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Deploying RAPIDS #39

Closed quasiben closed 1 year ago

quasiben commented 4 years ago

When deploying to GPUs I'd like the option of using the RAPIDS stack. This can be deployed either with a set of conda packages (with optional nightlies):

conda install -c rapidsai -c nvidia -c conda-forge rapids=0.14 cudatoolkit=$CUDA_VERSION

or official rapids images on dockerhub. In either case, deploying Dask+RAPIDS typically means using dask-cuda-workers instead of the dask-worker. dask-cuda-workers are opinionated in configuring GPUs for dask (1 worker/1 thread per GPU).

I'm not sure what is the best for users and coiled here. Some up front knowledge may be needed to be exposed to the user about the GPUs, specifically the CUDA VERSION on the machine: 10.1/10.2/11. We'd also want the option of using a different worker (maybe this is generalized to any executable ? though that's probably a big can of worms).

The RAPIDS nightly docker images is quite nice as it combines RAPIDS/DASK/XGBoost/etc and necessary dependencies. However, the conda env is store /opt/conda/rapids and I don't think coiled exposes a custom path/conda option for docker images at the moments

The next thing after RAPIDS is working nicely is getting BlazingSQL which can also be installed with conda/docker:

conda install -c blazingsql/label/cuda10.2 -c blazingsql -c rapidsai -c nvidia -c conda-forge -c defaults blazingsql python=3.7

From BSQL install docs.

mrocklin commented 4 years ago

In either case, deploying Dask+RAPIDS typically means using dask-cuda-workers instead of the dask-worker. dask-cuda-workers are opinionated in configuring GPUs for dask (1 worker/1 thread per GPU).

I've raised an issue internally with a design for supporting CUDAWorker (and other things along the way) I think that it will take about a day, but it might not be the first thing we start working on on Monday.

I'm curious if we can, short term, ask for tasks that have a single CPU core and if that would sufficiently mimic dask-cuda-worker for short-term use.

I'm not sure what is the best for users and coiled here. Some up front knowledge may be needed to be exposed to the user about the GPUs, specifically the CUDA VERSION on the machine: 10.1/10.2/11.

Yeah, I'm not sure what is best here yet. Let's think on this.

The RAPIDS nightly docker images is quite nice as it combines RAPIDS/DASK/XGBoost/etc and necessary dependencies. However, the conda env is store /opt/conda/rapids and I don't think coiled exposes a custom path/conda option for docker images at the moments

I don't suppose that the python command on the path points to the right executable, does it?

mrocklin commented 4 years ago

Hrm, I tried building a software environment, but I ran into the space-on-device issue again (which we're working to resolve)

coiled.create_software_environment(
    name='rapids', 
    conda={
        "channels": ["blazingsql/label/cuda10.2", "blazingsql", "rapidsai", "nvidia", "conda-forge", "defaults"], 
        "dependencies": ["blazingsql", "rapids=0.14", "cudatoolkit=10.2"]
    }
)
Traceback ```python-traceback ~/workspace/coiled/cloud/python-api/coiled/core.py in create_software_environment(name, conda, pip, container, log_output, post_build) 796 container=container, 797 post_build=post_build, --> 798 log_output=log_output, 799 ) 800 ~/workspace/coiled/cloud/python-api/coiled/core.py in create_software_environment(self, name, conda, pip, container, post_build, log_output) 437 container=container, 438 post_build=post_build, --> 439 log_output=log_output, 440 ) 441 ~/workspace/coiled/cloud/python-api/coiled/core.py in _sync(self, func, asynchronous, callback_timeout, *args, **kwargs) 276 else: 277 return sync( --> 278 self.loop, func, *args, callback_timeout=callback_timeout, **kwargs 279 ) 280 ~/workspace/distributed/distributed/utils.py in sync(loop, func, callback_timeout, *args, **kwargs) 337 if error[0]: 338 typ, exc, tb = error[0] --> 339 raise exc.with_traceback(tb) 340 else: 341 return result[0] ~/workspace/distributed/distributed/utils.py in f() 321 if callback_timeout is not None: 322 future = asyncio.wait_for(future, callback_timeout) --> 323 result[0] = yield future 324 except Exception as exc: 325 error[0] = sys.exc_info() ~/miniconda/lib/python3.7/site-packages/tornado/gen.py in run(self) 733 734 try: --> 735 value = future.result() 736 except Exception: 737 exc_info = sys.exc_info() ~/workspace/coiled/cloud/python-api/coiled/core.py in _create_software_environment(self, name, conda, pip, container, post_build, log_output) 520 error_details = await self._websocket_stream(ws, log_output, use_spinner=False) 521 if error_details: --> 522 raise ValueError(f"Unable to update Environment: {error_details}") 523 524 async def _list_software_environments(self, account=None): ValueError: Unable to update Environment: Docker build failed: STEP 1: FROM continuumio/miniconda3:4.8.2 STEP 2: COPY environment.yml environment.yml STEP 3: RUN conda env update -n base -f environment.yml && conda clean --all -y Collecting package metadata 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send2trash-1.5.0-py_0.tar.bz2 Removed tzcode-2020a-h516909a_0.tar.bz2 Removed pysocks-1.7.1-py37hc8dfbb8_1.tar.bz2 Removed libcudf-0.14.0-cuda10.2_0.tar.bz2 Removed xorg-xextproto-7.3.0-h14c3975_1002.tar.bz2 Removed tiledb-1.7.7-hcde45ca_0.tar.bz2 Removed libspatialite-4.3.0a-h2482549_1038.tar.bz2 Removed python_abi-3.7-1_cp37m.tar.bz2 Removed testpath-0.4.4-py_0.tar.bz2 Removed click-plugins-1.1.1-py_0.tar.bz2 Removed pyopenssl-19.1.0-py_1.tar.bz2 Removed cudf-0.14.0-py37_0.tar.bz2 Removed icu-64.2-he1b5a44_1.tar.bz2 Removed libgcrypt-1.8.4-hf484d3e_1000.tar.bz2 Removed prompt-toolkit-3.0.5-py_1.tar.bz2 Removed cudatoolkit-10.2.89-h6bb024c_0.tar.bz2 Removed grpc-cpp-1.23.0-h18db393_0.tar.bz2 Removed webencodings-0.5.1-py_1.tar.bz2 Removed xorg-libxrender-0.9.10-h516909a_1002.tar.bz2 Removed cligj-0.5.0-py_0.tar.bz2 Removed pyzmq-19.0.2-py37hac76be4_0.tar.bz2 Removed pexpect-4.8.0-py37hc8dfbb8_1.tar.bz2 Removed jupyter_core-4.6.3-py37hc8dfbb8_1.tar.bz2 Removed freetype-2.10.2-he06d7ca_0.tar.bz2 Removed cuxfilter-0.14.0-py37_0.tar.bz2 Removed jpype1-1.0.2-py37h99015e2_0.tar.bz2 Removed zlib-1.2.11-h516909a_1006.tar.bz2 Removed importlib_metadata-1.7.0-0.tar.bz2 Removed backports-1.0-py_2.tar.bz2 Removed _libgcc_mutex-0.1-conda_forge.tar.bz2 Removed double-conversion-3.1.5-he1b5a44_2.tar.bz2 WARNING: /root/.conda/pkgs does not exist Cache location: /opt/conda/pkgs Will remove the following packages: /opt/conda/pkgs --------------- rapids-0.14.1-cuda10.2_py37_0 12 KB python_abi-3.7-1_cp37m 10 KB importlib_metadata-1.7.0-0 8 KB _libgcc_mutex-0.1-conda_forge 6 KB parquet-cpp-1.5.1-2 8 KB rapids-xgboost-0.14.1-cuda10.2_py37_0 9 KB bsql-toolchain-0.14.0-0 17 KB libcblas-3.8.0-17_openblas 38 KB dask-2.22.0-py_0 12 KB libblas-3.8.0-17_openblas 39 KB liblapack-3.8.0-17_openblas 38 KB xgboost-1.1.0dev.rapidsai0.14-cuda10.2py37_0 37 KB pyct-0.4.6-py_0 7 KB pthread-stubs-0.4-h14c3975_1001 12 KB _openmp_mutex-4.5-1_gnu 93 KB --------------------------------------------------- Total: 347 KB removing rapids-0.14.1-cuda10.2_py37_0 removing python_abi-3.7-1_cp37m removing importlib_metadata-1.7.0-0 removing _libgcc_mutex-0.1-conda_forge removing parquet-cpp-1.5.1-2 removing rapids-xgboost-0.14.1-cuda10.2_py37_0 removing bsql-toolchain-0.14.0-0 removing libcblas-3.8.0-17_openblas removing dask-2.22.0-py_0 removing libblas-3.8.0-17_openblas removing liblapack-3.8.0-17_openblas removing xgboost-1.1.0dev.rapidsai0.14-cuda10.2py37_0 removing pyct-0.4.6-py_0 removing pthread-stubs-0.4-h14c3975_1001 removing _openmp_mutex-4.5-1_gnu STEP 4: COMMIT e49ee83ce0 ==> WARNING: A newer version of conda exists. <== current version: 4.8.2 latest version: 4.8.3 Please update conda by running $ conda update -n base -c defaults conda Getting image source signatures Copying blob sha256:f2cb0ecef392f2a630fa1205b874ab2e2aedf96de04d0b8838e4e728e28142da Copying blob sha256:875120aa853cf59c6c5bc24af9f448a55f9b64db0bab58c9ee18f8a92ed8ac33 Copying blob sha256:fcd8d39597dd39d0c68670479e4d240fa9dba04a1246587384df9e1aa31b17d4 Copying blob sha256:6cd19a4f6e7a004acd117342e7f1972ded4cb29be18b8624f00eb3ba07cc5a81 Copying config sha256:bff516e990195910efb4983a7390d6fedf180718eaff26b77f2d9b67ebb0b212 Writing manifest to image destination Storing signatures level=error msg="Error while applying layer: ApplyLayer exit status 1 stdout: stderr: write /opt/conda/bin/psql: no space left on device" error committing container for step {Env:[PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin LANG=C.UTF-8 LC_ALL=C.UTF-8] Command:run Args:[conda env update -n base -f environment.yml && conda clean --all -y] Flags:[] Attrs:map[] Message:RUN conda env update -n base -f environment.yml && conda clean --all -y Original:RUN conda env update -n base -f environment.yml && conda clean --all -y}: error copying layers and metadata for container "18f1241f314ec9557ec8c8e3554bb97c9984967030e726d0537af6c4ed1ce3c7": Error committing the finished image: error adding layer with blob "sha256:6cd19a4f6e7a004acd117342e7f1972ded4cb29be18b8624f00eb3ba07cc5a81": ApplyLayer exit status 1 stdout: stderr: write /opt/conda/bin/psql: no space left on device ```
quasiben commented 4 years ago

I don't suppose that the python command on the path points to the right executable, does it?

Yes, I think it is though the docker image, by default starts a jupyter lab session as well: https://github.com/rapidsai/docker/blob/branch-0.15/context/.run_in_rapids.sh

@jacobtomlinson and i were looking to. change some of the behaviors around Jupyterlab moving forward: https://github.com/rapidsai/docker/issues/133

Any progress on the space issue ?

jacobtomlinson commented 4 years ago

The container currently activates the correct conda environment as part of the entrypoint. So if you run the container with a custom command then python should be the correct one.

mrocklin commented 4 years ago

@jrbourbeau is working this afternoon on generalizing our use of dask-worker to make this customizable. We should be dask-cuda-worker friendly within a day or two.

I'm curious, have folks been able to get things running today with dask-worker? @quasiben I think that you had this up at some point. If you have a cluster configuration that I could start up I would welcome that.

cc also @sheer-coiled who might be interested in this topic.

mrocklin commented 4 years ago

Also, timing wise, I have a goal of having things up and running smoothly by next Tuesday, when I'm on the hook to give a multi-gpu RAPIDS talk and mini-tutorial with RAPIDS-Academy (we bumped it from tomorrow to next week).

As a stretch goal, I think that @TomAugspurger is participating in a Coiled live stream with Hugo on Thursday on machine learning. I'm not sure how much he's planning to talk about GPU stuff, but if we made this easy for him we might tempt him into it :)

quasiben commented 4 years ago

I tried creating an env this morning and I'm still seeing no space left on device. However, the env was created and the docker image moved onto cleanup after the install step

necaris commented 4 years ago

@quasiben just confirming this was on beta.coiledhq.com?

quasiben commented 4 years ago

Correct

On Wed, Aug 12, 2020, 9:44 AM Rami Chowdhury notifications@github.com wrote:

@quasiben https://github.com/quasiben just confirming this was on beta.coiledhq.com?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/coiled/coiled-issues/issues/39#issuecomment-672879250, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKWW6E7LLY2YXCR7SO2GWTSAKMDFANCNFSM4PYLSONA .

quasiben commented 4 years ago

On another coiled endpoint I was successful in building an env there cc @mrocklin

necaris commented 4 years ago

@quasiben I've pushed an update to the infrastructure so the no space left on device issue is hopefully vanquished.

necaris commented 4 years ago

I have a cluster configuration necaris/gputest on beta.coiledhq.com that will consistently launch. However, it's not able to run GPU code:

ImportError: CuPy is not correctly installed.

If you are using wheel distribution (cupy-cudaXX), make sure that the version of CuPy you installed matches with the version of CUDA on your host.
Also, confirm that only one CuPy package is installed:
  $ pip freeze

If you are building CuPy from source, please check your environment, uninstall CuPy and reinstall it with:
  $ pip install cupy --no-cache-dir -vvvv

Check the Installation Guide for details:
  https://docs.cupy.dev/en/latest/install.html

original error: libcuda.so.1: cannot open shared object file: No such file or directory

Software environment details:

{
  "channels": [
    "rapidsai",
    "nvidia",
    "conda-forge"
  ],
  "dependencies": [
    "cudatoolkit=10.1",
    "cudf",
    "cupy",
    "dask",
    "distributed",
    "pandas",
    "python=3.7"
  ]
}

Output of client.run(lambda: subprocess.check_output(['nvidia-smi'])):

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 418.87.00    Driver Version: 418.87.00    CUDA Version: N/A      |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  Tesla V100-SXM2...  On   | 00000000:00:1E.0 Off |                    0 |
| N/A   39C    P0    25W / 300W |      0MiB / 16130MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID   Type   Process name                             Usage      |
|=============================================================================|
|  No running processes found                                                 |
+-----------------------------------------------------------------------------+

Output of docker inspect on the container (with the TLS details snipped out):

[
    {
        "Id": "aad0062158911ed3f244ad55b9d36d87e5b3357960c120ea2dadee20c3ac6c39",
        "Created": "2020-08-12T16:09:32.709328463Z",
        "Path": "python",
        "Args": [
            "-m",
            "distributed.cli.dask_spec",
            "--spec",
            "{\"cls\": \"dask.distributed.Nanny\", \"opts\": {\"death_timeout\": \"60 seconds\", \"security\": {\"tls_ca_file\": \" \", \"tls_worker_key\": \" \", \"tls_worker_cert\": \" \"}}}"
        ],
        "State": {
            "Status": "exited",
            "Running": false,
            "Paused": false,
            "Restarting": false,
            "OOMKilled": false,
            "Dead": false,
            "Pid": 0,
            "ExitCode": 0,
            "Error": "",
            "StartedAt": "2020-08-12T16:09:55.100729755Z",
            "FinishedAt": "2020-08-12T16:14:53.793583622Z"
        },
        "Image": "sha256:30aa34e35c5e71194a6fa784c8f288b219b9f805ba9bc14320c0426f7ad423a1",
        "ResolvConfPath": "/var/lib/docker/containers/d37d21ed714415973db591b6e3d5e5321df3bd5b04db2ef382a5eae432f999d7/resolv.conf",
        "HostnamePath": "/var/lib/docker/containers/d37d21ed714415973db591b6e3d5e5321df3bd5b04db2ef382a5eae432f999d7/hostname",
        "HostsPath": "/var/lib/docker/containers/d37d21ed714415973db591b6e3d5e5321df3bd5b04db2ef382a5eae432f999d7/hosts",
        "LogPath": "",
        "Name": "/ecs-necaris-necaris-ba0c99ae-4-worker-1-dask-worker-9cdbf4f7efd0e29ee901",
        "RestartCount": 0,
        "Driver": "overlay2",
        "Platform": "linux",
        "MountLabel": "",
        "ProcessLabel": "",
        "AppArmorProfile": "",
        "ExecIDs": null,
        "HostConfig": {
            "Binds": [],
            "ContainerIDFile": "",
            "LogConfig": {
                "Type": "awslogs",
                "Config": {
                    "awslogs-create-group": "true",
                    "awslogs-credentials-endpoint": "/v2/credentials/b11ce8a5-25f7-47fa-aa8f-ef584a388e7e",
                    "awslogs-group": "necaris",
                    "awslogs-region": "us-east-2",
                    "awslogs-stream": "necaris-necaris-ba0c99ae-4-worker/dask-worker/f1f4ffb3bea341239dceb669a8848eee"
                }
            },
            "NetworkMode": "container:d37d21ed714415973db591b6e3d5e5321df3bd5b04db2ef382a5eae432f999d7",
            "PortBindings": {},
            "RestartPolicy": {
                "Name": "",
                "MaximumRetryCount": 0
            },
            "AutoRemove": false,
            "VolumeDriver": "",
            "VolumesFrom": [],
            "CapAdd": [],
            "CapDrop": [],
            "Capabilities": null,
            "Dns": null,
            "DnsOptions": null,
            "DnsSearch": null,
            "ExtraHosts": null,
            "GroupAdd": null,
            "IpcMode": "shareable",
            "Cgroup": "",
            "Links": null,
            "OomScoreAdj": 0,
            "PidMode": "",
            "Privileged": false,
            "PublishAllPorts": false,
            "ReadonlyRootfs": false,
            "SecurityOpt": null,
            "UTSMode": "",
            "UsernsMode": "",
            "ShmSize": 67108864,
            "Runtime": "nvidia",
            "ConsoleSize": [
                0,
                0
            ],
            "Isolation": "",
            "CpuShares": 8192,
            "Memory": 62277025792,
            "NanoCpus": 0,
            "CgroupParent": "/ecs/f1f4ffb3bea341239dceb669a8848eee",
            "BlkioWeight": 0,
            "BlkioWeightDevice": null,
            "BlkioDeviceReadBps": null,
            "BlkioDeviceWriteBps": null,
            "BlkioDeviceReadIOps": null,
            "BlkioDeviceWriteIOps": null,
            "CpuPeriod": 0,
            "CpuQuota": 0,
            "CpuRealtimePeriod": 0,
            "CpuRealtimeRuntime": 0,
            "CpusetCpus": "",
            "CpusetMems": "",
            "Devices": null,
            "DeviceCgroupRules": null,
            "DeviceRequests": null,
            "KernelMemory": 0,
            "KernelMemoryTCP": 0,
            "MemoryReservation": 62277025792,
            "MemorySwap": 124554051584,
            "MemorySwappiness": null,
            "OomKillDisable": false,
            "PidsLimit": null,
            "Ulimits": [
                {
                    "Name": "nofile",
                    "Hard": 4096,
                    "Soft": 1024
                }
            ],
            "CpuCount": 0,
            "CpuPercent": 0,
            "IOMaximumIOps": 0,
            "IOMaximumBandwidth": 0,
            "MaskedPaths": [
                "/proc/asound",
                "/proc/acpi",
                "/proc/kcore",
                "/proc/keys",
                "/proc/latency_stats",
                "/proc/timer_list",
                "/proc/timer_stats",
                "/proc/sched_debug",
                "/proc/scsi",
                "/sys/firmware"
            ],
            "ReadonlyPaths": [
                "/proc/bus",
                "/proc/fs",
                "/proc/irq",
                "/proc/sys",
                "/proc/sysrq-trigger"
            ]
        },
        "GraphDriver": {
            "Data": {
                "LowerDir": "/var/lib/docker/overlay2/4d16b73ba2f4dc30dc203975e3891b8fad671aa685d720a2e60abb4ba4882437-init/diff:/var/lib/docker/overlay2/3babeafe89f5396e24c1daa22b1a47cefdb694b1abead0e46a574b74f170b3a3/diff:/var/lib/docker/overlay2/4a224778196efd94a05012f35dbf61d8940581cf787c01bc6cf36361a89de4ed/diff:/var/lib/docker/overlay2/b742cdc99149eaf9a47b7ac7524b07a6e3d24dd7e91da8063fc26e517144f602/diff:/var/lib/docker/overlay2/daec24de05f77aa921c5781d1bbf5be1b6c15eec270aee51596c0ce7a9771c08/diff",
                "MergedDir": "/var/lib/docker/overlay2/4d16b73ba2f4dc30dc203975e3891b8fad671aa685d720a2e60abb4ba4882437/merged",
                "UpperDir": "/var/lib/docker/overlay2/4d16b73ba2f4dc30dc203975e3891b8fad671aa685d720a2e60abb4ba4882437/diff",
                "WorkDir": "/var/lib/docker/overlay2/4d16b73ba2f4dc30dc203975e3891b8fad671aa685d720a2e60abb4ba4882437/work"
            },
            "Name": "overlay2"
        },
        "Mounts": [],
        "Config": {
            "Hostname": "ip-10-1-11-29.us-east-2.compute.internal",
            "Domainname": "",
            "User": "",
            "AttachStdin": false,
            "AttachStdout": false,
            "AttachStderr": false,
            "Tty": false,
            "OpenStdin": false,
            "StdinOnce": false,
            "Env": [
                "NVIDIA_VISIBLE_DEVICES=GPU-3c4538b4-cf76-93eb-f2a4-c177171049b0",
                "ECS_CONTAINER_METADATA_URI=http://169.254.170.2/v3/16eb5756-1194-41dd-9d3c-7f04d9d4618a",
                "ECS_CONTAINER_METADATA_URI_V4=http://169.254.170.2/v4/16eb5756-1194-41dd-9d3c-7f04d9d4618a",
                "AWS_EXECUTION_ENV=AWS_ECS_EC2",
                "DASK_SCHEDULER_ADDRESS=tls://ip-10-1-11-50.us-east-2.compute.internal:8786",
                "AWS_CONTAINER_CREDENTIALS_RELATIVE_URI=/v2/credentials/256db1f9-d7b3-419e-b629-a671e74da494",
                "PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
                "LANG=C.UTF-8",
                "LC_ALL=C.UTF-8"
            ],
            "Cmd": [
                "python",
                "-m",
                "distributed.cli.dask_spec",
                "--spec",
                "{\"cls\": \"dask.distributed.Nanny\", \"opts\": {\"death_timeout\": \"60 seconds\", \"security\": {\"tls_ca_file\": \"\", \"tls_worker_key\": \"\", \"tls_worker_cert\": \"\"}}}"
            ],
            "Image": "769926636128.dkr.ecr.us-east-2.amazonaws.com/dev/necaris-gputest:3562f15cc0",
            "Volumes": null,
            "WorkingDir": "",
            "Entrypoint": null,
            "OnBuild": null,
            "Labels": {
                "com.amazonaws.ecs.cluster": "dev",
                "com.amazonaws.ecs.container-name": "dask-worker",
                "com.amazonaws.ecs.task-arn": "arn:aws:ecs:us-east-2:769926636128:task/dev/f1f4ffb3bea341239dceb669a8848eee",
                "com.amazonaws.ecs.task-definition-family": "necaris-necaris-ba0c99ae-4-worker",
                "com.amazonaws.ecs.task-definition-version": "1"
            }
        },
        "NetworkSettings": {
            "Bridge": "",
            "SandboxID": "",
            "HairpinMode": false,
            "LinkLocalIPv6Address": "",
            "LinkLocalIPv6PrefixLen": 0,
            "Ports": {},
            "SandboxKey": "",
            "SecondaryIPAddresses": null,
            "SecondaryIPv6Addresses": null,
            "EndpointID": "",
            "Gateway": "",
            "GlobalIPv6Address": "",
            "GlobalIPv6PrefixLen": 0,
            "IPAddress": "",
            "IPPrefixLen": 0,
            "IPv6Gateway": "",
            "MacAddress": "",
            "Networks": {}
        }
    }
]

Output of nvidia-smi on the host:

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 418.87.00    Driver Version: 418.87.00    CUDA Version: 10.1     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  Tesla V100-SXM2...  On   | 00000000:00:1E.0 Off |                    0 |
| N/A   36C    P0    24W / 300W |      0MiB / 16130MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID   Type   Process name                             Usage      |
|=============================================================================|
|  No running processes found                                                 |
+-----------------------------------------------------------------------------+

Host OS, etc:

❯ aws ec2 describe-images --image-ids ami-0733efab97426efd7
{
    "Images": [
        {
            "Architecture": "x86_64",
            "CreationDate": "2020-08-05T20:35:00.000Z",
            "ImageId": "ami-0733efab97426efd7",
            "ImageLocation": "amazon/amzn2-ami-ecs-gpu-hvm-2.0.20200805-x86_64-ebs",
            "ImageType": "machine",
            "Public": true,
            "OwnerId": "591542846629",
            "PlatformDetails": "Linux/UNIX",
            "UsageOperation": "RunInstances",
            "State": "available",
            "BlockDeviceMappings": [
                {
                    "DeviceName": "/dev/xvda",
                    "Ebs": {
                        "DeleteOnTermination": true,
                        "SnapshotId": "snap-07a4855bd8bf8b4af",
                        "VolumeSize": 30,
                        "VolumeType": "gp2",
                        "Encrypted": false
                    }
                }
            ],
            "Description": "Amazon Linux AMI 2.0.20200805 x86_64 ECS HVM GP2",
            "EnaSupport": true,
            "Hypervisor": "xen",
            "ImageOwnerAlias": "amazon",
            "Name": "amzn2-ami-ecs-gpu-hvm-2.0.20200805-x86_64-ebs",
            "RootDeviceName": "/dev/xvda",
            "RootDeviceType": "ebs",
            "SriovNetSupport": "simple",
            "VirtualizationType": "hvm"
        }
    ]
}
$ uname -a
Linux ip-10-1-11-216.us-east-2.compute.internal 4.14.186-146.268.amzn2.x86_64 #1 SMP Tue Jul 14 18:16:52 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
mrocklin commented 4 years ago
mrocklin@carbon-7:~$ coiled env inspect necaris/gputest
container:
None

conda:
{'channels': ['rapidsai', 'nvidia', 'conda-forge'],
 'dependencies': ['cudatoolkit=10.1',
                  'cudf',
                  'cupy',
                  'dask',
                  'distributed',
                  'pandas',
                  'python=3.7']}

It looks like you're using cudatoolkit 10.1 in the conda environment, but that maybe the CUDA drivers aren't accessible from the docker image?

Output of client.run(lambda: subprocess.check_output(['nvidia-smi'])):

+-----------------------------------------------------------------------------+
| NVIDIA-SMI 418.87.00    Driver Version: 418.87.00    CUDA Version: N/A      |

I wonder if we might need a different docker image base?

necaris commented 4 years ago

@mrocklin that seems like a possibility! I've created another cluster configuration necaris/gputest-rapids using a container-based software environment (necaris/rapids-docker using the rapidsai/rapidsai:0.14-cuda10.1-base-ubuntu18.04-py3.7 image) and it's doing basic GPU things:

In [7]: future = client.submit(cupy.ones, 1000)

In [8]: future = client.submit(cupy.sum, future)

In [9]: future.result()
Out[9]: array(1000.)
selshowk commented 4 years ago

@necaris I guess you could just switch all images to be built of the nvidia cuda base image (is the current base image based off ubuntu or the python docker env)? I'll probably hit into this soon with the stuff I'm doing (its pretty much my next step) so let me know if you'd like me to help in any way.

necaris commented 4 years ago

@sheer-coiled the current base image is based on continuumio/miniconda which I believe is based on Debian -- after talking to @quasiben it sounds like looking into nvidia/cuda is a logical next step for this too.

mrocklin commented 4 years ago

I think that Ben is trying to push a working software environment to the rapidsai account that is based off of a RAPIDS image, but then conda installs some things. I'll go ahead and add Rami and Sheer.

@jrbourbeau it would be useful in this case to be able to specify the conda environment into which we want to run conda install.

On Wed, Aug 12, 2020 at 11:14 AM Rami Chowdhury notifications@github.com wrote:

@sheer-coiled https://github.com/sheer-coiled the current base image is based on continuumio/miniconda which I believe is based on Debian -- after talking to @quasiben https://github.com/quasiben it sounds like looking into nvidia/cuda is a logical next step for this too.

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quasiben commented 4 years ago

I just tried this an coiled indeed does install into base and I want to install into rapids

In [28]: coiled.create_software_environment(name="rapidsai/blazingsql",container="rapidsai/rapidsai:0.14-cuda10.2-runtime-ubuntu18.04-p
    ...: y3.7",
    ...:     conda={
    ...:         "channels": ["blazingsql/label/cuda10.2", "blazingsql",
    ...:         "rapidsai", "nvidia", "conda-forge", "defaults"],
    ...:         "dependencies": ["blazingsql", "s3fs"],
    ...:     },
    ...: )
Updating software environment...
Solving conda environment...
Conda environment solved!
Building Docker image
(this takes a few minutes)
STEP 1: FROM rapidsai/rapidsai:0.14-cuda10.2-runtime-ubuntu18.04-py3.7
STEP 2: COPY environment.yml environment.yml
STEP 3: RUN conda env update -n base -f environment.yml && conda clean --all -y
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
jrbourbeau commented 4 years ago

I just tried this an coiled indeed does install into base and I want to install into rapids

Thanks @quasiben, we'll work to expose the name of the conda environment which conda env update uses

necaris commented 4 years ago

@quasiben would it make sense to create a "base" software environment on beta.coiledhq.com based on nvidia/cuda that we know works for the Coiled environment right now? Rather than having to build a custom Docker image and use that?

mrocklin commented 4 years ago

cc'ing also @jacobtomlinson

On Wed, Aug 12, 2020 at 2:50 PM Rami Chowdhury notifications@github.com wrote:

@quasiben https://github.com/quasiben would it make sense to create a "base" software environment on beta.coiledhq.com based on nvidia/cuda that we know works for the Coiled environment right now? Rather than having to build a custom Docker image and use that?

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jacobtomlinson commented 4 years ago

Thanks for the cc. Anything I can do in particular to help here?

mrocklin commented 4 years ago

Is there a combination docker image + conda/pip install + postbuild command that would get us to close to the RAPIDS docker image, but starting from a more barebones miniconda install? If so, constructing a software environment on Coiled around that would be useful.

coiled.create_software_environment(
    name="rapidsai/default",
    container="...",
    conda={"channels": [...], "dependencies": [...]},
    post_build=[...]
)

@jrbourbeau is the PR that would allow for use of CUDAWorker in a released version yet for folks to play with?

mrocklin commented 4 years ago

For context, starting from the rapids base image is awkward because

  1. Folks locally won't be able to reproduce it on their machines without docker
  2. It uses a different conda environment, which we aren't currently set up for

And the miniconda base image won't work because

  1. It doesn't have cuda magic.

So @necaris 's question was "Hey, could we start from nvidia/cuda and go from there with conda?

jacobtomlinson commented 4 years ago

You could definitely start from nvidia/cuda or the debian based continuumio/miniconda and install the missing pieces. It may help to trace all the image layers back to see what gets installed where. I think the RAPIDS image is built with the following layers:

I imagine to build all images from nvidia/cuda onwards you would need to be running NVIDIA Docker on a GPU powered build machine. Which is one of the main reasons why we recommend folks use the RAPIDS images.

necaris commented 4 years ago

Also, to be clear, I'm happy to dig into this and try and build that image, but I suspect that with your deeper insight into the cuda magic it'll take you much less time to come up with something workable.

jacobtomlinson commented 4 years ago

@necaris I suspect the main blocker here will be running the NVIDIA Docker runtime in order to build these images.

I expect the process will be to add the NVIDIA apt repo, install the drivers with apt, install miniconda with the shell script, install RAPIDS with conda.

mrocklin commented 4 years ago

I thought that it was possible to build RAPIDS on non-GPU machines, as long as the NVIDIA libraries were installed. I imagine that this is how conda-forge operates. My hope was that we could start from something like gpuci/miniconda-cuda and go from there.

On Thu, Aug 13, 2020 at 7:32 AM Jacob Tomlinson notifications@github.com wrote:

@necaris https://github.com/necaris I suspect the main blocker here will be running the NVIDIA Docker runtime in order to build these images.

I expect the process will be to add the NVIDIA apt repo, install the drivers with apt, install miniconda with the shell script, install RAPIDS with conda.

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necaris commented 4 years ago

@jacobtomlinson from your breakdown of the layers it seems like we could maybe start from gpuci/miniconda-cuda and go from there. Is that image available somewhere, or do we have to duplicate it?

jrbourbeau commented 4 years ago

is the PR that would allow for use of CUDAWorker in a released version yet for folks to play with?

It's not yet in a released version. I was planning to release tomorrow (Friday) after the distributed release, but we're in a release-able state now if it'd be useful to push something out for others use today

jacobtomlinson commented 4 years ago

@mrocklin I think you might be right. As long as you start from an image where all the GPU stuff is done you should be fine. Just note that tools like nvidia-smi are not available in any upstream image unless run with the NVIDIA Docker runtime. @quasiben got stuck in that hole recently trying to debug the image when it turned out to be the runtime.

@necaris AFAIK that image should be available on Docker Hub, so you can build directly from it.

FROM gpuci/miniconda-cuda

RUN ...
mrocklin commented 4 years ago

@jrbourbeau assuming that releasing is cheap then yes, let's go for it. Do we need to also deploy beta.coiled.io for this?

On Thu, Aug 13, 2020 at 7:40 AM Jacob Tomlinson notifications@github.com wrote:

@mrocklin https://github.com/mrocklin I think you might be right. As long as you start from an image where all the GPU stuff is done you should be fine. Just note that devices and tools like nvidia-smi are not available in any upstream image unless run with the NVIDIA Docker runtime. @quasiben https://github.com/quasiben got stuck in that hole recently trying to debug the image when it turned out to be the runtime.

@necaris https://github.com/necaris AFAIK that image should be available on Docker Hub https://hub.docker.com/r/gpuci/miniconda-cuda, so you can build directly from it.

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necaris commented 4 years ago

@jacobtomlinson we're reasonably sure we've ironed out the issues with ensuring the container is run with the right runtime :smile: so I'm looking into gpuci/miniconda-cuda now...

jrbourbeau commented 4 years ago

Yes, this will be a coiled release + re-deploy to beta

jacobtomlinson commented 4 years ago

Yeah I'm sure you're doing the right thing when it comes to running the container. The issue Ben and I had was when debugging something from a different machine/environment and thinking "oh I think the image is broken" when actually our debugging environment wasn't representative. Having binaries not exist when run with a different runtime can feel weird because usually everything is contained in the image. I just wanted to flag the trap more than anything.

necaris commented 4 years ago

@jacobtomlinson thanks for the extra warning! I banged my head against it a few times recently so I'm still cautious around the runtime (and the question of how exactly AWS passes the environment and arguments to Docker, too).

jrbourbeau commented 4 years ago

Just wanted to check in on this issue, do have a software environment for deploying rapids today?

necaris commented 4 years ago

@jrbourbeau on beta, dev/gpu-play deploys cupy and cudf, but I don't know about the rest of the RAPIDS stack.

mrocklin commented 4 years ago

It doesn't yet include dask-cudf unfortunately.

On Thu, Aug 20, 2020, 3:12 PM Rami Chowdhury notifications@github.com wrote:

@jrbourbeau https://github.com/jrbourbeau on beta, dev/gpu-play deploys cupy and cudf, but I don't know about the rest of the RAPIDS stack.

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quasiben commented 4 years ago

Should we try another round of testing ?

necaris commented 4 years ago

@quasiben I think we're in a good place for it :-)

quasiben commented 4 years ago

I tried on beta on get the following error:

``` In [7]: cluster = coiled.Cluster(n_workers=1, configuration="quasiben/rapids-015-test") Creating Cluster. This takes about a minute .../Checking environment images Valid environment image found --------------------------------------------------------------------------- ValueError Traceback (most recent call last) in ----> 1 cluster = coiled.Cluster(n_workers=1, configuration="quasiben/rapids-015-test") ~/miniconda3/envs/coiled/lib/python3.7/site-packages/coiled/cluster.py in __init__(self, n_workers, configuration, name, asynchronous, cloud, account, shutdown_on_close, region) 76 77 if not self.asynchronous: ---> 78 self.sync(self._start) 79 80 @property ~/miniconda3/envs/coiled/lib/python3.7/site-packages/distributed/deploy/cluster.py in sync(self, func, asynchronous, callback_timeout, *args, **kwargs) 172 return future 173 else: --> 174 return sync(self.loop, func, *args, **kwargs) 175 176 def _log(self, log): ~/miniconda3/envs/coiled/lib/python3.7/site-packages/distributed/utils.py in sync(loop, func, callback_timeout, *args, **kwargs) 337 if error[0]: 338 typ, exc, tb = error[0] --> 339 raise exc.with_traceback(tb) 340 else: 341 return result[0] ~/miniconda3/envs/coiled/lib/python3.7/site-packages/distributed/utils.py in f() 321 if callback_timeout is not None: 322 future = asyncio.wait_for(future, callback_timeout) --> 323 result[0] = yield future 324 except Exception as exc: 325 error[0] = sys.exc_info() ~/miniconda3/envs/coiled/lib/python3.7/site-packages/tornado/gen.py in run(self) 733 734 try: --> 735 value = future.result() 736 except Exception: 737 exc_info = sys.exc_info() ~/miniconda3/envs/coiled/lib/python3.7/site-packages/coiled/cluster.py in _start(self) 128 129 self.security, info = await self.cloud.security( --> 130 cluster_id=self.cluster_id, account=self.account # type: ignore 131 ) 132 ~/miniconda3/envs/coiled/lib/python3.7/site-packages/coiled/core.py in _security(self, cluster_id, account) 432 # cluster is stopped, probably very shortly after starting 433 raise ValueError( --> 434 "Unable to get security info, cluster status is unexpectedly STOPPED" 435 ) 436 if data["status"] != "pending" and data["public_address"]: ValueError: Unable to get security info, cluster status is unexpectedly STOPPED ```
mrocklin commented 4 years ago

Maybe try cluster.get_logs()

Also, I think that we should schedule some Ben and Rami together to go through things. I think that you both hold keys to unlocking this particular achievement.

On Thu, Sep 3, 2020 at 7:40 AM Benjamin Zaitlen notifications@github.com wrote:

I tried on beta on get the following error:

In [7]: cluster = coiled.Cluster(n_workers=1, configuration="quasiben/rapids-015-test") Creating Cluster. This takes about a minute .../Checking environment images Valid environment image found

ValueError Traceback (most recent call last)

in ----> 1 cluster = coiled.Cluster(n_workers=1, configuration="quasiben/rapids-015-test") ~/miniconda3/envs/coiled/lib/python3.7/site-packages/coiled/cluster.py in __init__(self, n_workers, configuration, name, asynchronous, cloud, account, shutdown_on_close, region) 76 77 if not self.asynchronous: ---> 78 self.sync(self._start) 79 80 @property ~/miniconda3/envs/coiled/lib/python3.7/site-packages/distributed/deploy/cluster.py in sync(self, func, asynchronous, callback_timeout, *args, **kwargs) 172 return future 173 else: --> 174 return sync(self.loop, func, *args, **kwargs) 175 176 def _log(self, log): ~/miniconda3/envs/coiled/lib/python3.7/site-packages/distributed/utils.py in sync(loop, func, callback_timeout, *args, **kwargs) 337 if error[0]: 338 typ, exc, tb = error[0] --> 339 raise exc.with_traceback(tb) 340 else: 341 return result[0] ~/miniconda3/envs/coiled/lib/python3.7/site-packages/distributed/utils.py in f() 321 if callback_timeout is not None: 322 future = asyncio.wait_for(future, callback_timeout) --> 323 result[0] = yield future 324 except Exception as exc: 325 error[0] = sys.exc_info() ~/miniconda3/envs/coiled/lib/python3.7/site-packages/tornado/gen.py in run(self) 733 734 try: --> 735 value = future.result() 736 except Exception: 737 exc_info = sys.exc_info() ~/miniconda3/envs/coiled/lib/python3.7/site-packages/coiled/cluster.py in _start(self) 128 129 self.security, info = await self.cloud.security( --> 130 cluster_id=self.cluster_id, account=self.account # type: ignore 131 ) 132 ~/miniconda3/envs/coiled/lib/python3.7/site-packages/coiled/core.py in _security(self, cluster_id, account) 432 # cluster is stopped, probably very shortly after starting 433 raise ValueError( --> 434 "Unable to get security info, cluster status is unexpectedly STOPPED" 435 ) 436 if data["status"] != "pending" and data["public_address"]: ValueError: Unable to get security info, cluster status is unexpectedly STOPPED — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub , or unsubscribe .
quasiben commented 4 years ago

I can't do cluster.get_logs() because the cluster did not get created.

Happy to spend some time with Rami. Let's coordinate over email

quasiben commented 4 years ago

@necaris and I were able to get things working now with Rapids Docker Images. We needed to fix a small issue in dask-cuda (thanks @necaris and @jrbourbeau ) and we also need to add a set a few things create_cluster_configuration (shown below). Two things which would help ergonomics:

  1. Running code remotely: https://github.com/dask/distributed/issues/4003
  2. Better output support (return/prints are little awkward if you don't have a GPU locally)
import coiled

coiled.create_software_environment(name="rapids-docker-016-nightly",
                                   container="rapidsai/rapidsai-nightly:0.16-cuda10.2-base-ubuntu18.04")

coiled.create_cluster_configuration(name='rapids-docker-example',
                                    worker_memory='15GiB',
                                    software='quasiben/rapids-docker-016-nightly',
                                    worker_options={'rmm_pool_size': '12GiB'},
                                    worker_class='dask_cuda.CUDAWorker',
                                    worker_gpu=1)

cluster = coiled.Cluster(n_workers=1, configuration="quasiben/rapids-docker-example")

from dask.distributed import Client
import dask.dataframe as dd

coiled.create_cluster_configuration(name='rapids-docker-example',
                                    worker_memory='15GiB',
                                    software='quasiben/rapids-docker-016-nightly',
                                    worker_options={'rmm_pool_size': '12GiB'},
                                    worker_class='dask_cuda.CUDAWorker',
                                    worker_gpu=1)
cluster = coiled.Cluster(n_workers=1, configuration="quasiben/rapids-docker-example")

# nvidia-smi from cli
def nvida_smi():
    import subprocess
    return subprocess.check_output(['nvidia-smi'])

for w, res in client.run(nvida_smi).items():
    print(w, ":")
    print(res.decode('utf8'))

#nvidia-smi from pynvml
def gpu_mem():
    from pynvml.smi import nvidia_smi
    nvsmi = nvidia_smi.getInstance()
    return nvsmi.DeviceQuery('memory.free, memory.total')

for w, res in client.run(gpu_mem).items():
    print(w, ":")
    print(res)

def tips():
    import cudf, io, requests
    from io import StringIO
    url = "https://github.com/plotly/datasets/raw/master/tips.csv"
    content = requests.get(url).content.decode('utf-8')
    tips_df = cudf.read_csv(StringIO(content))
    tips_df['tip_percentage'] = tips_df['tip'] / tips_df['total_bill'] * 100
    # display average tip by dining party size
    return str(tips_df.groupby('size').tip_percentage.mean())

for w, res in client.run(tips).items():
    print(w, ":")
    print(res)

def dask_cudf():
    import cudf
    cdf = cudf.datasets.timeseries()
    ddf = dd.from_pandas(cdf, npartitions=5)
    return ddf.groupby('name').agg(['mean', 'max', 'min']).compute().to_pandas()

for w, res in client.run(dask_cudf).items():
    print(w, ":")
    print(res)

I think we are now functional and now we need to document/experiment -- I'm +1 on closing. Thought?

mrocklin commented 4 years ago

This is very exciting! Thanks for putting this together @quasiben . I look forward to playing with it. Some thoughts:

  1. Any thoughts on claiming the rapidsai/nightly spot on Coiled for the RAPIDS nightly container?
  2. We might consider also using this with jobs or notebooks (cc @jrbourbeau) due to the lack of a local GPU

I'm inclined to keep this open until we have a doc page with an easy onramp for new users

necaris commented 4 years ago

I'm inclined to keep this open until we have a doc page with an easy onramp for new users

:+1: from me

mrocklin commented 4 years ago

I've put a rapidsai/nightly software environment and cluster configuration in the rapidsai account. So anyone should be able to do

import coiled
cluster = coiled.Cluster(configuration="rapidsai/nightly", account=...)

(where ... is some account with GPU access).

I started setting up an example to use this with Optuna (I was trying to play around earlier cc @jrbourbeau ), but needed to add a couple of packages. I did that with the following:

coiled.create_software_environment(
    name="mrocklin/dask-optuna", 
    container="rapidsai/rapidsai-nightly:0.16-cuda10.2-base-ubuntu18.04", 
    pip=["dask-optuna"], 
    conda={"channels": ["rapidsai-nightly", "nvidia", "conda-forge", "defaults"], "dependencies": ["optuna"]}, 
    conda_env_name="rapids"
)

However this appears to have overwritten a large number of conda packages, so I may have screwed something up.

mrocklin commented 4 years ago

@quasiben if I wanted to have all of the wonder GPU setup of the rapids image, but use my own conda environment, is there some sort of rapids-base docker image that would work?

necaris commented 4 years ago

@mrocklin gpuci/miniconda-cuda:10.1-runtime-ubuntu18.04 might fit your needs? I've used it to test a couple of software environments, e.g. see necaris/gpuci-223