Merge pull request #1359 from nv-morpheus/fea-sherlock

Merge fea-sherlock feature branch into branch-23.11

.clang-format

@@ -17,6 +17,7 @@ AllowShortBlocksOnASingleLine: true
 AllowShortCaseLabelsOnASingleLine: false # Allows placing breakpoint
 AllowShortFunctionsOnASingleLine: Empty
 AllowShortIfStatementsOnASingleLine: Never
+AllowShortLambdasOnASingleLine: Empty
 AllowShortLoopsOnASingleLine: false
 # This is deprecated
 AlwaysBreakAfterDefinitionReturnType: None
@@ -103,6 +104,7 @@ ObjCBinPackProtocolList: Never
 ObjCBlockIndentWidth: 2
 ObjCSpaceAfterProperty: false
 ObjCSpaceBeforeProtocolList: true
+PackConstructorInitializers: CurrentLine
 PenaltyBreakAssignment: 2
 PenaltyBreakBeforeFirstCallParameter: 1
 PenaltyBreakComment: 300

.gitattributes

@@ -1,11 +1,11 @@
 docs/source/developer_guide/guides/img/** filter=lfs diff=lfs merge=lfs -text
+docs/source/img/* filter=lfs diff=lfs merge=lfs -text
+examples/basic_usage/img/** filter=lfs diff=lfs merge=lfs -text
 examples/data/** filter=lfs diff=lfs merge=lfs -text
 examples/digital_fingerprinting/production/grafana/img/** filter=lfs diff=lfs merge=lfs -text
 examples/digital_fingerprinting/visualization/img/** filter=lfs diff=lfs merge=lfs -text
+git filter=lfs diff=lfs merge=lfs -text
 morpheus/_version.py export-subst
+status filter=lfs diff=lfs merge=lfs -text
 tests/mock_triton_server/payloads/** filter=lfs diff=lfs merge=lfs -text
 tests/tests_data/** filter=lfs diff=lfs merge=lfs -text
-examples/basic_usage/img/** filter=lfs diff=lfs merge=lfs -text
-docs/source/img/* filter=lfs diff=lfs merge=lfs -text
-git filter=lfs diff=lfs merge=lfs -text
-status filter=lfs diff=lfs merge=lfs -text

CMakeLists.txt

@@ -175,7 +175,7 @@ if(MORPHEUS_ENABLE_DEBUG_INFO)
 
   morpheus_utils_print_target_properties(
       TARGETS
-        morpheus
+        morpheus morpheus._lib.llm
       WRITE_TO_FILE
   )
 

ci/iwyu/mappings.imp

@@ -47,7 +47,8 @@
 { "include": [ "<google/protobuf/repeated_ptr_field.h>", private, "<google/protobuf/repeated_field.h>", "public" ] },
 
 # pybind11
-{ "include": [ "<pybind11/detail/common.h>", private, "<pybind11/pytypes.h>", "public" ] },
+{ "include": [ "<pybind11/detail/common.h>", "private", "<pybind11/pytypes.h>", "public" ] },
+{ "include": [ "<pybind11/cast.h>", "private", "<pybind11/pybind11.h>", "public" ] },
 
 # rxcpp
 # Hide includes that are exported by <rxcpp/rx.hpp>

ci/scripts/cpp_checks.sh

@@ -58,8 +58,10 @@ if [[ -n "${MORPHEUS_MODIFIED_FILES}" ]]; then
 
       CLANG_TIDY_DIFF=$(find_clang_tidy_diff)
 
-      # Run using a clang-tidy wrapper to allow warnings-as-errors and to eliminate any output except errors (since clang-tidy-diff.py doesn't return the correct error codes)
-      CLANG_TIDY_OUTPUT=`get_unified_diff ${CPP_FILE_REGEX} | ${CLANG_TIDY_DIFF} -j 0 -path ${BUILD_DIR} -p1 -quiet 2>&1`
+      # Run using a clang-tidy wrapper to allow warnings-as-errors and to eliminate any output except errors (since
+      # clang-tidy-diff.py doesn't return the correct error codes)
+      CLANG_TIDY_OUTPUT=`get_unified_diff ${CPP_FILE_REGEX} | ${CLANG_TIDY_DIFF} \
+         -extra-arg="-Wno-ignored-optimization-argument" -j 0 -path ${BUILD_DIR} -p1 -quiet 2>&1`
 
       if [[ -n "${CLANG_TIDY_OUTPUT}" && ${CLANG_TIDY_OUTPUT} != "No relevant changes found." ]]; then
          CLANG_TIDY_RETVAL=1

ci/scripts/github/common.sh

@@ -16,7 +16,7 @@
 
 function print_env_vars() {
     rapids-logger "Environ:"
-    env | grep -v -E "AWS_ACCESS_KEY_ID|AWS_SECRET_ACCESS_KEY|GH_TOKEN" | sort
+    env | grep -v -E "AWS_ACCESS_KEY_ID|AWS_SECRET_ACCESS_KEY|GH_TOKEN|NGC_API_KEY" | sort
 }
 
 rapids-logger "Env Setup"

ci/scripts/github/test.sh

@@ -98,7 +98,7 @@ done
 rapids-logger "Running Python tests"
 set +e
 
-python -I -m pytest --run_slow --run_kafka --fail_missing \
+python -I -m pytest --run_slow --run_kafka --run_milvus --fail_missing \
        --junit-xml=${REPORTS_DIR}/report_pytest.xml \
        --cov=morpheus \
        --cov-report term-missing \

docker/conda/environments/cuda11.8_dev.yml

@@ -24,6 +24,7 @@ channels:
 dependencies:
     ####### Morpheus Dependencies (keep sorted!) #######
     - automake=1.16.5
+    - beautifulsoup4=4.12
     - benchmark=1.6.1
     - boost-cpp=1.82
     - cachetools=5.0.0
@@ -34,8 +35,8 @@ dependencies:
     - configargparse=1.5
     - cuda-compiler=11.8
     - cuda-nvml-dev=11.8
+    - cuda-python>=11.8,<11.8.3 # workaround for https://github.com/nv-morpheus/Morpheus/issues/1317
     - cuda-toolkit=11.8
-    - cuda-python=11.8.2 # 11.8.3 breaks cuda helpers, pin to 11.8.2 for now.
     - cudf=23.06
     - cupy>=12.0.0
     - cxx-compiler
@@ -69,7 +70,7 @@ dependencies:
     - libwebp>=1.3.2 # Required for CVE mitigation: https://nvd.nist.gov/vuln/detail/CVE-2023-4863
     - mlflow>=2.2.1,<3
     - mrc=23.11
-    - networkx=3.1
+    - networkx>=2.8
     - ninja=1.10
     - nodejs=18.*
     - numba>=0.56.2
@@ -85,6 +86,7 @@ dependencies:
     - pydot
     - pylint>=2.17.4,<2.18 # 2.17.4 contains a fix for toml support
     - pytest
+    - pytest-asyncio
     - pytest-benchmark>=4.0
     - pytest-cov
     - python-confluent-kafka=1.9.2
@@ -94,6 +96,7 @@ dependencies:
     - pytorch=2.0.1
     - rapidjson=1.1.0
     - requests=2.31
+    - requests-cache=1.1
     - scikit-build=0.17.1
     - scikit-learn=1.2.2
     - sphinx
@@ -106,10 +109,18 @@ dependencies:
     - watchdog=2.1
     - websockets
     - yapf=0.40.1
+
+    ####### Pip Transitive Dependencies (keep sorted!) #######
+    # These are dependencies that are available on conda, but are required by the pip packages listed below. Its much
+    # better to install them with conda than pip to allow for better dependency resolution.
+    - kafka-python=2.0
+    - port-for=0.7
+    - py4j=0.10
+
     ####### Morpheus Pip Dependencies (keep sorted!) #######
     - pip:
         # Add additional dev dependencies here
         - databricks-connect
         - pytest-kafka==0.6.0
-        - pymilvus==2.3.1
-        - milvus
+        - pymilvus==2.3.2
+        - milvus==2.3.2

docker/conda/environments/cuda11.8_examples.yml

@@ -22,16 +22,41 @@
 channels:
     - rapidsai
     - nvidia
+    - huggingface
     - conda-forge
     - dglteam/label/cu118
 dependencies:
+    - arxiv=1.4
     - boto3
     - cuml=23.06
     - dask>=2023.1.1
     - dgl=1.0.2
     - dill=0.3.6
     - distributed>=2023.1.1
+    - huggingface_hub=0.10.1 # work-around for https://github.com/UKPLab/sentence-transformers/issues/1762
+    - langchain=0.0.190
     - libwebp>=1.3.2 # Required for CVE mitigation: https://nvd.nist.gov/vuln/detail/CVE-2023-4863
     - mlflow>=2.2.1,<3
+    - newspaper3k=0.2
+    - openai=0.28
     - papermill=2.3.4
+    - pypdf=3.16
+    - requests-cache=1.1
     - s3fs>=2023.6
+    - sentence-transformers
+    - transformers
+
+    ####### Pip Transitive Dependencies (keep sorted!) #######
+    # These are dependencies that are available on conda, but are required by the pip packages listed below. Its much
+    # better to install them with conda than pip to allow for better dependency resolution.
+    - environs=9.5
+    - minio=7.1
+    - python-dotenv=1.0
+    - ujson=5.8
+
+
+  ####### Pip Dependencies (keep sorted!) #######
+    - pip:
+        - google-search-results==2.4
+        - grpcio-status==1.58 # To keep in sync with 1.58 grpcio which is installed for Morpheus
+        - nemollm

docs/source/conf.py

@@ -129,7 +129,7 @@
         BUILTIN_STL_SUPPORT = YES
         DOT_IMAGE_FORMAT = svg
         EXCLUDE_PATTERNS = */tests/* */include/nvtext/* */__pycache__/* */doca/*
-        EXCLUDE_SYMBOLS = "@*" "cudf*" "py::literals" "RdKafka" "mrc*" "std*"
+        EXCLUDE_SYMBOLS = "@*" "cudf*" "py::literals" "RdKafka" "mrc*" "std*" "PYBIND11_NAMESPACE*"
         EXTENSION_MAPPING = cu=C++ cuh=C++
         EXTRACT_ALL = YES
         FILE_PATTERNS = *.c *.cc *.cpp *.h *.hpp *.cu *.cuh *.md
@@ -138,6 +138,11 @@
         INPUT = ../../morpheus/_lib
         INTERACTIVE_SVG = YES
         SOURCE_BROWSER = YES
+        ENABLE_PREPROCESSING = YES
+        MACRO_EXPANSION = YES
+        EXPAND_ONLY_PREDEF = NO
+        PREDEFINED = "MORPHEUS_EXPORT=" \
+                     "DOXYGEN_SHOULD_SKIP_THIS=1"
     ''')
 }
 
@@ -165,6 +170,7 @@
     "cudf",  # Avoid loading GPU libraries during the documentation build
     "cupy",  # Avoid loading GPU libraries during the documentation build
     "databricks.connect",
+    "langchain",
     "merlin",
     "morpheus.cli.commands",  # Dont document the CLI in Sphinx
     "nvtabular",

docs/source/examples.md

@@ -24,3 +24,8 @@ limitations under the License.
 * [Example Ransomware Detection Morpheus Pipeline for AppShield Data](./examples/ransomware_detection/README.md)
 * [Root Cause Analysis Acceleration & Predictive Maintenance Example](./examples/root_cause_analysis/README.md)
 * [SID Visualization Example](./examples/sid_visualization/README.md)
+* [Large Language Models (LLMs)](./examples/llm/README.md)
+  * [Agents](./examples/llm/agents/README.md)
+  * [Completion](./examples/llm/completion/README.md)
+  * [VDB Upload](./examples/llm/vdb_upload/README.md)
+  * [Retreival Augmented Generation (RAG)](./examples/llm/rag/README.md)

docs/source/examples/index.rst

@@ -25,6 +25,7 @@ Examples
    abp_nvsmi_detection/README.md
    abp_pcap_detection/README.md
    gnn_fraud_detection_pipeline/README.md
+   llm/index
    log_parsing/README.md
    nlp_si_detection/README.md
    ransomware_detection/README.md
@@ -35,3 +36,4 @@ Examples
    :hidden:
 
    ../examples
+

docs/source/examples/llm/README.md

@@ -0,0 +1,23 @@
+<!--
+SPDX-FileCopyrightText: Copyright (c) 2022-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+SPDX-License-Identifier: Apache-2.0
+
+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.
+-->
+
+# LLM
+
+- [completion](./completion/README.md)
+- [vdb_upload](./vdb_upload/README.md)
+- [rag](./rag/README.md)
+- [agents](./agents/README.md)

docs/source/examples/llm/agents/README.md

@@ -0,0 +1 @@
+../../../../../examples/llm/agents/README.md

docs/source/examples/llm/completion/README.md

@@ -0,0 +1 @@
+../../../../../examples/llm/completion/README.md

docs/source/examples/llm/index.rst

@@ -0,0 +1,30 @@
+..
+   SPDX-FileCopyrightText: Copyright (c) 2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+   SPDX-License-Identifier: Apache-2.0
+
+   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.
+
+
+===
+LLM
+===
+
+.. toctree::
+   :maxdepth: 20
+
+   ./README.md
+   ./completion/README.md
+   ./vdb_upload/README.md
+   ./rag/README.md
+   ./agents/README.md
+

docs/source/examples/llm/rag/README.md

@@ -0,0 +1,18 @@
+<!--
+SPDX-FileCopyrightText: Copyright (c) 2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+SPDX-License-Identifier: Apache-2.0
+
+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.
+-->
+
+# LLM RAG

docs/source/examples/llm/vdb_upload/README.md

@@ -0,0 +1,18 @@
+<!--
+SPDX-FileCopyrightText: Copyright (c) 2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+SPDX-License-Identifier: Apache-2.0
+
+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.
+-->
+
+# LLM VDB Upload

examples/digital_fingerprinting/production/morpheus/dfp/stages/multi_file_source.py

@@ -143,8 +143,8 @@ def _polling_generate_frames_fsspec(self) -> typing.Iterable[fsspec.core.OpenFil
                 if file.full_name not in files_seen:
                     filtered_files.append(file)
 
-            # Replace files_seen with the new set of files. This prevents a memory leak that could occurr if files are
-            # deleted from the input directory. In addition if a file with a given name was created, seen/processed by
+            # Replace files_seen with the new set of files. This prevents a memory leak that could occur if files are
+            # deleted from the input directory. In addition, if a file with a given name was created, seen/processed by
             # the stage, and then deleted, and a new file with the same name appeared sometime later, the stage will
             # need to re-ingest that new file.
             files_seen = file_set