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fix doc link
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Signed-off-by: Yuan Zhou <[email protected]>
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70 changes: 70 additions & 0 deletions docs/ApacheArrowInstallation.md
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# llvm-7.0:
Arrow Gandiva depends on LLVM, and I noticed current version strictly depends on llvm7.0 if you installed any other version rather than 7.0, it will fail.
``` shell
wget http://releases.llvm.org/7.0.1/llvm-7.0.1.src.tar.xz
tar xf llvm-7.0.1.src.tar.xz
cd llvm-7.0.1.src/
cd tools
wget http://releases.llvm.org/7.0.1/cfe-7.0.1.src.tar.xz
tar xf cfe-7.0.1.src.tar.xz
mv cfe-7.0.1.src clang
cd ..
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
cmake --build . -j
cmake --build . --target install
# check if clang has also been compiled, if no
cd tools/clang
mkdir build
cd build
cmake ..
make -j
make install
```

# cmake:
Arrow will download package during compiling, in order to support SSL in cmake, build cmake is optional.
``` shell
wget https://github.com/Kitware/CMake/releases/download/v3.15.0-rc4/cmake-3.15.0-rc4.tar.gz
tar xf cmake-3.15.0-rc4.tar.gz
cd cmake-3.15.0-rc4/
./bootstrap --system-curl --parallel=64 #parallel num depends on your server core number
make -j
make install
cmake --version
cmake version 3.15.0-rc4
```

# Apache Arrow
``` shell
git clone https://github.com/Intel-bigdata/arrow.git
cd arrow && git checkout branch-0.17.0-oap-1.0
mkdir -p arrow/cpp/release-build
cd arrow/cpp/release-build
cmake -DARROW_DEPENDENCY_SOURCE=BUNDLED -DARROW_GANDIVA_JAVA=ON -DARROW_GANDIVA=ON -DARROW_PARQUET=ON -DARROW_HDFS=ON -DARROW_BOOST_USE_SHARED=ON -DARROW_JNI=ON -DARROW_DATASET=ON -DARROW_WITH_PROTOBUF=ON -DARROW_WITH_SNAPPY=ON -DARROW_WITH_LZ4=ON -DARROW_FILESYSTEM=ON -DARROW_JSON=ON ..
make -j
make install

# build java
cd ../../java
# change property 'arrow.cpp.build.dir' to the relative path of cpp build dir in gandiva/pom.xml
mvn clean install -P arrow-jni -am -Darrow.cpp.build.dir=../cpp/release-build/release/ -DskipTests
# if you are behine proxy, please also add proxy for socks
mvn clean install -P arrow-jni -am -Darrow.cpp.build.dir=../cpp/release-build/release/ -DskipTests -DsocksProxyHost=${proxyHost} -DsocksProxyPort=1080
```

run test
``` shell
mvn test -pl adapter/parquet -P arrow-jni
mvn test -pl gandiva -P arrow-jni
```

# Copy binary files to oap-native-sql resources directory
Because oap-native-sql plugin will build a stand-alone jar file with arrow dependency, if you choose to build Arrow by yourself, you have to copy below files as a replacement from the original one.
You can find those files in Apache Arrow installation directory or release directory. Below example assume Apache Arrow has been installed on /usr/local/lib64
``` shell
cp /usr/local/lib64/libarrow.so.17 $native-sql-engine-dir/cpp/src/resources
cp /usr/local/lib64/libgandiva.so.17 $native-sql-engine-dir/cpp/src/resources
cp /usr/local/lib64/libparquet.so.17 $native-sql-engine-dir/cpp/src/resources
```
29 changes: 29 additions & 0 deletions docs/Configuration.md
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# Spark Configurations for Native SQL Engine

Add below configuration to spark-defaults.conf

```
##### Columnar Process Configuration
spark.sql.sources.useV1SourceList avro
spark.sql.join.preferSortMergeJoin false
spark.sql.extensions com.intel.oap.ColumnarPlugin
spark.shuffle.manager org.apache.spark.shuffle.sort.ColumnarShuffleManager
# note native sql engine depends on arrow data source
spark.driver.extraClassPath $HOME/miniconda2/envs/oapenv/oap_jars/spark-columnar-core-<version>-jar-with-dependencies.jar:$HOME/miniconda2/envs/oapenv/oap_jars/spark-arrow-datasource-standard-<version>-jar-with-dependencies.jar
spark.executor.extraClassPath $HOME/miniconda2/envs/oapenv/oap_jars/spark-columnar-core-<version>-jar-with-dependencies.jar:$HOME/miniconda2/envs/oapenv/oap_jars/spark-arrow-datasource-standard-<version>-jar-with-dependencies.jar
spark.executorEnv.LIBARROW_DIR $HOME/miniconda2/envs/oapenv
spark.executorEnv.CC $HOME/miniconda2/envs/oapenv/bin/gcc
######
```

Before you start spark, you must use below command to add some environment variables.

```
export CC=$HOME/miniconda2/envs/oapenv/bin/gcc
export LIBARROW_DIR=$HOME/miniconda2/envs/oapenv/
```

About arrow-data-source.jar, you can refer [Unified Arrow Data Source ](https://oap-project.github.io/arrow-data-source/).
30 changes: 30 additions & 0 deletions docs/Installation.md
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# Spark Native SQL Engine Installation

For detailed testing scripts, please refer to [solution guide](https://github.com/Intel-bigdata/Solution_navigator/tree/master/nativesql)

## Install Googletest and Googlemock

``` shell
yum install gtest-devel
yum install gmock
```

## Build Native SQL Engine

``` shell
git clone -b ${version} https://github.com/oap-project/native-sql-engine.git
cd oap-native-sql
cd cpp/
mkdir build/
cd build/
cmake .. -DTESTS=ON
make -j
```

``` shell
cd ../../core/
mvn clean package -DskipTests
```

### Additonal Notes
[Notes for Installation Issues](./InstallationNotes.md)
47 changes: 47 additions & 0 deletions docs/InstallationNotes.md
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### Notes for Installation Issues
* Before the Installation, if you have installed other version of oap-native-sql, remove all installed lib and include from system path: libarrow* libgandiva* libspark-columnar-jni*

* libgandiva_jni.so was not found inside JAR

change property 'arrow.cpp.build.dir' to $ARROW_DIR/cpp/release-build/release/ in gandiva/pom.xml. If you do not want to change the contents of pom.xml, specify it like this:

```
mvn clean install -P arrow-jni -am -Darrow.cpp.build.dir=/root/git/t/arrow/cpp/release-build/release/ -DskipTests -Dcheckstyle.skip
```

* No rule to make target '../src/protobuf_ep', needed by `src/proto/Exprs.pb.cc'

remove the existing libprotobuf installation, then the script for find_package() will be able to download protobuf.

* can't find the libprotobuf.so.13 in the shared lib

copy the libprotobuf.so.13 from $OAP_DIR/oap-native-sql/cpp/src/resources to /usr/lib64/

* unable to load libhdfs: libgsasl.so.7: cannot open shared object file

libgsasl is missing, run `yum install libgsasl`

* CentOS 7.7 looks like didn't provide the glibc we required, so binaries packaged on F30 won't work.

```
20/04/21 17:46:17 WARN TaskSetManager: Lost task 0.1 in stage 1.0 (TID 2, 10.0.0.143, executor 6): java.lang.UnsatisfiedLinkError: /tmp/libgandiva_jni.sobe729912-3bbe-4bd0-bb96-4c7ce2e62336: /lib64/libm.so.6: version `GLIBC_2.29' not found (required by /tmp/libgandiva_jni.sobe729912-3bbe-4bd0-bb96-4c7ce2e62336)
```

* Missing symbols due to old GCC version.

```
[root@vsr243 release-build]# nm /usr/local/lib64/libparquet.so | grep ZN5boost16re_detail_10710012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcSsEESaINS_9sub_matchIS6_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE14construct_initERKNS_11basic_regexIcSD_EENS_15regex_constants12_match_flagsE
_ZN5boost16re_detail_10710012perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcSsEESaINS_9sub_matchIS6_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE14construct_initERKNS_11basic_regexIcSD_EENS_15regex_constants12_match_flagsE
```

Need to compile all packags with newer GCC:

```
[root@vsr243 ~]# export CXX=/usr/local/bin/g++
[root@vsr243 ~]# export CC=/usr/local/bin/gcc
```

* Can not connect to hdfs @sr602

vsr606, vsr243 are both not able to connect to hdfs @sr602, need to skipTests to generate the jar

109 changes: 109 additions & 0 deletions docs/OAP-Developer-Guide.md
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# OAP Developer Guide

This document contains the instructions & scripts on installing necessary dependencies and building OAP.
You can get more detailed information from OAP each module below.

* [SQL Index and Data Source Cache](https://github.com/oap-project/sql-ds-cache/blob/master/docs/Developer-Guide.md)
* [PMem Common](https://github.com/oap-project/pmem-common)
* [PMem Shuffle](https://github.com/oap-project/pmem-shuffle#5-install-dependencies-for-shuffle-remote-pmem-extension)
* [Remote Shuffle](https://github.com/oap-project/remote-shuffle)
* [OAP MLlib](https://github.com/oap-project/oap-mllib)
* [Arrow Data Source](https://github.com/oap-project/arrow-data-source)
* [Native SQL Engine](https://github.com/oap-project/native-sql-engine)

## Building OAP

### Prerequisites for Building

OAP is built with [Apache Maven](http://maven.apache.org/) and Oracle Java 8, and mainly required tools to install on your cluster are listed below.

- [Cmake](https://help.directadmin.com/item.php?id=494)
- [GCC > 7](https://gcc.gnu.org/wiki/InstallingGCC)
- [Memkind](https://github.com/memkind/memkind/tree/v1.10.1-rc2)
- [Vmemcache](https://github.com/pmem/vmemcache)
- [HPNL](https://github.com/Intel-bigdata/HPNL)
- [PMDK](https://github.com/pmem/pmdk)
- [OneAPI](https://software.intel.com/content/www/us/en/develop/tools/oneapi.html)
- [Arrow](https://github.com/Intel-bigdata/arrow)

- **Requirements for Shuffle Remote PMem Extension**
If enable Shuffle Remote PMem extension with RDMA, you can refer to [PMem Shuffle](https://github.com/oap-project/pmem-shuffle) to configure and validate RDMA in advance.

We provide scripts below to help automatically install dependencies above **except RDMA**, need change to **root** account, run:

```
# git clone -b <tag-version> https://github.com/Intel-bigdata/OAP.git
# cd OAP
# sh $OAP_HOME/dev/install-compile-time-dependencies.sh
```

Run the following command to learn more.

```
# sh $OAP_HOME/dev/scripts/prepare_oap_env.sh --help
```

Run the following command to automatically install specific dependency such as Maven.

```
# sh $OAP_HOME/dev/scripts/prepare_oap_env.sh --prepare_maven
```


### Building

To build OAP package, run command below then you can find a tarball named `oap-$VERSION-bin-spark-$VERSION.tar.gz` under directory `$OAP_HOME/dev/release-package `.
```
$ sh $OAP_HOME/dev/compile-oap.sh
```

Building Specified OAP Module, such as `oap-cache`, run:
```
$ sh $OAP_HOME/dev/compile-oap.sh --oap-cache
```


### Running OAP Unit Tests

Setup building environment manually for intel MLlib, and if your default GCC version is before 7.0 also need export `CC` & `CXX` before using `mvn`, run

```
$ export CXX=$OAP_HOME/dev/thirdparty/gcc7/bin/g++
$ export CC=$OAP_HOME/dev/thirdparty/gcc7/bin/gcc
$ export ONEAPI_ROOT=/opt/intel/inteloneapi
$ source /opt/intel/inteloneapi/daal/2021.1-beta07/env/vars.sh
$ source /opt/intel/inteloneapi/tbb/2021.1-beta07/env/vars.sh
$ source /tmp/oneCCL/build/_install/env/setvars.sh
```

Run all the tests:

```
$ mvn clean test
```

Run Specified OAP Module Unit Test, such as `oap-cache`:

```
$ mvn clean -pl com.intel.oap:oap-cache -am test
```

### Building SQL Index and Data Source Cache with PMem

#### Prerequisites for building with PMem support

When using SQL Index and Data Source Cache with PMem, finish steps of [Prerequisites for building](#prerequisites-for-building) to ensure needed dependencies have been installed.

#### Building package

You can build OAP with PMem support with command below:

```
$ sh $OAP_HOME/dev/compile-oap.sh
```
Or run:

```
$ mvn clean -q -Ppersistent-memory -Pvmemcache -DskipTests package
```
69 changes: 69 additions & 0 deletions docs/OAP-Installation-Guide.md
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# OAP Installation Guide
This document introduces how to install OAP and its dependencies on your cluster nodes by ***Conda***.
Follow steps below on ***every node*** of your cluster to set right environment for each machine.

## Contents
- [Prerequisites](#prerequisites)
- [Installing OAP](#installing-oap)
- [Configuration](#configuration)

## Prerequisites

- **OS Requirements**
We have tested OAP on Fedora 29 and CentOS 7.6 (kernel-4.18.16). We recommend you use **Fedora 29 CentOS 7.6 or above**. Besides, for [Memkind](https://github.com/memkind/memkind/tree/v1.10.1-rc2) we recommend you use **kernel above 3.10**.

- **Conda Requirements**
Install Conda on your cluster nodes with below commands and follow the prompts on the installer screens.:
```bash
$ wget -c https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
$ chmod +x Miniconda2-latest-Linux-x86_64.sh
$ bash Miniconda2-latest-Linux-x86_64.sh
```
For changes to take effect, close and re-open your current shell. To test your installation, run the command `conda list` in your terminal window. A list of installed packages appears if it has been installed correctly.

## Installing OAP

Dependencies below are required by OAP and all of them are included in OAP Conda package, they will be automatically installed in your cluster when you Conda install OAP. Ensure you have activated environment which you created in the previous steps.

- [Arrow](https://github.com/Intel-bigdata/arrow)
- [Plasma](http://arrow.apache.org/blog/2017/08/08/plasma-in-memory-object-store/)
- [Memkind](https://anaconda.org/intel/memkind)
- [Vmemcache](https://anaconda.org/intel/vmemcache)
- [HPNL](https://anaconda.org/intel/hpnl)
- [PMDK](https://github.com/pmem/pmdk)
- [OneAPI](https://software.intel.com/content/www/us/en/develop/tools/oneapi.html)


Create a conda environment and install OAP Conda package.
```bash
$ conda create -n oapenv -y python=3.7
$ conda activate oapenv
$ conda install -c conda-forge -c intel -y oap=1.0.0
```

Once finished steps above, you have completed OAP dependencies installation and OAP building, and will find built OAP jars under `$HOME/miniconda2/envs/oapenv/oap_jars`

#### Extra Steps for Shuffle Remote PMem Extension

If you use one of OAP features -- [PMmem Shuffle](https://github.com/oap-project/pmem-shuffle) with **RDMA**, you need to configure and validate RDMA, please refer to [PMem Shuffle](https://github.com/oap-project/pmem-shuffle#4-configure-and-validate-rdma) for the details.


## Configuration

Once finished steps above, make sure libraries installed by Conda can be linked by Spark, please add the following configuration settings to `$SPARK_HOME/conf/spark-defaults.conf`.

```
spark.executorEnv.LD_LIBRARY_PATH $HOME/miniconda2/envs/oapenv/lib
spark.executor.extraLibraryPath $HOME/miniconda2/envs/oapenv/lib
spark.driver.extraLibraryPath $HOME/miniconda2/envs/oapenv/lib
spark.executor.extraClassPath $HOME/miniconda2/envs/oapenv/oap_jars/$OAP_FEATURE.jar
spark.driver.extraClassPath $HOME/miniconda2/envs/oapenv/oap_jars/$OAP_FEATURE.jar
```

And then you can follow the corresponding feature documents for more details to use them.






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