Merge branch 'NGC_containers_' into 'preview'

Ngc containers

Closes #22

See merge request zih/hpcsupport/hpc-compendium!339

doc.zih.tu-dresden.de/docs/software/ngc_containers.md

+# GPU-accelerated Containers for Deep Learning (NGC Containers)
+
+A [container](containers.md) is an executable and portable unit of software.
+On ZIH systems, [Singularity](https://sylabs.io/) is used as a standard container solution.
+
+[NGC](https://developer.nvidia.com/ai-hpc-containers),
+a registry of highly GPU-optimized software,
+has been enabling scientists and researchers by providing regularly updated
+and validated containers of HPC and AI applications.
+NGC containers are **GPU-optimized** containers
+for deep learning, machine learning, visualization:
+
+- Built-in libraries and dependencies;
+- Faster training with Automatic Mixed Precision (AMP);
+- Opportunity to scale up from single-node to multi-node systems;
+- Performance optimized.
+
+!!! note "Advantages of NGC containers"
+    - NGC containers were highly optimized for cluster usage.
+        The performance provided by NGC containers is comparable to the performance
+        provided by the modules on the ZIH system (which is potentially the most performant way).
+        NGC containers are a quick and efficient way to apply the best models
+        on your dataset on a ZIH system;
+    - NGC containers allow using an exact version of the software
+        without installing it with all prerequisites manually.
+        Manual installation can result in poor performance (e.g. using conda to install a software).
+
+## Run NGC Containers on the ZIH System
+
+The first step is a choice of the necessary software (container) to run.
+The [NVIDIA NGC catalog](https://ngc.nvidia.com/catalog)
+contains a host of GPU-optimized containers for deep learning,
+machine learning, visualization, and HPC applications that are tested
+for performance, security, and scalability.
+It is necessary to register to have full access to the catalog.
+
+To find a container that fits the requirements of your task, please check
+the [official examples page](https://github.com/NVIDIA/DeepLearningExamples)
+with the list of main containers with their features and peculiarities.
+
+### Run NGC container on a Single GPU
+
+!!! note
+    Almost all NGC containers can work with a single GPU.
+
+To use NGC containers, it is necessary to understand the main Singularity commands.
+
+If you are not familiar with Singularity's syntax, please find the information on the
+[official page](https://sylabs.io/guides/3.0/user-guide/quick_start.html#interact-with-images).
+However, some main commands will be explained.
+
+Create a container from the image from the NGC catalog.
+(For this example, the alpha is used):
+
+```console
+marie@login$ srun --partition=alpha --nodes=1 --ntasks-per-node=1 --ntasks=1 --gres=gpu:1 --time=08:00:00 --pty --mem=50000 bash 
+
+marie@compute$ cd /scratch/ws/<name_of_your_workspace>/containers   #please create a Workspace
+
+marie@compute$ singularity pull pytorch:21.08-py3.sif docker://nvcr.io/nvidia/pytorch:21.08-py3
+```
+
+Now, you have a fully functional PyTorch container.
+
+Please pay attention, using `srun` directly on the shell will lead to
+background by using batch jobs.
+For that, you can conveniently put the parameters directly into the job file,
+which you can submit using `sbatch` command.
+
+In the majority of cases, the container doesn't contain the dataset for training models.
+To download the dataset, please follow the
+[instructions](https://github.com/NVIDIA/DeepLearningExamples) for the exact container.
+Also, you can find the instructions in a README file which you can find inside the container:
+
+```console
+marie@compute$ singularity exec pytorch:21.06-py3_beegfs vim /workspace/examples/resnet50v1.5/README.md
+```
+
+It is recommended to run the container with a single command.
+However, for the educational purpose, the separate commands will be presented below:
+
+```console
+marie@login$ srun --partition=alpha --nodes=1 --ntasks-per-node=1 --ntasks=1 --gres=gpu:1 --time=08:00:00 --pty --mem=50000 bash
+```
+
+Run a shell within a container with the `singularity shell` command:
+
+```console
+marie@compute$ singularity shell --nv -B /scratch/imagenet:/data/imagenet pytorch:21.06-py3
+```
+
+The flag `--nv` in the command above was used to enable Nvidia support for GPU usage
+and a flag `-B` for a user-bind path specification.
+
+Run the training inside the container:
+
+```console
+marie@container$ python /workspace/examples/resnet50v1.5/multiproc.py --nnodes=1 --nproc_per_node=1 \
+                --node_rank=0 /workspace/examples/resnet50v1.5/main.py --data-backend dali-cpu \
+                --raport-file raport.json -j16 -p 100 --lr 2.048 --optimizer-batch-size 2048 --warmup 8 \
+                --arch resnet50 -c fanin --label-smoothing 0.1 --lr-schedule cosine --mom 0.875 \
+                --wd 3.0517578125e-05 -b 256 --epochs 90 /data/imagenet
+```
+
+!!! warning
+    Please keep in mind that it is necessary to specify the amount of resources that you use inside
+    the container, especially if you have allocated more resources in the cluster. Regularly, you
+    can do it with flags such as `--nproc_per_node`. You can find more information in the README
+    file inside the container.
+
+As an example, please find the full command to run the ResNet50 model
+on the ImageNet dataset inside the PyTorch container:
+
+```console
+marie@login$ srun --partition=alpha --nodes=1 --ntasks-per-node=1 --ntasks=1 --gres=gpu:1 --time=08:00:00 --pty --mem=50000 \
+                singularity exec --nv -B /scratch/ws/0/anpo879a-ImgNet/imagenet:/data/imagenet pytorch:21.06-py3 \
+                python /workspace/examples/resnet50v1.5/multiproc.py --nnodes=1 --nproc_per_node 1 \
+                --node_rank=0 /workspace/examples/resnet50v1.5/main.py --data-backend dali-cpu --raport-file raport.json \
+                -j16 -p 100 --lr 2.048 --optimizer-batch-size 2048 --warmup 8 --arch resnet50 -c fanin --label-smoothing 0.1 \
+                --lr-schedule cosine --mom 0.875 --wd 3.0517578125e-05 -b 256 --epochs 90 /data/imagenet
+```
+
+### Multi-GPU Usage
+
+The majority of the NGC containers allow you to use multiple GPUs from one node
+to run the model inside the container.
+However, the NGC containers were made by Nvidia for the Nvidia cluster,
+which is not ZIH system.
+Moreover, editing NGC containers requires root privileges,
+which can be done only with [containers](containers.md) on ZIH systems.
+Thus, there is no guarantee that all NGC containers work right out of the box.
+
+However, PyTorch and TensorFlow containers support multi-GPU usage.
+
+An example of using the PyTorch container for the training of the ResNet50 model
+on the classification task on the ImageNet dataset is presented below:
+
+```console
+marie@login$ srun --partition=alpha --nodes=1 --ntasks-per-node=8 --ntasks=8 --gres=gpu:8 --time=08:00:00 --pty --mem=700G bash
+```
+
+```console
+marie@alpha$ singularity exec --nv -B /scratch/ws/0/marie-ImgNet/imagenet:/data/imagenet pytorch:21.06-py3 \
+                python /workspace/examples/resnet50v1.5/multiproc.py --nnodes=1 --nproc_per_node 8 \
+                --node_rank=0 /workspace/examples/resnet50v1.5/main.py --data-backend dali-cpu \
+                --raport-file raport.json -j16 -p 100 --lr 2.048 --optimizer-batch-size 2048 --warmup 8 \
+                --arch resnet50 -c fanin --label-smoothing 0.1 --lr-schedule cosine --mom 0.875 \
+                --wd 3.0517578125e-05 -b 256 --epochs 90 /data/imagenet
+```
+
+Please pay attention to the parameter `--nproc_per_node`.
+The value is equal to 8 because 8 GPUs per node were allocated with `--gres=gpu:8`.
+
+### Multi-node Usage
+
+There are few NGC containers with Multi-node support
+[available](https://github.com/NVIDIA/DeepLearningExamples).
+Moreover, the realization of the multi-node usage depends on the authors
+of the exact container.
+Thus, right now, it is not possible to run NGC containers with multi-node support
+on the ZIH system without changing the source code inside the container.

doc.zih.tu-dresden.de/mkdocs.yml

@@ -32,6 +32,7 @@ nav:
       - Singularity Recipes and Hints: software/singularity_recipe_hints.md
       - Virtual Machines Tools: software/virtual_machines_tools.md
       - Virtual Machines: software/virtual_machines.md
+      - NGC Containers: software/ngc_containers.md
     - Applications:
       - Licenses: software/licenses.md
       - Computational Fluid Dynamics (CFD): software/cfd.md

doc.zih.tu-dresden.de/wordlist.aspell

@@ -222,6 +222,7 @@ parallelize
 parfor
 pdf
 Perf
+performant
 PESSL
 PGI
 PiB
@@ -252,6 +253,7 @@ README
 reproducibility
 requeueing
 resnet
+ResNet
 RHEL
 Rmpi
 rome
@@ -268,6 +270,7 @@ Sandybridge
 Saxonid
 sbatch
 ScaDS
+scalability
 scalable
 ScaLAPACK
 Scalasca