sfu-dis/fptree

An open-source FPTree implementation

FPTree

An open-source FPTree implementation

I. Oukid, J. Lasperas, A. Nica, T. Willhalm, and W. Lehner. FPTree: A Hybrid SCM-DRAM Persistent and Concurrent B-Tree for Storage Class Memory. 
In Proceedings of the 2016 International Conference on Management of Data, SIGMOD’16, pages 371–386. ACM, 2016

Important information before build !

FPTree use Intel Threading Building Blocks (oneTBB) for concurrency control. The default retry threshold for oneTBB is only 10 for read write mutex.

1. To achieve better scalability, we are using customized TBB library for FPTree (which is also the approach taken by the original author).
   Here are the steps to generate libtbb.so:
   
   • Clone oneTBB from github (https://github.com/oneapi-src/oneTBB.git)
     to this repo (i.e., /path/to/your/fptree/oneTBB).
   • Modify the read/write retry from 10 to 256 in oneTBB/src/tbb/rtm_mutex.cpp and oneTBB/src/tbb/rtm_rw_mutex.cpp
     
   • cd oneTBB && mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release .. && make -j
     
   • Check that libtbb.so exists in oneTBB/build/gnu_11.1_cxx11_64_release
     
   • Modify CMakeLists.txt located in FPTree folder to use custom TBB
     
     • delete -ltbb flag in CMAKE_CXX_FLAGS which link to your default TBB built
       
     • add and modify them in the proper place in CMakeLists.txt

     link_directories(oneTBB/build/gnu_11.1_cxx11_64_release) # gnu version and cxx version could vary
     include_directories(oneTBB/include)
     

   • After the line that adds fptree pibench wrapper library, do target link below.

     target_link_libraries(fptree_pibench_wrapper libtbb.so)
     

   • Change header files in fptree.h to include those from custom tbb like this:

     // #include <tbb/spin_mutex.h>
     // #include <tbb/spin_rw_mutex.h>
     #include "oneapi/tbb/spin_mutex.h"
     #include "oneapi/tbb/spin_rw_mutex.h"
     

2. Modify #define PMEMOBJ_POOL_SIZE in fptree.h if BACKEND = PMEM (defined in CMakeLists.txt)
   
3. Modify #define MAX_INNER_SIZE 128 and #define MAX_LEAF_SIZE 64 in fptree.h if you want. These are tunable variable.
4. To use HTM, you will need to turn on TSX on your machine. If you execute lscpu and see Vulnerability Tsx async abort: Vulnerable, then TSX is turned on. Otherwise, here is an example of how to turn on TSX on archlinux.

• Make sure everything's up-to-date and consistent. Use pacman to do an update.
• Add this line to /etc/default/grub: GRUB_CMDLINE_LINUX_DEFAULT="tsx=on tsx_async_abort=off loglevel=3 quiet"
• Run these commands:

grub-mkconfig -o /boot/grub/grub.cfg
systemctl reboot

Build (check out the next section for running pibench with the fptree wrapper)

Build PMEM Version

mkdir build && cd build
cmake -DPMEM_BACKEND=PMEM ..

Build DRAM Version

mkdir build && cd build
cmake -DPMEM_BACKEND=DRAM ..

All executables are in build/src folder

Inspector executable

mkdir build && cd build
cmake -DPMEM_BACKEND=${BACKEND} -DBUILD_INSPECTOR=1 ..

Run inspector to check the correctness of single/multi-threaded insert, delete operations for both leaf nodes and inner nodes

If you want to check performance of this implementation, please see PiBench instruction below

Other build options

-DBUILD_INSPECTOR=1 to build inspector executable which can check the correctness of single/multi-threaded operations (insert, delete..)

-DTEST_MODE=1 to set the size of leaf nodes & inner nodes. (TEST MODE: MAX_INNER_SIZE=3 MAX_LEAF_SIZE=4 for debug usage)

Benchmark on PiBench

We officially support FPTree wrapper for pibench:

Checkout PiBench here: https://github.com/sfu-dis/pibench

Build/Create FPTree shared lib

mkdir Release && cd Release
cmake -DPMEM_BACKEND=<PMEM|DRAM> -DTEST_MODE=0 -DBUILD_INSPECTOR=0 ..

Troubleshooting

(1) If you see the error below when you try to run PiBench with this wrapper:

Error in dlopen(): /lib/x86_64-linux-gnu/libjemalloc.so.2: cannot allocate memory in static TLS block

You can try adding LD_PRELOAD before the PiBench executable:

LD_PRELOAD=/path/to/your/libjemalloc.so ./PiBench ...

(2) libpmemobj.so error.

Error in dlopen(): /path/to/libfptree_pibench_wrapper.so: undefined symbol: _pobj_cache_invalidate

Add /path/to/libpmemobj.so to LD_PRELOAD.

fptree's Issues

SIGILL when running DRAM versioned fptree

Hello! I am trying to run fptree but has a SIGILL issue.
I built a DRAM version as I don't have persistent memory and I removed all linked PM libraries in CMakeLists.txt.
When I ran fptree, sometimes it can print out the tree (100 KV pairs) but sometimes it is SIGILL. And if I decide to delete some key, it always ends in "Illegal instruction (core dumped)". Could you share the basic system requirements to run fptree and what could be the possible reason for my issue?
Thanks a lot!

Can't turn on TSX support in my Ubuntu2204

Hello, I tried to build the FPTree project, but encountered an issue while enabling TSX support. I add "tsx=on tsx_async_abort=off" to /etc/default/grub and update grub. Then I reboot my machine, it seems like not working. My machine's CPU is Intel Xeon Gold 5320, and the Intel documentation mentions support for TSX

OS:

Reboot Info:

lscpu: