Add batch multinode parallel jobs support

docs/source/batch.rst

@@ -4,14 +4,14 @@ AWS Batch Integration
 =======================
 
 AWS Batch allows to efficiently execute batch computing jobs on AWS by dynamically provisioning the required underlying EC2 instances on which Docker-based jobs are executed.
-SCAR allows to transparently integrate the execution of the jobs through `AWS Batch <https://aws.amazon.com/batch/>`_. 
+SCAR allows to transparently integrate the execution of the jobs through `AWS Batch <https://aws.amazon.com/batch/>`_.
 Three execution modes are now available in SCAR:
 
   * `lambda`: This is the default execution mode. All executions will be run on AWS Lambda.
   * `lambda-batch`: Executions will be run on AWS Lambda. If the default timeout is reached, then the execution is automatically delegated to AWS Batch.
   * `batch`: Executions will be automatically diverted to AWS Batch.
 
-This way, you can use AWS Lambda as a highly-scalable cache for burts of short computational jobs while longer executions can be automatically delegated to AWS Batch. 
+This way, you can use AWS Lambda as a highly-scalable cache for burts of short computational jobs while longer executions can be automatically delegated to AWS Batch.
 The very same `programming model <https://scar.readthedocs.io/en/latest/prog_model.html>`_ is maintained regardless of the service employed to perform the computation.
 
 Set up your configuration file
@@ -47,20 +47,20 @@ The variables responsible for batch configuration are::
     },
     "service_role": "arn:aws:iam::{account_id}:role/service-role/AWSBatchServiceRole"
   }
-  
-Since AWS Batch deploys Amazon EC2 instances, the REQUIRED variables are: 
+
+Since AWS Batch deploys Amazon EC2 instances, the REQUIRED variables are:
  * `security_group_ids`: The EC2 security group that is associated with the instances launched in the compute environment. This allows to define the inbound and outbound network rules in order to allow or disallow TCP/UDP traffic generated from (or received by) the EC2 instance. You can choose the default VPC security group.
  * `subnets`:  The VPC subnet(s) identifier(s) on which the EC2 instances will be deployed. This allows to use multiple Availability Zones for enhanced fault-tolerance.
 
-The remaining variables have default values that should be enough to manage standard batch jobs. 
+The remaining variables have default values that should be enough to manage standard batch jobs.
 The default `fdl file <https://github.com/grycap/scar/blob/master/fdl-example.yaml>`_ explains briefly the remaining Batch variables and how are they used.
 
 Additional info about the variables and the different values that can be assigned can be found in the `AWS API Documentation <https://docs.aws.amazon.com/batch/latest/APIReference/API_CreateComputeEnvironment.html>`_.
 
 Set up your Batch IAM role
 --------------------------
 
-The default IAM role used in the creation of the EC2 for the Batch Compute Environment is **arn:aws:iam::$ACCOUNT_ID:instance-profile/**ecsInstanceRole****. Thus, if you want to provide S3 access to your Batch jobs you have to specify the corresponding policies in the aforementioned role. 
+The default IAM role used in the creation of the EC2 for the Batch Compute Environment is **arn:aws:iam::$ACCOUNT_ID:instance-profile/**ecsInstanceRole****. Thus, if you want to provide S3 access to your Batch jobs you have to specify the corresponding policies in the aforementioned role.
 If you have a role aleredy configured, you can set it in the configuration file by changin the variable `batch.compute_resources.instance_role`.
 
 
@@ -105,10 +105,10 @@ And trigger the execution of the function by uploading a file to be processed to
 
 SCAR automatically creates the compute environment in AWS Batch and submits a job to be executed. Input and output data files are transparently managed as well according to the programming model.
 
-The CloudWatch logs will reveal the execution of the Lambda function as well as the execution of the AWS Batch job. 
-Notice that whenever the execution of the AWS Batch job has finished, the EC2 instances will be eventually terminated. 
+The CloudWatch logs will reveal the execution of the Lambda function as well as the execution of the AWS Batch job.
+Notice that whenever the execution of the AWS Batch job has finished, the EC2 instances will be eventually terminated.
 Also, the number of EC2 instances will increase and shrink to handle the incoming number of jobs.
- 
+
 Combine AWS Lambda and AWS Batch executions
 -------------------------------------------
 As explained in the section :doc:`/prog_model`, if you define an output bucket as the input bucket of another function, a workflow can be created.
@@ -127,3 +127,13 @@ To create the AWS Batch job, the Lambda function defines a Job with the payload
 The payload limit can be avoided by redefining the script used and passing the large payload files using other service (e.g S3 or some bash command like 'wget' or 'curl' to download the information in execution time). As we didi with the plant classification example, where a `bootstrap script <https://github.com/grycap/scar/blob/master/examples/plant-classification/bootstrap-plants.sh>`_ was used to download the `executed script <https://github.com/grycap/scar/blob/master/examples/plant-classification/plant-classification-run.sh>`_.
 
 Also, AWS Batch does not allow to override the container entrypoint so containers with an entrypoint defined can not execute an user script.
+
+Multinode parallel jobs
+-----------------------
+You can execute multinode parallel jobs in batch by enabling this mode either in the scar.cfg file or in the configuration file for the job (functions->aws->batch->multi_node_parallel->enable).
+You can also set the number of nodes and the index of the main node.
+Please take into account that the index of the main node starts from 0 up to the number of nodes -1.
+
+We included an `example <https://github.com/grycap/scar/tree/master/examples/mpi>`_ of MPI job that can be executed as multinode parallel job, showing a hello world from each CPU/node available for execution.
+Both work in Amazon Lambda and Batch single node, you can use the included configuration files as a starting point.
+For more details, please check the README.md that comes with the example.

examples/mpi/Dockerfile

@@ -0,0 +1,48 @@
+FROM debian:stretch-slim
+
+ARG ADD_BASE_DIR=examples/mpi
+ARG BUILD_PACKAGES=' wget git make gcc g++ iproute2 cmake  build-essential gfortran curl  '
+
+ENV DEBIAN_FRONTEND=noninteractive
+## Set to either lambda or batch
+ENV EXEC_TYPE=lambda
+
+ENV APP_PARAMS=""
+ENV GIT_REPO=https://github.com/mpitutorial/mpitutorial
+ENV GIT_REPO_REL_PATH_SRC=mpitutorial/tutorials/mpi-hello-world/code
+ENV GIT_REPO_REL_PATH_EXEC=mpitutorial/tutorials/mpi-hello-world/code/mpi_hello_world
+ENV APP_BIN=/opt/$GIT_REPO_REL_PATH_EXEC
+ENV SSH_PRIV_FILE_KEY=ssh_host_rsa_key
+ENV SSH_PUB_FILE_KEY=ssh_host_rsa_key.pub
+
+ENV LANG en_US.UTF-8
+
+ADD ${ADD_BASE_DIR}/run.sh  /opt/
+
+RUN apt-get update \
+  && apt-get install -q -o=Dpkg::Use-Pty=0 -y $BUILD_PACKAGES perl locales \
+  && locale-gen en_US.UTF-8 \
+  && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+  && dpkg-reconfigure --frontend=noninteractive locales \
+  && update-locale LANG=en_US.UTF-8 \
+  && wget -q --no-check-certificate -qO- https://download.open-mpi.org/release/open-mpi/v1.4/openmpi-1.4.3.tar.bz2 | tar xvfj - -C /tmp/ \
+  && cd /tmp/openmpi-1.4.3/ \
+  && ./configure --disable-pty-support --disable-doc \
+  && make -j`nproc` \
+  && make install \
+  && ldconfig \
+  && cd /opt/ \
+  && git clone $GIT_REPO \
+  && cd /opt/$GIT_REPO_REL_PATH_SRC \
+  && make \
+  && apt-get remove --purge -y $BUILD_PACKAGES gnupg* gnupg-agent* \
+  && apt-get autoremove --purge -y \
+  && rm -rf /tmp/* /var/lib/apt/lists/* \
+  && ulimit -n 1024 \
+  && chmod 755 /opt/$GIT_REPO_REL_PATH_EXEC \
+  && chmod 755 /opt/run.sh \
+  && echo $(date) > /build_date \
+  && echo "Build date: $(cat  /build_date)"
+
+
+CMD /opt/run.sh

examples/mpi/LICENSE

@@ -0,0 +1,201 @@
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