Serializer_refactor - MOD-4196 #262

meiravgri · 2022-10-19T05:42:34Z

Describe the changes in the pull request

In this PR we refactored the serializer class. it is no longer holding an index instance as a data member.
If an index is supposed to be serialized it should inherit the serializer and implement:

save to file function
A construct that initializes the index attributes from a file.

to avoid adding unnecessary functions and memory, the inheritance and serializing related functions can be declared and implemented under the BUILD_TESTS preprocessor flag.

-When using encoding version 1 we need to explicitly generate the HNSWParams struct with the same attributes as the loaded index.

from encoding version 2 we serialize also VecSimIndexAbstract class data members (dim, vector data type, metric, etc.) so we can initialize HNSWParams for the ctor from the file.

Which issues this PR fixes

Resources management is better because we don't need to worry that the index will be freed before the serializer.
General API of the serializer enables serializing all types of indices in the future.
from v2 - we don't need to know the index attributes before loading it.

Main objects this PR modified

Serializer class is totally refactored and moved to the utils directory.
moved some serializing functions that are specific to hnsw index to hnsw class

Mark if applicable

This PR introduces API changes
This PR introduces serialization changes

codecov · 2022-10-19T06:16:32Z

Codecov Report

Base: 95.35% // Head: 95.35% // No change to project coverage 👍

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meiravgri · 2022-10-20T05:41:00Z

src/VecSim/algorithms/brute_force/brute_force.h

@@ -331,7 +331,7 @@ VecSimIndexInfo BruteForceIndex<DataType, DistType>::info() const {
    info.bfInfo.indexSize = this->count;
    info.bfInfo.indexLabelCount = this->indexLabelCount();
    info.bfInfo.blockSize = this->blockSize;
-    info.bfInfo.memory = this->allocator->getAllocationSize();
+    info.bfInfo.memory = this->getAllocationSize();


getAllocationSize() was added to vecsim_interface

meiravgri · 2022-10-21T11:32:48Z

tests/benchmark/bm_utils.h

+    static const char *hnsw_index_file;
+    static inline std::string GetSerializedIndexLocation(const char *file_name) {
+        return std::string(getenv("ROOT")) + "/" + file_name;
+    }
+};


serializer already includes stream opening logic

std::string(getenv("ROOT")) throws an exception when ROOT is not defined (and getenv returns null). Consider passing a default value instead ("." or calling pwd).

src/VecSim/algorithms/hnsw/hnsw.h

src/VecSim/utils/serializer.cpp

meiravgri · 2022-10-24T08:06:17Z

tests/unit/test_hnsw_multi.cpp

+
+    VecSimIndex_Free(index);
+
+    // Create new index, set it into the serializer and extract the data to it.


ill fix the comment along with the review fixes

tests/unit/test_hnsw.cpp

alonre24

Good job! See the comments and let me know what you think. While most of the comments are minor, I do want us to discuss if we should change how we load index entirety, so that loading will be an alternative constructor for the index.

alonre24 · 2022-10-26T08:07:15Z

src/VecSim/utils/serializer.h

+    } EncodingVersion;
+
+    // Persist index into a file in the specified location.
+    void saveIndex(const std::string &location, EncodingVersion version = EncodingVersion_V1);


Should we change the default EncodingVersion to EncodingVersion_V2?

yes, i forgot to change this 😄

alonre24 · 2022-10-26T08:48:31Z

src/VecSim/utils/serializer.h

+    // Restore the index from the file in the specified location.
+    void loadIndex(const std::string &location);
+    // Check if the serialized index is valid.
+    virtual bool serializingIsValid() const = 0;


Suggested change

virtual bool serializingIsValid() const = 0;

virtual bool checkIndexIntergrity() const = 0;

alonre24 · 2022-10-26T08:50:30Z

src/VecSim/memory/vecsim_malloc.h

@@ -33,7 +33,7 @@ struct VecSimAllocator {
    void operator delete(void *p, size_t size);
    void operator delete[](void *p, size_t size);

-    int64_t getAllocationSize();
+    int64_t getAllocationSize() const;


How is that related to this PR?

checkIntegrity() uses this as const so i cant call getAllocationSize() if its not const...

alonre24 · 2022-10-26T08:53:43Z

src/VecSim/vec_sim_interface.h

@@ -154,4 +155,6 @@ struct VecSimIndexInterface : public VecsimBaseObject {
    inline static void setTimeoutCallbackFunction(timeoutCallbackFunction callback) {
        VecSimIndexInterface::timeoutCallback = callback;
    }
+
+    inline int64_t getAllocationSize() const { return this->allocator->getAllocationSize(); }


Why this addition?

this is just a shortcut

consider moving this to VecsimBaseObject

alonre24 · 2022-10-26T09:01:58Z

src/VecSim/algorithms/hnsw/hnsw.h

+void HNSWIndex<DataType, DistType>::saveIndexIMP(std::ofstream &output,
+                                                 EncodingVersion version) const {
+    // We already checked in the serializer that this is a valid version number.
+    // Now checking the version number to decide which data to write.
+    if (version != EncodingVersion_V1) {
+        saveIndexFields_v2(output);
+    }
+
+    this->saveIndexFields(output);
+    this->saveGraph(output);
+}


General comment for serialization and versioning - when we introduce a new version, we don't need to keep old versions of encoding functions, (unlike the old decoding functions that we do keep). That is since if we save an index using this code, we always want it to be in the latest version. However, if we load a serialized index, we wan't to allow it whether it was serialized with an older versions as well.

alonre24 · 2022-10-26T11:31:14Z

tests/unit/test_allocator.cpp

@@ -360,16 +360,15 @@ TYPED_TEST(IndexAllocatorTest, test_hnsw_reclaim_memory) {
    ASSERT_EQ(allocator->getAllocationSize(), initial_memory_size + accumulated_mem_delta);
    // Also validate that there are no unidirectional connections (these add memory to the incoming
    // edges sets).
-    // auto serializer = HNSWIndexSerializer(hnswIndex);
-    // ASSERT_EQ(serializer.checkIntegrity().unidirectional_connections, 0);
+    // ASSERT_EQ(hnswIndex->checkIntegrity().unidirectional_connections, 0);


Do you know why was this commented out?

it was moved to a separate test, not templated

alonre24 · 2022-10-26T11:46:41Z

tests/unit/test_common.cpp

+    this->file_name = std::string(getenv("ROOT")) + "/tests/unit/data/test_common_hnsw";
+    ASSERT_EQ(this->GetFileSize(), 0);


Isn't there a simpler way to validate that a file under this name doesn't exist? Or am I missing something here?

i think i put this line here by mistake 😅

alonre24 · 2022-10-26T11:53:26Z

tests/unit/test_common.cpp

+    VecSimIndex *index = test_utils::CreateNewIndex(params, VecSimType_FLOAT32);
+    HNSWIndex<float, float> *hnsw_index = reinterpret_cast<HNSWIndex<float, float> *>(index);
+
+    this->file_name = std::string(getenv("ROOT")) + "/tests/unit/data/test_common_hnsw";


Suggested change

this->file_name = std::string(getenv("ROOT")) + "/tests/unit/data/test_common_hnsw";

this->file_name = std::string(getenv("ROOT")) + "/tests/unit/data/bad_index.hnsw

alonre24 · 2022-10-26T12:11:18Z

tests/unit/test_hnsw.cpp

+    // Save index.
+    EXPECT_THROW(hnsw_index->saveIndex(this->file_name, Serializer::EncodingVersion_NOT_VALID),
+                 std::runtime_error);
+    hnsw_index->saveIndex(this->file_name, Serializer::EncodingVersion_V2);


You have this check already in test_common no?

alonre24 · 2022-10-26T12:16:51Z

tests/unit/test_hnsw.cpp

+    index = this->CreateNewIndex(other_params);
+
+    VecSimIndexInfo other_index_info = VecSimIndex_Info(index);
+    // Make sure that this index is different
+    ASSERT_NE(serialized_index_info.hnswInfo.dim, other_index_info.hnswInfo.dim);
+    ASSERT_NE(serialized_index_info.hnswInfo.blockSize, other_index_info.hnswInfo.blockSize);
+    ASSERT_NE(serialized_index_info.hnswInfo.M, other_index_info.hnswInfo.M);
+    ASSERT_NE(serialized_index_info.hnswInfo.efConstruction,
+              other_index_info.hnswInfo.efConstruction);
+    ASSERT_NE(serialized_index_info.hnswInfo.efRuntime, other_index_info.hnswInfo.efRuntime);
+    ASSERT_NE(serialized_index_info.hnswInfo.epsilon, other_index_info.hnswInfo.epsilon);
+
+    hnsw_index = this->CastToHNSW(index);
+    hnsw_index->loadIndex(this->file_name);


Looking at this test makes me think that we should use the loadIndex as an alternative constructor. Creating an index and then loading it from file was the temporary solution at the time, but now it looks awkward to use loadIndex to override index data. Let's discuss it...

alonre24

Great job! :)
See some comments and questions that I had. Also, I would add some more tests such as - serializing and loading an empty index, searching before and after serialization (only in v2...)

alonre24 · 2022-11-03T15:35:56Z

src/VecSim/utils/serializer.cpp

+void Serializer::saveIndex(const std::string &location, EncodingVersion version) {
+    // Only V1 and V2 are supported
+    if (version >= EncodingVersion_INVALID) {
+        throw std::runtime_error("Cannot load index: bad encoding version");
+    }


Always save with EncodingVersion_V2 no?

alonre24 · 2022-11-03T15:37:46Z

src/VecSim/vec_sim_index.h

@@ -42,6 +42,12 @@ struct VecSimIndexAbstract : public VecSimIndexInterface {
        spaces::SetDistFunc(metric, dim, &dist_func);
    }

+#ifdef BUILD_TESTS
+    VecSimIndexAbstract(std::shared_ptr<VecSimAllocator> allocator)


Consider adding a comment here that explains what this constructor exists for

i didn't use it eventually

alonre24 · 2022-11-03T15:40:52Z

src/VecSim/algorithms/hnsw/hnsw_serializer_declarations.h

+HNSWIndexMetaData checkIntegrity() const;
+
+// Index memory size might be changed during index saving.
+virtual void saveIndexIMP(std::ofstream &output, EncodingVersion version) override;


This is not virtual, right? we wouldn't override it

it is pure virtual in the serializer class so it can call it from saveIndex function

alonre24 · 2022-11-03T15:42:50Z

src/VecSim/algorithms/hnsw/hnsw_factory.cpp

@@ -8,7 +8,7 @@ namespace HNSWFactory {
 template <typename DataType, typename DistType = DataType>
 inline VecSimIndex *NewIndex_ChooseMultiOrSingle(const HNSWParams *params,
                                                 std::shared_ptr<VecSimAllocator> allocator) {
-    // check if single and return new bf_index
+    // check if single and return new hnsw_index


nice catch :)

alonre24 · 2022-11-03T15:53:28Z

src/VecSim/algorithms/hnsw/hnsw_factory.cpp

+    case Serializer::EncodingVersion_V1: {
+        assert(params);
+        file_params.type = params->type;
+        file_params.dim = params->dim;
+        file_params.metric = params->metric;
+        file_params.multi = params->multi;
+        file_params.blockSize = params->blockSize;
+        file_params.epsilon = params->epsilon;
+        break;


nit picking: what if the last 3 params are empty? What will be the default behavior?

Good question
maybe epsilon and block size can have default values because they don't affect the loading process, but all the others must be the same as the loaded index since we cant get them from the file.

alonre24 · 2022-11-03T16:06:45Z

src/VecSim/algorithms/hnsw/hnsw_serializer_imp.h

+        input.ignore(sizeof(unsigned long));
+    }
+
+    // for V2 and up we don't serialize the level generator, so we just returb and


typo return

alonre24 · 2022-11-03T16:12:35Z

tests/benchmark/bm_datasets.py

@@ -29,7 +29,8 @@ def get_data_set(dataset_name):


 # Create an HNSW index from dataset based on specific params.
-def create_hnsw_index(dataset, ef_construction, M):
+def load_or_create_hnsw_index(dataset, index_file_name, ef_construction, M):


Did you ran this script locally to see that these changes work?

yes i ran make benchmark

alonre24 · 2022-11-03T16:38:25Z

tests/unit/test_common.cpp

+
+    std::string file_name;
+};
+TEST_F(SerializerTest, HNSWSerialzer) {


Suggested change

TEST_F(SerializerTest, HNSWSerialzer) {

TEST_F(SerializerTest, HNSWSerialzerErrors) {

Also, try to see if you can increase the coverage in some additional cases where we send invalid params to the new constructor (bad M, bad type etc...), and test the error message itself in addition to the exception type

alonre24 · 2022-11-03T16:42:55Z

tests/unit/test_hnsw.cpp

-    serializer.saveIndex(file_name);
-    VecSimIndex_Free(new_index);
+        // Load the index from the file.
+        VecSimIndex *serialized_index = HNSWFactory::NewIndex(file_name, &params);


Why sending params? I thought that for V2 you don't need them.

alonre24 · 2022-11-03T16:44:43Z

tests/unit/test_hnsw.cpp

+    size_t ef = 10;
+    double epsilon = 0.004;
+    size_t blockSize = 1;
+    bool is_multi[] = {false, true};


We have multi in v1?

Theoretically we can have

meiravgri · 2022-11-06T16:06:02Z

src/VecSim/algorithms/hnsw/hnsw_serializer_imp.h

+                    // Check if we found an invalid neighbor.
+                    if (data[j] > this->max_id || data[j] == i) {
+                        res.valid_state = false;
+                        return res;


was never covered

meiravgri · 2022-11-06T16:06:18Z

src/VecSim/algorithms/hnsw/hnsw_serializer_imp.h

+                // Check if a certain neighbor appeared more than once.
+                if (s.size() != size) {
+                    res.valid_state = false;
+                    return res;


was never covered

meiravgri · 2022-11-06T16:06:27Z

src/VecSim/algorithms/hnsw/hnsw_serializer_imp.h

+            : 0;
+    if (incoming_edges_sets_sizes + double_connections != connections_checked) {
+        res.valid_state = false;
+        return res;


was never covered

alonre24

You did it! :)

GuyAv46

Nicely done!
regarding adding invalid values to enums, IMO we should avoid it

GuyAv46 · 2022-11-14T11:59:02Z

src/VecSim/vec_sim_interface.h

@@ -154,4 +155,6 @@ struct VecSimIndexInterface : public VecsimBaseObject {
    inline static void setTimeoutCallbackFunction(timeoutCallbackFunction callback) {
        VecSimIndexInterface::timeoutCallback = callback;
    }
+
+    inline int64_t getAllocationSize() const { return this->allocator->getAllocationSize(); }


consider moving this to VecsimBaseObject

GuyAv46 · 2022-11-14T12:00:18Z

src/VecSim/vec_sim_interface.h

 #include "VecSim/memory/vecsim_base.h"
 #include "info_iterator_struct.h"

+#include <stddef.h>
+#include <stdexcept>


Why include <stdexcept>?

don't remember but I removed it and it's ok

ok i don't why it doesn't crush locally but the default flow it says that the it doesn't know std::runtime_error

GuyAv46 · 2022-11-14T12:39:52Z

src/VecSim/utils/serializer.cpp

+    // Only V1 and V2 are supported
+    if (version >= EncodingVersion_INVALID) {


what about version 0?

i thought it is no longer supported
@alonre24 ?

you're right @meiravgri. But we don't return an error if version==0. You can just add this validation to this if

I can add EncodingVersion_V0 and it won't throw because it is smaller than EncodingVersion_INVALID
typedef enum EncodingVersion { EncodingVersion_V1 = 1, EncodingVersion_V2 = 2, EncodingVersion_INVALID, // This should always be last. } EncodingVersion;

but it will return when we try to initialize params. So I don't quite understand how to handle v0 without returning an error

I think you SHOULD return an error for version==0

Agrees.

Suggested change

// Only V1 and V2 are supported

if (version >= EncodingVersion_INVALID) {

// Only V1 and V2 are supported

if (version <= 0 || version >= EncodingVersion_INVALID) {

oh got it 😅

GuyAv46 · 2022-11-14T13:25:25Z

src/VecSim/algorithms/hnsw/hnsw_multi.h

+    virtual void AddToLabelLookup(labelType label, idType id) override {
+        if (label_lookup_.find(label) == label_lookup_.end()) {
+            label_lookup_.emplace(label, vecsim_stl::vector<idType>{this->allocator});
+        }
+        setVectorId(label, id);
+    }


Adding this function complicates things for no reason (my bad). I think it is better to move this check to setVectorId itself and remove it from addVector. we call this function once anyway

this function is called by the parent class so if we dont want to affect performance when we are not in tests mode we need the virtual function wrapper anyway

It won’t effect performance because it is called once every insertion anyway

GuyAv46 · 2022-11-14T13:30:45Z

src/VecSim/algorithms/hnsw/hnsw_serializer_imp.h

@@ -0,0 +1,307 @@
+#pragma once


consider calling this file hnsw_serializer.h

GuyAv46 · 2022-11-14T14:10:05Z

tests/unit/test_common.cpp

+};
+TEST_F(SerializerTest, HNSWSerialzer) {
+
+    this->file_name = std::string(getenv("ROOT")) + "/tests/unit/data/bad_index.hnsw";


std::string(getenv("ROOT")) throws an exception when ROOT is not defined (and getenv returns null). Consider passing a default value instead ("." or calling pwd).

GuyAv46 · 2022-11-14T14:10:24Z

tests/unit/test_hnsw.cpp

+        // Set index type.
+        params.multi = is_multi[i];
+
+        auto file_name = std::string(getenv("ROOT")) + "/tests/unit/data/1k-d4-L2-M8-ef_c10_" +


std::string(getenv("ROOT")) throws an exception when ROOT is not defined (and getenv returns null). Consider passing a default value instead ("." or calling pwd).

GuyAv46 · 2022-11-14T14:11:22Z

tests/unit/test_utils.h

@@ -105,3 +105,18 @@ inline double GetInfVal(VecSimType type) {
        throw std::invalid_argument("This type is not supported");
    }
 }
+
+// Test a specific exception type is thrown and prints the right message.
+#define ASSERT_EXCEPTION_MESSAGE(VALUE, EXCEPTION_TYPE, MESSAGE)                                   \


GuyAv46 · 2022-11-14T14:16:24Z

tests/unit/test_utils.h

+        VALUE;                                                                                     \
+        FAIL() << "exception '" << MESSAGE << "' not thrown at all!";                              \
+    } catch (const EXCEPTION_TYPE &e) {                                                            \
+        EXPECT_EQ(std::string(MESSAGE), e.what())                                                  \


There is a macro for comparing c-strings if you prefer.

GuyAv46 · 2022-11-14T14:18:48Z

tests/benchmark/bm_utils.h

+    static const char *hnsw_index_file;
+    static inline std::string GetSerializedIndexLocation(const char *file_name) {
+        return std::string(getenv("ROOT")) + "/" + file_name;
+    }
+};


std::string(getenv("ROOT")) throws an exception when ROOT is not defined (and getenv returns null). Consider passing a default value instead ("." or calling pwd).

GuyAv46

Nicely done!
regarding adding invalid values to enums, IMO we should avoid it

…ing, added multi test

added hnsw ctor for the serializer(required also new ctor for VecSimIndexAbstract) and factory functions to call this ctor, added VecSimAlgo_INVALID, removed friend class SerializerTest_HNSWSerialzer_Test, added serilized index v1 to unit data and the v1 only loads it

put ser test in the begining of hnsw, commented some in the end commented ser in hnsw multi tests fixed common test commented out all the unit tests except hnsw and allocator in hnsw::resize chnaged visited_nodes_handler from unique ptr to shared

… version = v2, hnsw ctor to load from file get params as argument for v1, also gets the version to intialize serializer level_generator is not saved from V2 and up, and skipped whin lodaing v1, new files for v2 unit tests datasets in bm support loading from files if existed

fixed test common

…ex arguments (always saving version 2), added default value to the v1 unit test

removed AddToLabelLookup (calling directly set vector id) checking if the label already exists or should be emplaced from add vector to set vector id

meiravgri force-pushed the serializer_refactor branch from b0a99a0 to 9755881 Compare October 19, 2022 05:44

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meiravgri force-pushed the serializer_refactor branch from 496083c to 3ad3cad Compare October 21, 2022 06:20

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meiravgri force-pushed the serializer_refactor branch 2 times, most recently from 9125357 to 74b8879 Compare October 31, 2022 05:12

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meiravgri changed the title ~~Serializer_refactor~~ Serializer_refactor - MOD-4196 Nov 10, 2022

alonre24 previously approved these changes Nov 13, 2022

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meiravgri added the run-micro-benchmarks label Nov 13, 2022

meiravgri requested a review from GuyAv46 November 13, 2022 09:27

meiravgri dismissed alonre24’s stale review via e760a06 November 13, 2022 14:42

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meiravgri force-pushed the serializer_refactor branch from c3c9611 to e64f1ca Compare November 17, 2022 14:56

meiravgri removed the benchmark label Nov 17, 2022

meiravgri added 21 commits November 24, 2022 07:28

moved clear label look up before resize, initialized vars before read…

086477c

…ing, added multi test

fixed updated bm file

95b6e71

modified binding with the new srialization API

f60d39a

rebase+ changed to n that is not working

d8c2d56

removed indexisvalid and left onlu check integrity

9ff605d

fixed memory saving, added serialized indices, fixed bindings

cfe6907

format

46c26e1

updated xcode

70c7652

added save and load index unit test

e8ec8fe

fixed test common

added check exception msg t test utils, removed version from save ind…

87d4a25

…ex arguments (always saving version 2), added default value to the v1 unit test

checking params in V1 unit test

38243de

fixed updated index intialize

50b2a44

review fixes (not all)

ee5c788

removed vecsim inbvalid type

d6f3a7e

removed AddToLabelLookup (calling directly set vector id) checking if the label already exists or should be emplaced from add vector to set vector id

removed VecSimAlgo_INVALID

9b6b8e3

added #include <stdexcept> back

28411d2

added #include <stdexcept> to the right place...

5ba98f3

replaced add to label id with setbector id

e79690c

meiravgri force-pushed the serializer_refactor branch from 0971995 to e79690c Compare November 24, 2022 05:29

meiravgri requested a review from GuyAv46 November 24, 2022 05:30

meiravgri added run-micro-benchmarks and removed benchmark labels Nov 24, 2022

GuyAv46 approved these changes Nov 24, 2022

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meiravgri merged commit 5e1f503 into main Nov 27, 2022

meiravgri deleted the serializer_refactor branch November 27, 2022 15:21

alonre24 pushed a commit that referenced this pull request Apr 4, 2023

Serializer_refactor - MOD-4196 (#262)

22297e0

alonre24 pushed a commit that referenced this pull request Apr 4, 2023

Serializer_refactor - MOD-4196 (#262)

e117303


		VecSimIndex_Free(index);

		// Create new index, set it into the serializer and extract the data to it.

	virtual bool serializingIsValid() const = 0;
	virtual bool checkIndexIntergrity() const = 0;

		this->file_name = std::string(getenv("ROOT")) + "/tests/unit/data/test_common_hnsw";
		ASSERT_EQ(this->GetFileSize(), 0);

	TEST_F(SerializerTest, HNSWSerialzer) {
	TEST_F(SerializerTest, HNSWSerialzerErrors) {

		// Only V1 and V2 are supported
		if (version >= EncodingVersion_INVALID) {

Serializer_refactor - MOD-4196 #262

Serializer_refactor - MOD-4196 #262

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meiravgri commented Oct 19, 2022 • edited Loading

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meiravgri Nov 15, 2022 • edited Loading

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meiravgri commented Oct 19, 2022 •

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codecov bot commented Oct 19, 2022 •

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meiravgri Oct 26, 2022 •

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meiravgri Nov 15, 2022 •

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