slorado

Building CUDA version of slorado on x84_64

1. To build for the NVIDIA GPU, you need to have the CUDA toolkit installed. See below for the CUDA toolkit versions we have tested.

2. A minimum g++ version as listed below is required due to libtorch. You check check your g++ version by invoking g++ --version.

3. Install zlib development files needed for slow5lib:

    On Debian/Ubuntu : sudo apt-get install zlib1g-dev
    On Fedora/CentOS : sudo dnf/yum install zlib-devel
   

4. Clone the slorado repository recursively

    git clone --recursive https://github.com/BonsonW/slorado
    cd slorado
   

5. Run the script that downloads and extracts torchlib.

    scripts/install-torch2.sh cuda
   

   This will download the torch version marked default in table below. You can specify a different torch version in this table, for example scripts/install-torch2.sh cuda 2.0.0.

6. Invoke make

    make cuda=1 -j
   

   Note that if the particular torch version in table below states “yes” for cxx11_abi, you should invoke as make cuda=1 -j cxx11_abi=1

7. See the slorado version

    ./slorado --version
   

Advanced building options

• By default it is assumed that you have CUDA on the standard system location (/usr/local/cuda/). There should be the nvcc compiler at /usr/local/cuda/bin/nvcc. The library files (.a files) should be present under /usr/local/cuda/lib64/. If the CUDA location is different, you can specify the path manually as:

   make cuda=1 CUDA_ROOT=/path/to/cuda/
  

  Make sure you have nvcc at /path/to/cuda/bin/nvcc and library files at /path/to/cuda/lib64.

• You can provide the CUDA architecture as make cuda=1 CUDA_ARCH=-arch=sm_xy

• Custom libtorch path:

    make LIBTORCH_DIR=/path/to/libtorch
  

• C++11 ABI (if you are using torch version with C++11 ABI):

    make cxx11_abi=1
  

• You can optionally enable zstd support for built-in slow5lib when building slorado by invoking make zstd=1. This requires zstd 1.3 development libraries installed on your system (libzstd1-dev package for apt, libzstd-devel for yum/dnf).

Tested versions and requirements

Note that we have tested compilation on a limited number of combinations and the approximate minimum g++ requirements are as below.

Slorado version	tested libtorch	tested CUDA	minimum g++ (approximate)	cxx11_abi	comments
0.4.0-beta	2.0.0	11	5.4	no	Flash Attention unsupported for SUP >= v5.0.0
0.4.0-beta	2.4.0 (default)	11	9	no	Fused RMSNorm unsupported for SUP >= v5.0.0
0.4.0-beta	2.9.0	12	9	yes
0.2.0-beta,0.3.0-beta	2.0.0	10,11,12	5.4	no

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