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lukeseawalkerlukeseawalker
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Merge pull request #338 from aws/develop
Merge Release 2.4.0
2 parents 7568a23 + 4afb7d6 commit e94e9c2

38 files changed

+1251
-199
lines changed

‎.kitchen.cloud.yml‎

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@@ -2,6 +2,7 @@
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driver_config:
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retryable_sleep: 15
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retryable_tries: 20
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retry_limit: 6
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aws_ssh_key_id: <%= ENV['AWS_KEYPAIR_NAME'] %>
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region: <%= ENV['AWS_DEFAULT_REGION'] %>
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instance_type: <%= ENV['AWS_FLAVOR_ID'] %>
@@ -16,6 +17,8 @@ driver_config:
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provisioner:
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name: chef_zero
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require_chef_omnibus: 14.2.0
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# use custom chef install URL to cope with issue https://github.com/chef/bento/issues/609
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chef_omnibus_url: https://raw.githubusercontent.com/aws/aws-parallelcluster-cookbook/develop/util/chef-install.sh
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retry_on_exit_code:
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- 35 # 35 is the exit code signaling that the node is rebooting
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max_retries: 1

‎.kitchen.yml‎

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@@ -68,11 +68,14 @@ suites:
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cfn_ephemeral_dir: <%= ENV['CFN_EPHEMERAL_DIR'] %>
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cfn_shared_dir: <%= ENV['CFN_SHARED_DIR'] %>
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cfn_cluster_user: <%= ENV['CFN_CLUSTER_USER'] %>
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custom_node_package: <%= ENV['PARALLELCLUSTER_NODE_URL'] %>
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os: <%= ENV['OS'] %>
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- name: sge_config_MasterServer
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run_list:
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- recipe[aws-parallelcluster::_prep_env]
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- recipe[aws-parallelcluster::sge_config]
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- recipe[aws-parallelcluster::finalize]
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- recipe[aws-parallelcluster::tests]
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attributes:
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cfncluster:
@@ -87,11 +90,14 @@ suites:
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cfn_cluster_user: <%= ENV['CFN_CLUSTER_USER'] %>
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cfn_sqs_queue: <%= ENV['CFN_SQS_QUEUE'] %>
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cfn_ddb_table: <%= ENV['CFN_DDB_TABLE'] %>
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custom_node_package: <%= ENV['PARALLELCLUSTER_NODE_URL'] %>
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os: <%= ENV['OS'] %>
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- name: torque_config_MasterServer
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run_list:
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- recipe[aws-parallelcluster::_prep_env]
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- recipe[aws-parallelcluster::torque_config]
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- recipe[aws-parallelcluster::finalize]
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- recipe[aws-parallelcluster::tests]
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attributes:
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cfncluster:
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cfn_cluster_user: <%= ENV['CFN_CLUSTER_USER'] %>
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cfn_sqs_queue: <%= ENV['CFN_SQS_QUEUE'] %>
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cfn_ddb_table: <%= ENV['CFN_DDB_TABLE'] %>
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custom_node_package: <%= ENV['PARALLELCLUSTER_NODE_URL'] %>
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os: <%= ENV['OS'] %>
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- name: slurm_config_MasterServer
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run_list:
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- recipe[aws-parallelcluster::_prep_env]
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- recipe[aws-parallelcluster::slurm_config]
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- recipe[aws-parallelcluster::finalize]
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- recipe[aws-parallelcluster::tests]
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attributes:
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cfncluster:
@@ -125,11 +134,14 @@ suites:
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cfn_cluster_user: <%= ENV['CFN_CLUSTER_USER'] %>
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cfn_sqs_queue: <%= ENV['CFN_SQS_QUEUE'] %>
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cfn_ddb_table: <%= ENV['CFN_DDB_TABLE'] %>
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custom_node_package: <%= ENV['PARALLELCLUSTER_NODE_URL'] %>
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os: <%= ENV['OS'] %>
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- name: sge_config_ComputeFleet
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run_list:
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- recipe[aws-parallelcluster::_prep_env]
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- recipe[aws-parallelcluster::sge_config]
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- recipe[aws-parallelcluster::finalize]
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- recipe[aws-parallelcluster::tests]
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attributes:
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cfncluster:
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cfn_cluster_user: <%= ENV['CFN_CLUSTER_USER'] %>
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cfn_sqs_queue: <%= ENV['CFN_SQS_QUEUE'] %>
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cfn_master: <%= ENV['CFN_MASTER'] %>
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custom_node_package: <%= ENV['PARALLELCLUSTER_NODE_URL'] %>
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os: <%= ENV['OS'] %>
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- name: torque_config_ComputeFleet
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run_list:
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- recipe[aws-parallelcluster::_prep_env]
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- recipe[aws-parallelcluster::torque_config]
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- recipe[aws-parallelcluster::finalize]
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- recipe[aws-parallelcluster::tests]
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attributes:
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cfncluster:
@@ -163,11 +178,14 @@ suites:
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cfn_cluster_user: <%= ENV['CFN_CLUSTER_USER'] %>
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cfn_sqs_queue: <%= ENV['CFN_SQS_QUEUE'] %>
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cfn_master: <%= ENV['CFN_MASTER'] %>
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custom_node_package: <%= ENV['PARALLELCLUSTER_NODE_URL'] %>
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os: <%= ENV['OS'] %>
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- name: slurm_config_ComputeFleet
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run_list:
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- recipe[aws-parallelcluster::_prep_env]
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- recipe[aws-parallelcluster::slurm_config]
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- recipe[aws-parallelcluster::finalize]
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- recipe[aws-parallelcluster::tests]
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attributes:
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cfncluster:
@@ -182,3 +200,5 @@ suites:
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cfn_cluster_user: <%= ENV['CFN_CLUSTER_USER'] %>
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cfn_sqs_queue: <%= ENV['CFN_SQS_QUEUE'] %>
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cfn_master: <%= ENV['CFN_MASTER'] %>
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custom_node_package: <%= ENV['PARALLELCLUSTER_NODE_URL'] %>
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os: <%= ENV['OS'] %>

‎CHANGELOG.md‎

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@@ -3,6 +3,36 @@ aws-parallelcluster-cookbook CHANGELOG
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This file is used to list changes made in each version of the AWS ParallelCluster cookbook.
55

6+
2.4.0
7+
-----
8+
9+
**ENHANCEMENTS**
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- Add support for EFA on Centos 7, Amazon Linux and Ubuntu 1604
11+
- Add support for Ubuntu in China region `cn-northwest-1`
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13+
**CHANGES**
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- SGE: changed following parameters in global configuration
15+
- `max_unheard 00:03:00`: allows a faster reaction in case of faulty nodes
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- `reschedule_unknown 00:00:30`: enables rescheduling of jobs running on failing nodes
17+
- `qmaster_params ENABLE_FORCED_QDEL_IF_UNKNOWN`: forces job deletion on unresponsive nodes
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- `qmaster_params ENABLE_RESCHEDULE_KILL`: forces rescheduling or killing of jobs running on failing nodes
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- Slurm: decrease SlurmdTimeout to 120 seconds to speed up replacement of faulty nodes
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- Always use full master FQDN when mounting NFS on compute nodes. This solves some issues occurring with some networking
21+
setups and custom DNS configurations
22+
- Set soft and hard ulimit on open files to 10000 for all supported OSs
23+
- Pin python `supervisor` version to 3.4.0
24+
- Remove unused `compute_instance_type` from jobwatcher.cfg
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- Removed unused `max_queue_size` from sqswatcher.cfg
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- Remove double quoting of the post_install args
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28+
**BUG FIXES**
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- Fix issue that was preventing Torque from being used on Centos 7
30+
- Start node daemons at the end of instance initialization. The time spent for post-install script and node
31+
initialization is not counted as part of node idletime anymore.
32+
- Fix issue which was causing an additional and invalid EBS mount point to be added in case of multiple EBS
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- Install Slurm libpmpi/libpmpi2 that is distributed in a separate package since Slurm 17
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2.3.1
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-----
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‎amis/packer_alinux.json‎

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"pause_before": "2m",
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"json" : {
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"cfncluster" : {
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"cfn_region": "{{user `region`}}",
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"nvidia" : {
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"enabled" : "{{user `nvidia_enabled`}}"
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},
@@ -246,7 +247,6 @@
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},
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{
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"type" : "shell",
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"only": ["custom-alinux"],
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"inline" : [
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"sudo /usr/local/sbin/ami_cleanup.sh"
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]

‎amis/packer_centos6.json‎

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"pause_before": "2m",
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"json" : {
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"cfncluster" : {
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"cfn_region": "{{user `region`}}",
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"nvidia" : {
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"enabled" : "{{user `nvidia_enabled`}}"
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},
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"inline" : [
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"region=\"{{user `region`}}\"",
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"bucket=\"s3.amazonaws.com\"",
254-
"[[ ${region} =~ ^cn- ]] && bucket=\"s3.cn-north-1.amazonaws.com.cn\"",
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"[[ ${region} =~ ^cn- ]] && bucket=\"s3.cn-north-1.amazonaws.com.cn/cn-north-1-aws-parallelcluster\"",
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"curl --retry 3 -L -o /tmp/aws-cfn-bootstrap-latest.tar.gz https://${bucket}/cloudformation-examples/aws-cfn-bootstrap-latest.tar.gz",
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"sudo pip install /tmp/aws-cfn-bootstrap-latest.tar.gz"
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]
@@ -265,7 +266,6 @@
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},
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{
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"type" : "shell",
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"only": ["custom-centos6"],
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"inline" : [
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"sudo /usr/local/sbin/ami_cleanup.sh"
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]

‎amis/packer_centos7.json‎

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"pause_before": "2m",
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"json" : {
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"cfncluster" : {
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"cfn_region": "{{user `region`}}",
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"nvidia" : {
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"enabled" : "{{user `nvidia_enabled`}}"
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},
@@ -256,7 +257,7 @@
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"inline" : [
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"region=\"{{user `region`}}\"",
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"bucket=\"s3.amazonaws.com\"",
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"[[ ${region} =~ ^cn- ]] && bucket=\"s3.cn-north-1.amazonaws.com.cn\"",
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"[[ ${region} =~ ^cn- ]] && bucket=\"s3.cn-north-1.amazonaws.com.cn/cn-north-1-aws-parallelcluster\"",
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"curl --retry 3 -L -o /tmp/aws-cfn-bootstrap-latest.tar.gz https://${bucket}/cloudformation-examples/aws-cfn-bootstrap-latest.tar.gz",
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"which pip2",
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"if [ $? -eq 0 ]; then sudo pip2 install /tmp/aws-cfn-bootstrap-latest.tar.gz; else sudo pip install /tmp/aws-cfn-bootstrap-latest.tar.gz; fi"
@@ -277,7 +278,6 @@
277278
},
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{
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"type" : "shell",
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"only": ["custom-centos7"],
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"inline" : [
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"sudo /usr/local/sbin/ami_cleanup.sh"
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]

‎amis/packer_ubuntu1404.json‎

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"pause_before": "2m",
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"json" : {
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"cfncluster" : {
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"cfn_region": "{{user `region`}}",
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"nvidia" : {
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"enabled" : "{{user `nvidia_enabled`}}"
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},
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"inline" : [
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"region=\"{{user `region`}}\"",
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"bucket=\"s3.amazonaws.com\"",
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"[[ ${region} =~ ^cn- ]] && bucket=\"s3.cn-north-1.amazonaws.com.cn\"",
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"[[ ${region} =~ ^cn- ]] && bucket=\"s3.cn-north-1.amazonaws.com.cn/cn-north-1-aws-parallelcluster\"",
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"curl --retry 3 -L -o /tmp/aws-cfn-bootstrap-latest.tar.gz https://${bucket}/cloudformation-examples/aws-cfn-bootstrap-latest.tar.gz",
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"sudo pip install /tmp/aws-cfn-bootstrap-latest.tar.gz"
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]
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},
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{
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"type" : "shell",
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"only": ["custom-ubuntu1404"],
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"inline" : [
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"sudo /usr/local/sbin/ami_cleanup.sh"
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]

‎amis/packer_ubuntu1604.json‎

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"pause_before": "2m",
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"json" : {
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"cfncluster" : {
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"cfn_region": "{{user `region`}}",
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"nvidia" : {
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"enabled" : "{{user `nvidia_enabled`}}"
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},
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"inline" : [
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"region=\"{{user `region`}}\"",
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"bucket=\"s3.amazonaws.com\"",
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"[[ ${region} =~ ^cn- ]] && bucket=\"s3.cn-north-1.amazonaws.com.cn\"",
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"[[ ${region} =~ ^cn- ]] && bucket=\"s3.cn-north-1.amazonaws.com.cn/cn-north-1-aws-parallelcluster\"",
264265
"curl --retry 3 -L -o /tmp/aws-cfn-bootstrap-latest.tar.gz https://${bucket}/cloudformation-examples/aws-cfn-bootstrap-latest.tar.gz",
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"sudo pip install /tmp/aws-cfn-bootstrap-latest.tar.gz"
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]
@@ -274,7 +275,6 @@
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},
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{
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"type" : "shell",
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"only": ["custom-ubuntu1604"],
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"inline" : [
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"sudo /usr/local/sbin/ami_cleanup.sh"
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]

‎amis/packer_variables.json‎

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{
2-
"parallelcluster_version": "2.3.1",
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"parallelcluster_cookbook_version": "2.3.1",
2+
"parallelcluster_version": "2.4.0",
3+
"parallelcluster_cookbook_version": "2.4.0",
44
"chef_version": "14.2.0",
55
"ridley_version": "5.1.1",
66
"berkshelf_version": "7.0.4"

‎attributes/default.rb‎

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1919
default['cfncluster']['scripts_dir'] = "#{node['cfncluster']['base_dir']}/scripts"
2020
default['cfncluster']['license_dir'] = "#{node['cfncluster']['base_dir']}/licenses"
2121
# Python packages
22-
default['cfncluster']['cfncluster-version'] = '2.3.1'
23-
default['cfncluster']['cfncluster-node-version'] = '2.3.1'
24-
default['cfncluster']['cfncluster-supervisor-version'] = '3.3.1'
22+
default['cfncluster']['cfncluster-version'] = '2.4.0'
23+
default['cfncluster']['cfncluster-node-version'] = '2.4.0'
24+
default['cfncluster']['supervisor-version'] = '3.4.0'
2525
# URLs to software packages used during install recipes
2626
# Gridengine software
2727
default['cfncluster']['sge']['version'] = '8.1.9'
@@ -45,6 +45,8 @@
4545
default['cfncluster']['nvidia']['enabled'] = 'no'
4646
default['cfncluster']['nvidia']['driver_url'] = 'http://download.nvidia.com/XFree86/Linux-x86_64/418.56/NVIDIA-Linux-x86_64-418.56.run'
4747
default['cfncluster']['nvidia']['cuda_url'] = 'https://developer.nvidia.com/compute/cuda/10.0/Prod/local_installers/cuda_10.0.130_410.48_linux'
48+
# EFA
49+
default['cfncluster']['efa']['installer_url'] = 'https://s3-us-west-2.amazonaws.com/aws-efa-installer/aws-efa-installer-latest.tar.gz'
4850

4951
# Reboot after default_pre recipe
5052
default['cfncluster']['default_pre_reboot'] = 'true'
@@ -83,7 +85,7 @@
8385
if node['platform_version'].to_i >= 7
8486
default['cfncluster']['base_packages'] = %w[vim ksh tcsh zsh openssl-devel ncurses-devel pam-devel net-tools openmotif-devel
8587
libXmu-devel hwloc-devel libdb-devel tcl-devel automake autoconf pyparted libtool
86-
httpd boost-devel redhat-lsb mlocate lvm2 mpich-devel openmpi-devel R atlas-devel
88+
httpd boost-devel redhat-lsb mlocate lvm2 mpich-devel R atlas-devel
8789
blas-devel fftw-devel libffi-devel openssl-devel dkms mariadb-devel libedit-devel
8890
libical-devel postgresql-devel postgresql-server sendmail libxml2-devel libglvnd-devel mdadm]
8991
if node['platform_version'].split('.')[1] == '6'
@@ -105,7 +107,7 @@
105107
when 'amazon'
106108
default['cfncluster']['base_packages'] = %w[vim ksh tcsh zsh openssl-devel ncurses-devel pam-devel net-tools openmotif-devel
107109
libXmu-devel hwloc-devel db4-devel tcl-devel automake autoconf pyparted libtool
108-
httpd boost-devel redhat-lsb mlocate mpich-devel openmpi-devel R atlas-devel fftw-devel
110+
httpd boost-devel redhat-lsb mlocate mpich-devel R atlas-devel fftw-devel
109111
libffi-devel openssl-devel dkms mysql-devel libedit-devel postgresql-devel postgresql-server
110112
sendmail cmake byacc libglvnd-devel mdadm]
111113
end
@@ -123,8 +125,11 @@
123125
default['cfncluster']['base_packages'] = %w[vim ksh tcsh zsh libssl-dev ncurses-dev libpam-dev net-tools libhwloc-dev dkms
124126
tcl-dev automake autoconf python-parted libtool librrd-dev libapr1-dev libconfuse-dev
125127
apache2 libboost-dev libdb-dev tcsh libssl-dev libncurses5-dev libpam0g-dev libxt-dev
126-
libmotif-dev libxmu-dev libxft-dev libhwloc-dev man-db lvm2 libmpich-dev libopenmpi-dev
128+
libmotif-dev libxmu-dev libxft-dev libhwloc-dev man-db lvm2 libmpich-dev
127129
r-base libatlas-dev libblas-dev libfftw3-dev libffi-dev libssl-dev libxml2-dev mdadm]
130+
if node['platform_version'] == '14.04'
131+
default['cfncluster']['base_packages'].push('libopenmpi-dev')
132+
end
128133
default['cfncluster']['kernel_generic_pkg'] = "linux-generic"
129134
default['cfncluster']['kernel_extra_pkg'] = "linux-image-extra-#{node['kernel']['release']}"
130135
default['cfncluster']['ganglia']['apache_user'] = 'www-data'
@@ -166,7 +171,6 @@
166171
default['cfncluster']['cfn_shared_dir'] = '/shared'
167172
default['cfncluster']['cfn_efs_shared_dir'] = 'NONE'
168173
default['cfncluster']['cfn_efs'] = nil
169-
default['cfncluster']['cfn_node_type'] = nil
170174
default['cfncluster']['cfn_master'] = nil
171175
default['cfncluster']['cfn_cluster_user'] = 'ec2-user'
172176
default['cfncluster']['cfn_fsx_options'] = 'NONE'

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