Merge pull request #31 from oracle-quickstart/2.10.4

2.10.4

Author: arnaudfroidmont

README.md

@@ -240,6 +240,7 @@ sleep 1000
 
 - Instance Type: You can specify the OCI instance type that you’d like to run on as a constraint. This will make sure that you run on the right shape and also generate the right cluster. Instance types are defined in the `/opt/oci-hpc/conf/queues.conf` file in yml format. Leave all of the field in there even if they are not used. You can define multiple queues and multiple instance type in each queue. If you do not select an instance type when creating your job, it will use the default one.
 
+- cpu-bind: On Ubuntu 22.04, we are switching to Cgroup v2 and we did notice that when hyperthreading is turned off. The default cpu-bind may give some issues. If you get an error like `error: task_g_set_affinity: Invalid argument`, you can try running your job with --cpu-bind=none or --cpu-bind=sockets
 ## Clusters folders: 
 ```
 /opt/oci-hpc/autoscaling/clusters/clustername

autoscaling/crontab/autoscale_slurm.sh

@@ -41,7 +41,7 @@ def getTopology(clusterName):
 # Get the list of Jobs in all states
 def getJobs():
     # changing the position of Dependency as it is giving blank instead of null. to handle that, putting it at the end.
-    out = subprocess.Popen(['squeue','-O','STATE,JOBID,FEATURE:100,NUMNODES,Partition,UserName,Dependency'], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True)
+    out = subprocess.Popen(['squeue','-r','-O','STATE,JOBID,FEATURE:100,NUMNODES,Partition,UserName,Dependency'], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True)
     stdout,stderr = out.communicate()
     return stdout.split("\n")[1:]
 
@@ -433,4 +433,4 @@ try:
 
 except Exception:
     traceback.print_exc()
-os.remove(lockfile)
+os.remove(lockfile)

autoscaling/tf_init/bastion_update.tf

@@ -54,8 +54,10 @@ resource "local_file" "inventory" {
     spack = var.spack,
     ldap = var.ldap,
     bastion_block = var.bastion_block,
+    login_block = var.login_block,
     scratch_nfs_type = local.scratch_nfs_type,
     bastion_mount_ip = var.bastion_mount_ip,
+    login_mount_ip = var.login_mount_ip,
     cluster_mount_ip = local.mount_ip,
     cluster_name = local.cluster_name,
     shape = var.cluster_network ? var.cluster_network_shape : var.instance_pool_shape,
@@ -72,7 +74,8 @@ resource "local_file" "inventory" {
     bastion_username = var.bastion_username,
     compute_username = var.compute_username,
     pam = var.pam,
-    sacct_limits = var.sacct_limits
+    sacct_limits = var.sacct_limits,
+    use_compute_agent=var.use_compute_agent
     })
   filename   = "${local.bastion_path}/inventory"
 }

autoscaling/tf_init/cluster-network-configuration.tf

@@ -18,8 +18,32 @@ resource "oci_core_instance_configuration" "cluster-network-instance_configurati
         user_data           = base64encode(data.template_file.config.rendered)
       }
       agent_config {
-        is_management_disabled = true
+
+        are_all_plugins_disabled = false
+        is_management_disabled   = true
+        is_monitoring_disabled   = false
+
+        plugins_config {
+          desired_state = "DISABLED"
+          name          = "OS Management Service Agent"
+          }
+        dynamic plugins_config {
+          
+          for_each = var.use_compute_agent ? ["ENABLED"] : ["DISABLED"]
+          content {
+          name = "Compute HPC RDMA Authentication"
+          desired_state = plugins_config.value
+           }
+         }
+        dynamic plugins_config {
+          for_each = var.use_compute_agent ? ["ENABLED"] : ["DISABLED"]
+          content {
+          name = "Compute HPC RDMA Auto-Configuration"
+          desired_state = plugins_config.value
+          }
+
         }
+      }
       shape = var.cluster_network_shape
       source_details {
         source_type             = "image"

autoscaling/tf_init/inventory.tpl

@@ -41,8 +41,10 @@ pyxis = ${pyxis}
 enroot = ${enroot}
 spack = ${spack} 
 bastion_block = ${bastion_block} 
+login_block = ${login_block} 
 scratch_nfs_type = ${scratch_nfs_type}
 bastion_mount_ip = ${bastion_mount_ip}
+login_mount_ip = ${login_mount_ip}
 cluster_mount_ip = ${cluster_mount_ip}
 autoscaling = true
 force = no
@@ -68,4 +70,5 @@ latency_check=${latency_check}
 compute_username=${compute_username}
 bastion_username=${bastion_username}
 pam = ${pam}
-sacct_limits=${sacct_limits}
+sacct_limits=${sacct_limits}
+use_compute_agent=${use_compute_agent}

autoscaling/tf_init/marketplace.tf

@@ -1,6 +1,6 @@
 locals {
-    mp_listing_id = var.use_marketplace_image ? var.use_old_marketplace_image ? var.old_marketplace_listing_id : substr(var.marketplace_listing,0,3) == "HPC" ? var.marketplace_listing_id_HPC : var.marketplace_listing_id_GPU : ""
-    mp_version_id = var.use_old_marketplace_image ? var.marketplace_version_id[split(".", var.marketplace_listing)[0]] : var.marketplace_version_id[var.marketplace_listing]
+    mp_listing_id = var.use_marketplace_image ? substr(var.marketplace_listing,0,3) == "HPC" ? var.marketplace_listing_id_HPC : var.marketplace_listing_id_GPU : ""
+    mp_version_id = var.marketplace_version_id[var.marketplace_listing]
 }
 
 /* 

bastion.tf

@@ -15,6 +15,7 @@ resource "oci_core_volume_attachment" "bastion_volume_attachment" {
   instance_id     = oci_core_instance.bastion.id
   display_name    = "${local.cluster_name}-bastion-volume-attachment"
   device          = "/dev/oracleoci/oraclevdb"
+  is_shareable    = true
 } 
 
 resource "oci_core_volume_backup_policy" "bastion_boot_volume_backup_policy" {
@@ -200,7 +201,7 @@ resource "null_resource" "bastion" {
   }
 
   provisioner "file" {
-    content     = tls_private_key.ssh.private_key_pem
+    content     = tls_private_key.ssh.private_key_openssh
     destination = "/home/${var.bastion_username}/.ssh/cluster.key"
     connection {
       host        = local.host
@@ -209,6 +210,17 @@ resource "null_resource" "bastion" {
       private_key = tls_private_key.ssh.private_key_pem
     }
   }
+
+    provisioner "file" {
+    content     = tls_private_key.ssh.public_key_openssh
+    destination = "/home/${var.bastion_username}/.ssh/id_rsa.pub"
+    connection {
+      host        = local.host
+      type        = "ssh"
+      user        = var.bastion_username
+      private_key = tls_private_key.ssh.private_key_pem
+    }
+  }
 }
 resource "null_resource" "cluster" { 
   depends_on = [null_resource.bastion, null_resource.backup, oci_core_compute_cluster.compute_cluster, oci_core_cluster_network.cluster_network, oci_core_instance.bastion, oci_core_volume_attachment.bastion_volume_attachment ] 
@@ -246,14 +258,17 @@ resource "null_resource" "cluster" {
       log_vol = var.log_vol,
       redundancy = var.redundancy,
       cluster_network = var.cluster_network,
+      use_compute_agent = var.use_compute_agent,
       slurm = var.slurm,
       rack_aware = var.rack_aware,
       slurm_nfs_path = var.slurm_nfs ? var.nfs_source_path : var.cluster_nfs_path
       spack = var.spack,
       ldap = var.ldap,
       bastion_block = var.bastion_block, 
+      login_block = var.login_block, 
       scratch_nfs_type = local.scratch_nfs_type,
       bastion_mount_ip = local.bastion_mount_ip,
+      login_mount_ip = local.login_mount_ip,
       cluster_mount_ip = local.mount_ip,
       autoscaling = var.autoscaling,
       cluster_name = local.cluster_name,
@@ -324,11 +339,11 @@ resource "null_resource" "cluster" {
   provisioner "file" {
     content        = templatefile("${path.module}/queues.conf", {  
       cluster_network = var.cluster_network,
+      use_compute_agent = var.use_compute_agent,
       compute_cluster = var.compute_cluster,
-      marketplace_listing = var.use_old_marketplace_image ? var.old_marketplace_listing : var.marketplace_listing,
+      marketplace_listing = var.marketplace_listing,
       image = local.image_ocid,
       use_marketplace_image = var.use_marketplace_image,
-      use_old_marketplace_image = var.use_old_marketplace_image,
       boot_volume_size = var.boot_volume_size,
       shape = var.cluster_network ? var.cluster_network_shape : var.instance_pool_shape,
       region = var.region,
@@ -376,8 +391,10 @@ resource "null_resource" "cluster" {
       spack = var.spack,
       ldap = var.ldap,
       bastion_block = var.bastion_block, 
+      login_block = var.login_block, 
       scratch_nfs_type = local.scratch_nfs_type,
       bastion_mount_ip = local.bastion_mount_ip,
+      login_mount_ip = local.login_mount_ip,
       cluster_mount_ip = local.mount_ip,
       scratch_nfs_type_cluster = var.scratch_nfs_type_cluster,
       scratch_nfs_type_pool = var.scratch_nfs_type_pool,
@@ -390,8 +407,6 @@ resource "null_resource" "cluster" {
       ssh_cidr = var.ssh_cidr,
       use_cluster_nfs = var.use_cluster_nfs,
       cluster_nfs_path = var.cluster_nfs_path,
-      bastion_block = var.bastion_block,
-      bastion_mount_ip = local.bastion_mount_ip,
       home_nfs = var.home_nfs,
       create_fss = var.create_fss,
       home_fss = var.home_fss,
@@ -417,7 +432,8 @@ resource "null_resource" "cluster" {
       bastion_username = var.bastion_username,
       compute_username = var.compute_username,
       pam = var.pam,
-      sacct_limits = var.sacct_limits
+      sacct_limits = var.sacct_limits, 
+      use_compute_agent = var.use_compute_agent
       })
 
     destination   = "/opt/oci-hpc/conf/variables.tf"
@@ -467,6 +483,7 @@ provisioner "file" {
       "chmod a+x /opt/oci-hpc/bin/*.sh",
       "timeout --foreground 60m /opt/oci-hpc/bin/bastion.sh",
       "chmod 755 /opt/oci-hpc/autoscaling/crontab/*.sh",
+      "chmod 755 /opt/oci-hpc/samples/*.sh",
       "chmod 600 /opt/oci-hpc/autoscaling/credentials/key.pem",
       "echo ${var.configure} > /tmp/configure.conf",
       "timeout 2h /opt/oci-hpc/bin/configure.sh | tee /opt/oci-hpc/logs/initial_configure.log",
@@ -487,30 +504,27 @@ data "oci_objectstorage_namespace" "compartment_namespace" {
 }
 
 locals {
-  rdma_nic_metric_bucket_name = "RDMA_NIC_metrics"
+  current_timestamp           = timestamp()
+  current_timestamp_formatted = formatdate("YYYYMMDDhhmmss", local.current_timestamp)
+  rdma_nic_metric_bucket_name = format("%s_%s","RDMA_NIC_metrics",local.current_timestamp_formatted)
   par_path = ".."
 }
 /*
 saving the PAR into file: ../PAR_file_for_metrics.
 this PAR is used by the scripts to upload NIC metrics to object storage (i.e. script: upload_rdma_nic_metrics.sh)
 */
 
-data "oci_objectstorage_bucket" "RDMA_NIC_Metrics_bucket_check" {
-  name           = local.rdma_nic_metric_bucket_name
-  namespace      = data.oci_objectstorage_namespace.compartment_namespace.namespace
-}
-
 
 resource "oci_objectstorage_bucket" "RDMA_NIC_metrics_bucket" {
-  count = (var.bastion_object_storage_par && data.oci_objectstorage_bucket.RDMA_NIC_Metrics_bucket_check.bucket_id == null) ? 1 : 0
+  count = (var.bastion_object_storage_par) ? 1 : 0
   compartment_id = var.targetCompartment
   name           = local.rdma_nic_metric_bucket_name
   namespace      = data.oci_objectstorage_namespace.compartment_namespace.namespace
   versioning     = "Enabled"
 }
 
 resource "oci_objectstorage_preauthrequest" "RDMA_NIC_metrics_par" {
-  count = (var.bastion_object_storage_par && data.oci_objectstorage_bucket.RDMA_NIC_Metrics_bucket_check.bucket_id == null) ? 1 : 0
+  count = (var.bastion_object_storage_par) ? 1 : 0
   depends_on  = [oci_objectstorage_bucket.RDMA_NIC_metrics_bucket]
   access_type = "AnyObjectWrite"
   bucket      = local.rdma_nic_metric_bucket_name
@@ -522,12 +536,12 @@ resource "oci_objectstorage_preauthrequest" "RDMA_NIC_metrics_par" {
 
 output "RDMA_NIC_metrics_url" {
  depends_on = [oci_objectstorage_preauthrequest.RDMA_NIC_metrics_par]
- value = (var.bastion_object_storage_par && data.oci_objectstorage_bucket.RDMA_NIC_Metrics_bucket_check.bucket_id == null) ? "https://objectstorage.${var.region}.oraclecloud.com${oci_objectstorage_preauthrequest.RDMA_NIC_metrics_par[0].access_uri}" : ""
+ value = (var.bastion_object_storage_par) ? "https://objectstorage.${var.region}.oraclecloud.com${oci_objectstorage_preauthrequest.RDMA_NIC_metrics_par[0].access_uri}" : ""
 }
 
 
 resource "local_file" "PAR" {
-    count = (var.bastion_object_storage_par && data.oci_objectstorage_bucket.RDMA_NIC_Metrics_bucket_check.bucket_id == null) ? 1 : 0
+    count = (var.bastion_object_storage_par) ? 1 : 0
     depends_on = [oci_objectstorage_preauthrequest.RDMA_NIC_metrics_par]
     content     = "https://objectstorage.${var.region}.oraclecloud.com${oci_objectstorage_preauthrequest.RDMA_NIC_metrics_par[0].access_uri}"
     filename = "${local.par_path}/PAR_file_for_metrics"

bin/bastion.sh

@@ -43,15 +43,15 @@ if [ $ID == "ol" ] || [ $ID == "centos" ] ; then
     sudo mkdir /etc/ansible
     sudo ln -s /usr/local/bin/ansible-playbook /bin/ansible-playbook
     sudo ln -s /usr/local/bin/ansible /bin/ansible
-    sudo python3 -m pip install -U pip
-    sudo python3 -m pip install netaddr --upgrade
-    sudo python3 -m pip install setuptools_rust --upgrade
-    sudo python3 -m pip install requests --upgrade
-    sudo python3 -m pip install urllib3 --upgrade
   fi
   sudo yum-config-manager --add-repo https://rpm.releases.hashicorp.com/RHEL/hashicorp.repo
   sudo yum install -y terraform
-   sudo python3 -m pip install oci-cli --upgrade
+  sudo python3 -m pip install -U pip
+  sudo python3 -m pip install netaddr --upgrade
+  sudo python3 -m pip install setuptools_rust --upgrade
+  sudo python3 -m pip install requests --upgrade
+  sudo python3 -m pip install urllib3 --upgrade
+  sudo python3 -m pip install oci-cli --upgrade
 
 
 elif [ $ID == "debian" ] || [ $ID == "ubuntu" ] ; then 
@@ -91,24 +91,41 @@ elif [ $ID == "debian" ] || [ $ID == "ubuntu" ] ; then
   sudo apt -y --fix-broken install
 
   fix_apt
-
+  
+  sudo add-apt-repository --yes --update ppa:ansible/ansible
   sudo apt-get -y install ansible 
   output=$?
   if [ $output -ne 0 ]
   then
       fix_apt
+      sleep 60s
       sudo apt-get -y install ansible 
   fi
   fix_apt
-  sudo apt-get -y install python python-netaddr python3 python3-pip
+
+  if [ $ID == "ubuntu" ] && [ $VERSION_ID == "22.04" ] ; then
+    sudo sed -i 's/#$nrconf{restart} = '"'"'i'"'"';/$nrconf{restart} = '"'"'a'"'"';/g' /etc/needrestart/needrestart.conf
+    sudo apt-get -y install python3 python3-netaddr python3-pip
+    sudo ln -s /usr/bin/python3 /usr/bin/python
+  else
+    sudo apt-get -y install python python-netaddr python3 python3-pip
+  fi
   output=$?
   if [ $output -ne 0 ]
   then
       fix_apt
-      sudo apt-get -y install python python-netaddr python3 python3-pip
+        if [ $ID == "ubuntu" ] && [ $VERSION_ID == "22.04" ] ; then
+          sudo apt-get -y install python3 python3-netaddr python3-pip
+
+        else
+          sudo apt-get -y install python python-netaddr python3 python3-pip
+        fi
   fi
   fix_apt
-
+  sudo python3 -m pip install -U pip
+  sudo python3 -m pip install netaddr --upgrade
+  sudo python3 -m pip install requests --upgrade
+  sudo python3 -m pip install urllib3 --upgrade
   pip install pip --upgrade
   pip install pyopenssl --upgrade
 
@@ -153,11 +170,22 @@ ansible-galaxy collection install community.crypto --force > /dev/null
 threads=$(nproc)
 forks=$(($threads * 8))
 
-sudo sed -i "s/^#forks.*/forks = ${forks}/" /etc/ansible/ansible.cfg
-sudo sed -i "s/^#fact_caching=.*/fact_caching=jsonfile/" /etc/ansible/ansible.cfg
-sudo sed -i "s/^#fact_caching_connection.*/fact_caching_connection=\/tmp\/ansible/" /etc/ansible/ansible.cfg
-sudo sed -i "s/^#bin_ansible_callbacks.*/bin_ansible_callbacks=True/" /etc/ansible/ansible.cfg
-sudo sed -i "s/^#stdout_callback.*/stdout_callback=yaml/" /etc/ansible/ansible.cfg
-sudo sed -i "s/^#retries.*/retries=5/" /etc/ansible/ansible.cfg
-sudo sed -i "s/^#connect_timeout.*/connect_timeout=300/" /etc/ansible/ansible.cfg
-sudo sed -i "s/^#command_timeout.*/command_timeout=120/" /etc/ansible/ansible.cfg
+if [ ! -d /etc/ansible ] ; then
+  sudo mkdir /etc/ansible
+  if [ $ID == "ubuntu" ] ; then
+    sudo chown ubuntu:ubuntu /etc/ansible
+  else
+    sudo chown opc:opc /etc/ansible
+  fi
+fi
+
+ansible-config init --disabled -t all | sudo tee /etc/ansible/ansible.cfg
+sudo sed -i "s/^\(#\|;\)forks.*/forks = ${forks}/" /etc/ansible/ansible.cfg
+sudo sed -i "s/^\(#\|;\)fact_caching=.*/fact_caching=jsonfile/" /etc/ansible/ansible.cfg
+sudo sed -i "0,/^\(#\|;\)fact_caching_connection.*/s//fact_caching_connection=\/tmp\/ansible/" /etc/ansible/ansible.cfg
+sudo sed -i "s/^\(#\|;\)bin_ansible_callbacks.*/bin_ansible_callbacks=True/" /etc/ansible/ansible.cfg
+sudo sed -i "s/^\(#\|;\)stdout_callback.*/stdout_callback=yaml/" /etc/ansible/ansible.cfg
+sudo sed -i "s/^\(#\|;\)retries.*/retries=5/" /etc/ansible/ansible.cfg
+sudo sed -i "s/^\(#\|;\)connect_timeout.*/connect_timeout=300/" /etc/ansible/ansible.cfg
+sudo sed -i "s/^\(#\|;\)command_timeout.*/command_timeout=120/" /etc/ansible/ansible.cfg
+

bin/create_cluster.sh

@@ -42,7 +42,6 @@ targetCompartment=`yq eval ".queues.[] | select(.name == \"$4\") | .instance_typ
 ADNames=`yq eval ".queues.[] | select(.name == \"$4\") | .instance_types.[] | select(.name == \"$3\") |.ad " $queues_conf`
 boot_volume_size=`yq eval ".queues.[] | select(.name == \"$4\") | .instance_types.[] | select(.name == \"$3\") |.boot_volume_size " $queues_conf`
 use_marketplace_image=`yq eval ".queues.[] | select(.name == \"$4\") | .instance_types.[] | select(.name == \"$3\") |.use_marketplace_image " $queues_conf`
-use_old_marketplace_image=`yq eval ".queues.[] | select(.name == \"$4\") | .instance_types.[] | select(.name == \"$3\") |.use_old_marketplace_image " $queues_conf`
 image=`yq eval ".queues.[] | select(.name == \"$4\") | .instance_types.[] | select(.name == \"$3\") |.image " $queues_conf`
 instance_pool_ocpus=`yq eval ".queues.[] | select(.name == \"$4\") | .instance_types.[] | select(.name == \"$3\") |.instance_pool_ocpus " $queues_conf`
 instance_pool_memory=`yq eval ".queues.[] | select(.name == \"$4\") | .instance_types.[] | select(.name == \"$3\") |.instance_pool_memory " $queues_conf`
@@ -68,7 +67,7 @@ do
 
   echo $1 $3 $4 >> currently_building
   echo $3 $4 > cluster_options
-  sed "s~##NODES##~$1~g;s~##NAME##~$2~g;s~##SHAPE##~$shape~g;s~##CN##~$cluster_network~g;s~##QUEUE##~${4}~g;s~##COMP##~${targetCompartment}~g;s~##AD##~${ADName}~g;s~##BOOT##~${boot_volume_size}~g;s~##USEMP##~${use_marketplace_image}~g;s~##USEOLDMP##~${use_old_marketplace_image}~g;s~##IMAGE##~${image}~g;s~##OCPU##~${instance_pool_ocpus}~g;s~##MEM##~${instance_pool_memory}~g;s~##CUSTOM_MEM##~${instance_pool_custom_memory}~g;s~##MP_LIST##~${marketplace_listing}~g;s~##HT##~${hyperthreading}~g;s~##INST_TYPE##~$3~g;s~##TAGS##~$tags~g;s~##REGION##~${region}~g;s~##PRIVATE_SUBNET_ID##~${private_subnet_id}~g;s~##PRIVATE_SUBNET##~${private_subnet}~g;s~##CC##~$compute_cluster~g" $conf_folder/variables.tf > variables.tf
+  sed "s~##NODES##~$1~g;s~##NAME##~$2~g;s~##SHAPE##~$shape~g;s~##CN##~$cluster_network~g;s~##QUEUE##~${4}~g;s~##COMP##~${targetCompartment}~g;s~##AD##~${ADName}~g;s~##BOOT##~${boot_volume_size}~g;s~##USEMP##~${use_marketplace_image}~g;s~##IMAGE##~${image}~g;s~##OCPU##~${instance_pool_ocpus}~g;s~##MEM##~${instance_pool_memory}~g;s~##CUSTOM_MEM##~${instance_pool_custom_memory}~g;s~##MP_LIST##~${marketplace_listing}~g;s~##HT##~${hyperthreading}~g;s~##INST_TYPE##~$3~g;s~##TAGS##~$tags~g;s~##REGION##~${region}~g;s~##PRIVATE_SUBNET_ID##~${private_subnet_id}~g;s~##PRIVATE_SUBNET##~${private_subnet}~g;s~##CC##~$compute_cluster~g" $conf_folder/variables.tf > variables.tf
 
   echo "Started to build $2"
   start=`date -u +%s`