kind',
@@ -57,6 +58,7 @@
     'NumericType',
     'OrbitalData',
     'PortableCode',
+    'PortableContainerizedCode',
     'ProjectionData',
     'RemoteData',
     'RemoteStashData',

aiida/orm/nodes/data/code/__init__.py

@@ -7,6 +7,7 @@
 # pylint: disable=wildcard-import
 
 from .abstract import *
+from .containerized import *
 from .installed import *
 from .legacy import *
 from .portable import *
@@ -15,7 +16,9 @@
     'AbstractCode',
     'Code',
     'InstalledCode',
+    'InstalledContainerizedCode',
     'PortableCode',
+    'PortableContainerizedCode',
 )
 
 # yapf: enable