Merge pull request #868 from GoogleCloudPlatform/release-candidate

Release v1.12.0

Author: cboneti

SECURITY.md

@@ -0,0 +1,6 @@
+To report a security issue, please email hpc-toolkit-security@google.com
+with a description of the issue, the steps you took to create the issue,
+affected versions, and, if known, mitigations for the issue. Our vulnerability
+management team will respond within 3 working days of your email. If the issue
+is confirmed as a vulnerability, we will open a Security Advisory. This project
+follows a 90 day disclosure timeline.

cmd/root.go

@@ -49,7 +49,7 @@ HPC deployments on the Google Cloud Platform.`,
 				log.Fatalf("cmd.Help function failed: %s", err)
 			}
 		},
-		Version:     "v1.11.0",
+		Version:     "v1.12.0",
 		Annotations: annotation,
 	}
 )

community/examples/fluent-tutorial.yaml

@@ -0,0 +1,167 @@
+# Copyright 2023 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+---
+
+blueprint_name: ansys-fluent
+
+vars:
+  project_id:  ## Set GCP Project ID Here ##
+  deployment_name: fluent-wl
+  region: us-central1
+  zone: us-central1-c
+
+deployment_groups:
+- group: primary
+  modules:
+  - source: modules/scripts/startup-script
+    kind: terraform
+    id: startup_login
+    settings:
+      runners:
+      - type: shell
+        content: |
+          #!/bin/bash
+          google_mpi_tuning --hpcthroughput
+          google_mpi_tuning --nomitigation
+          yum -y install mesa-libGLU-devel libExt nmap openssl libXrandr mesa-libGL libX11-devel libSM-devel libICE-devel libXinerama libXcursor hdf5-devel dkms zlib-devel libXext-devel libGLU-devel libXt-devel libXrender-devel libXinerama-devel libpng-devel libXrandr-devel libXi-devel libXft-devel libjpeg-turbo-devel libXcursor-devel readline-devel ncurses-devel python python-devel cmake qt-devel qt-assistant mpfr-devel gmp-devel htop wget screen vim xorg-x11-drv-dummy xorg-x11-server-utils libXp-devel xorg-x11-fonts-cyrillic.noarch xterm.x86_64 motif-devel compat-libstdc++-33.x86_64 libstdc++.x86_64 libstdc++.i686 gcc-c++.x86_64 compat-libstdc++-33.i686 libstdc++-devel.x86_64 libstdc++-devel.i686 compat-gcc-34.x86_64 gtk2.i686 libXxf86vm.i686 libSM.i686 xorg-x11-fonts-ISO8859-1-75dpi.no xorg-x11-fonts-iso8859-1-75dpi.no gdm gnome-session gnome-classic-session gnome-session-xsession xorg-x11-server-Xorg xorg-x11-drv-dummy xorg-x11-fonts-Type1 xorg-x11-utils gnome-terminal gnu-free-fonts-common gnu-free-mono-fonts gnu-free-sans-fonts gnu-free-serif-fonts alsa-plugins-pulseaudio alsa-utils hdf5-devel
+
+        destination: /tmp/install-deps.sh
+      - type: shell
+        content: |
+          #!/bin/bash
+          cat <<- "EOF" >> /etc/bashrc
+          export LD_LIBRARY_PATH=/shared/apps/fluent/v222/TurboGrid/tools/Prime/lib/:${LD_LIBRARY_PATH}
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/shared/apps/fluent/v222/commonfiles/fluids/lib/linx64/
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/shared/apps/fluent/v222/commonfiles/fluids/lib/linx64/
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/shared/apps/fluent/v222/fluent/fluent22.2.0/multiport/lnamd64/mpi/shared/
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/shared/apps/fluent/shared_files/syslib/linx64
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/shared/apps/fluent/v222/aisol/lib/linx64/
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/shared/apps/fluent/v222/polyflow/polyflow22.2.0/lnamd64/libs/
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/shared/apps/fluent/v222/tp/IntelMKL/2021.3.0/linx64/lib/intel64/
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/shared/apps/fluent/v222/fluent/lib/lnamd64/
+          export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/shared/apps/fluent/v222/dcs/
+          export INTELMPI_ROOT=/shared/apps/intel/compilers_and_libraries_2018.5.274/linux/mpi/intel64
+          source /shared/apps/intel/parallel_studio_xe_2018.4.057/psxevars.sh
+          EOF
+
+        destination: /tmp/install-bashrc.sh
+      - type: shell
+        content: |
+          #!/bin/bash
+          mkdir /tmp/intel
+          cd /tmp/intel
+          wget https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13741/l_mpi_2018.4.274.tgz
+          tar xvf l_mpi_2018.4.274.tgz
+          cd l_mpi_2018.4.274
+          patch silent.cfg <<- "EOF1"
+          16:07:46.199308305 +0000
+          @@ -6,13 +6,13 @@
+           # snpat       - the serial number pattern (ABCD-01234567)
+
+           # Accept EULA, valid values are: {accept, decline}
+          -ACCEPT_EULA=decline
+          +ACCEPT_EULA=accept
+
+           # Optional error behavior, valid values are: {yes, no}
+           CONTINUE_WITH_OPTIONAL_ERROR=yes
+
+           # Install location, valid values are: {/opt/intel, filepat}
+          -PSET_INSTALL_DIR=/opt/intel
+          +PSET_INSTALL_DIR=/shared/apps/intel
+
+           # Continue with overwrite of existing installation directory, valid values are: {yes, no}
+           CONTINUE_WITH_INSTALLDIR_OVERWRITE=yes
+          EOF1
+
+          sudo ./install.sh -s silent.cfg
+
+        destination: /tmp/install-mpi.sh
+
+  - source: modules/scripts/startup-script
+    kind: terraform
+    id: startup
+    settings:
+      runners:
+      - type: shell
+        content: |
+          #!/bin/bash
+          google_mpi_tuning --hpcthroughput
+          google_mpi_tuning --nomitigation
+          yum -y install mesa-libGLU-devel libExt nmap openssl libXrandr mesa-libGL libX11-devel libSM-devel libICE-devel libXinerama libXcursor hdf5-devel dkms zlib-devel libXext-devel libGLU-devel libXt-devel libXrender-devel libXinerama-devel libpng-devel libXrandr-devel libXi-devel libXft-devel libjpeg-turbo-devel libXcursor-devel readline-devel ncurses-devel python python-devel cmake qt-devel qt-assistant mpfr-devel gmp-devel htop wget screen vim xorg-x11-drv-dummy xorg-x11-server-utils libXp-devel xorg-x11-fonts-cyrillic.noarch xterm.x86_64 motif-devel compat-libstdc++-33.x86_64 libstdc++.x86_64 libstdc++.i686 gcc-c++.x86_64 compat-libstdc++-33.i686 libstdc++-devel.x86_64 libstdc++-devel.i686 compat-gcc-34.x86_64 gtk2.i686 libXxf86vm.i686 libSM.i686 xorg-x11-fonts-ISO8859-1-75dpi.no xorg-x11-fonts-iso8859-1-75dpi.no gdm gnome-session gnome-classic-session gnome-session-xsession xorg-x11-server-Xorg xorg-x11-drv-dummy xorg-x11-fonts-Type1 xorg-x11-utils gnome-terminal gnu-free-fonts-common gnu-free-mono-fonts gnu-free-sans-fonts gnu-free-serif-fonts alsa-plugins-pulseaudio alsa-utils hdf5-devel
+
+        destination: /tmp/install-deps.sh
+      - type: shell
+        content: |
+          #!/bin/bash
+          hostname >> /home/hosts.txt
+        destination: /tmp/install-hosts.sh
+
+  - source: modules/file-system/filestore
+    kind: terraform
+    id: homefs
+    settings:
+      network_name: "default"
+      size_gb: 1024
+      filestore_tier: "BASIC_HDD"
+      local_mount: /home
+
+  - source: modules/file-system/filestore
+    kind: terraform
+    id: sharefs
+    settings:
+      network_name: "default"
+      size_gb: 1024
+      filestore_tier: "BASIC_HDD"
+      local_mount: /shared
+
+  - source: modules/compute/vm-instance
+    kind: terraform
+    id: compute_1
+    use:
+    - homefs
+    - sharefs
+    - startup
+    settings:
+      threads_per_core: 1
+      disable_public_ips: false
+      bandwidth_tier: "gvnic_enabled"
+      machine_type: c2-standard-60
+      instance_count: 4
+      name_prefix: fluent-compute
+      placement_policy:
+        vm_count: 4  # Note: should match instance count
+        collocation: "COLLOCATED"
+        availability_domain_count: null
+
+  - source: modules/compute/vm-instance
+    kind: terraform
+    id: login
+    use:
+    - homefs
+    - sharefs
+    - startup_login
+    settings:
+      threads_per_core: 1
+      disable_public_ips: false
+      bandwidth_tier: "gvnic_enabled"
+      machine_type: c2-standard-8
+      instance_count: 1
+      name_prefix: fluent-login
+
+  - source: community/modules/scripts/wait-for-startup
+    kind: terraform
+    id: wait
+    settings:
+      instance_name: ((module.compute_1.name[0]))

community/examples/intel/README.md

@@ -261,7 +261,7 @@ Follow `ghpc` instructions to deploy the environment
 
 The `community/examples/intel/daos-cluster.yaml` blueprint does not contain configuration for DAOS pools and containers. Therefore, pools and containers will need to be created manually.
 
-Before pools and containers can be created the storage system must be formatted. Formatting the storage is done automatically by the startup script that runs on the *daos-server-0001* instance. The startup script will run the [dmg storage format](https://docs.daos.io/v2.0/admin/deployment/?h=dmg+storage#storage-formatting) command. It may take a few minutes for all daos server instances to join.
+Before pools and containers can be created the storage system must be formatted. Formatting the storage is done automatically by the startup script that runs on the *daos-server-0001* instance. The startup script will run the [dmg storage format](https://docs.daos.io/v2.2/admin/deployment/?h=dmg+storage#storage-formatting) command. It may take a few minutes for all daos server instances to join.
 
 Verify that the storage system has been formatted and that the daos-server instances have joined.
 
@@ -286,9 +286,9 @@ Both daos-server instances should show a state of *Joined*.
 
 #### About the DAOS Command Line Tools
 
-The DAOS Management tool `dmg` is used by System Administrators to manange the DAOS storage [system](https://docs.daos.io/v2.0/overview/architecture/#daos-system) and DAOS [pools](https://docs.daos.io/v2.0/overview/storage/#daos-pool). Therefore, `sudo` must be used when running `dmg`.
+The DAOS Management tool `dmg` is used by System Administrators to manange the DAOS storage [system](https://docs.daos.io/v2.2/overview/architecture/#daos-system) and DAOS [pools](https://docs.daos.io/v2.2/overview/storage/#daos-pool). Therefore, `sudo` must be used when running `dmg`.
 
-The DAOS CLI `daos` is used by both users and System Administrators to create and manage [containers](https://docs.daos.io/v2.0/overview/storage/#daos-container). It is not necessary to use `sudo` with the `daos` command.
+The DAOS CLI `daos` is used by both users and System Administrators to create and manage [containers](https://docs.daos.io/v2.2/overview/storage/#daos-container). It is not necessary to use `sudo` with the `daos` command.
 
 #### Determine Free Space
 
@@ -323,7 +323,7 @@ Set ACLs to allow any user to create a container in *pool1*.
 sudo dmg pool update-acl -e A::EVERYONE@:rcta pool1
 ```
 
-See the [Pool Operations](https://docs.daos.io/v2.0/admin/pool_operations) section of the of the DAOS Administration Guide for more information about creating pools.
+See the [Pool Operations](https://docs.daos.io/v2.2/admin/pool_operations) section of the of the DAOS Administration Guide for more information about creating pools.
 
 #### Create a Container
 
@@ -336,10 +336,10 @@ For the purpose of this demo create the container without specifying ACLs. The c
 daos cont create pool1 \
   --label cont1 \
   --type POSIX \
-  --properties rf:1
+  --properties rf:0
 ```
 
-See the [Container Management](https://docs.daos.io/v2.0/user/container) section of the of the DAOS User Guide for more information about creating containers.
+See the [Container Management](https://docs.daos.io/v2.2/user/container) section of the of the DAOS User Guide for more information about creating containers.
 
 #### Mount the DAOS Container
 
@@ -371,7 +371,7 @@ time LD_PRELOAD=/usr/lib64/libioil.so \
 dd if=/dev/zero of=./test20GiB.img iflag=fullblock bs=1G count=20
 ```
 
-See the [File System](https://docs.daos.io/v2.0/user/filesystem/) section of the DAOS User Guide for more information about DFuse.
+See the [File System](https://docs.daos.io/v2.2/user/filesystem/) section of the DAOS User Guide for more information about DFuse.
 
 ### Unmount the DAOS Container
 
@@ -387,7 +387,7 @@ Verify that the container is unmounted
 df -h -t fuse.daos
 ```
 
-See the [DFuse (DAOS FUSE)](https://docs.daos.io/v2.0/user/filesystem/?h=dfuse#dfuse-daos-fuse) section of the DAOS User Guide for more information about mounting POSIX containers.
+See the [DFuse (DAOS FUSE)](https://docs.daos.io/v2.2/user/filesystem/?h=dfuse#dfuse-daos-fuse) section of the DAOS User Guide for more information about mounting POSIX containers.
 
 ### Delete the DAOS infrastructure when not in use
 
@@ -596,7 +596,7 @@ Verify that the container is unmounted
 df -h -t fuse.daos
 ```
 
-See the [DFuse (DAOS FUSE)](https://docs.daos.io/v2.0/user/filesystem/?h=dfuse#dfuse-daos-fuse) section of the DAOS User Guide for more information about mounting POSIX containers.
+See the [DFuse (DAOS FUSE)](https://docs.daos.io/v2.2/user/filesystem/?h=dfuse#dfuse-daos-fuse) section of the DAOS User Guide for more information about mounting POSIX containers.
 
 ### Delete the DAOS/Slurm Cluster infrastructure when not in use
 

community/examples/intel/daos-cluster.yaml

@@ -35,7 +35,7 @@ deployment_groups:
   # https://github.com/daos-stack/google-cloud-daos/tree/main/images
   # more info: https://github.com/daos-stack/google-cloud-daos/tree/main/terraform/modules/daos_server
   - id: daos-server
-    source: github.com/daos-stack/google-cloud-daos.git//terraform/modules/daos_server?ref=v0.2.1
+    source: github.com/daos-stack/google-cloud-daos.git//terraform/modules/daos_server?ref=v0.3.0
     use: [network1]
     settings:
       number_of_instances: 2
@@ -45,7 +45,7 @@ deployment_groups:
   # https://github.com/daos-stack/google-cloud-daos/tree/main/images
   # more info: https://github.com/daos-stack/google-cloud-daos/tree/main/terraform/modules/daos_client
   - id: daos-client
-    source: github.com/daos-stack/google-cloud-daos.git//terraform/modules/daos_client?ref=v0.2.1
+    source: github.com/daos-stack/google-cloud-daos.git//terraform/modules/daos_client?ref=v0.3.0
     use: [network1, daos-server]
     settings:
       number_of_instances: 2

community/examples/intel/daos-slurm.yaml

@@ -41,7 +41,7 @@ deployment_groups:
   # https://github.com/daos-stack/google-cloud-daos/tree/main/images
   # more info: https://github.com/daos-stack/google-cloud-daos/tree/main/terraform/modules/daos_server
   - id: daos
-    source: github.com/daos-stack/google-cloud-daos.git//terraform/modules/daos_server?ref=v0.2.1
+    source: github.com/daos-stack/google-cloud-daos.git//terraform/modules/daos_server?ref=v0.3.0
     use: [network1]
     settings:
       labels: {ghpc_role: file-system}

community/front-end/ofe/website/ghpcfe/models.py

@@ -643,10 +643,10 @@ class Cluster(CloudResource):
     )
     login_node_disk_size = models.PositiveIntegerField(
         # login node disk must be large enough to hold the SlurmGCP
-        # image: >=30GB
-        validators=[MinValueValidator(30)],
+        # image: >=50GB
+        validators=[MinValueValidator(50)],
         help_text="Boot disk size (in GB)",
-        default=30,
+        default=50,
         blank=True,
     )
     grafana_dashboard_url = models.CharField(

community/front-end/ofe/website/nginx.conf

@@ -39,8 +39,8 @@ http {
             set $gitScript /usr/libexec/git-core/git-http-backend;
         }
 
-        location /static {
-            alias ../hpc-toolkit/community/front-end/website/static/;
+        location /static/ {
+            alias ../hpc-toolkit/community/front-end/ofe/website/static/;
         }
 
         location / {

community/modules/compute/SchedMD-slurm-on-gcp-partition/README.md

@@ -27,6 +27,11 @@ The following code snippet creates a partition module with:
     machine_type: c2-standard-30
 ```
 
+## GPU Support
+
+More information on GPU support in Slurm on GCP and other HPC Toolkit modules
+can be found at [docs/gpu-support.md](../../../../docs/gpu-support.md)
+
 ## Support
 The HPC Toolkit team maintains the wrapper around the [slurm-on-gcp] terraform
 modules. For support with the underlying modules, see the instructions in the

community/modules/compute/pbspro-execution/README.md

@@ -31,6 +31,11 @@ concert with the [pbspro-preinstall], [pbspro-server], and [filestore] modules.
 [pbspro-preinstall]: ../../scripts/pbspro-preinstall/README.md
 [filestore]: ../../../../modules/file-system/filestore/README.md
 
+## GPU Support
+
+More information on GPU support in PBS Pro and other HPC Toolkit modules
+can be found at [docs/gpu-support.md](../../../../docs/gpu-support.md)
+
 ## Support
 
 PBS Professional is licensed and supported by [Altair][pbspro]. This module is