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Python to C

When installing via miniconda3 the the web site states “Due to technical limitations, the conda package does not support GPUs at the moment. If you want to use a GPU, you have to build galario by hand.”

A compilation by hand yields two standalone libraries and presumably GPU functionality. There is an example of an invocation using -llibgalario_cuda.

But we have python code so my thought was to pass these two standalone libraries via environment variable to the compiler. source was downloaded and used directly.

  cd /usr/local/src/tmp/
  tar zxvf /zfshomes/hmeij/amhughes/Nuitka-
  cd Nuitka-
  ln -s /zfshomes/hmeij/amhughes/

#  make sure  pip installe cpython in the python of choice
#  miniconda3's python 3.8 (source the code initialization block)

# be sure to get a recent gcc compiler

  export PATH=/share/apps/CENTOS6/gcc/9.2.0/bin:$PATH
  export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/9.2.0/lib64:$LD_LIBRARY_PATH
  export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/9.2.0/lib:$LD_LIBRARY_PATH

# then generate a centos 7 binary

  python  bin/nuitka --follow-imports

That all worked and a sample job scheduler is listed below. It is claimed that the C binary will run 300% faster than the python code. We'll see what the users say.

Now to try to pass the standalone libraries I tried this …

# cuda 9.2
export CUDAHOME=/usr/local/n37-cuda-9.2
export PATH=/usr/local/n37-cuda-9.2/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/n37-cuda-9.2/lib64:$LD_LIBRARY_PATH
which nvcc

# fftw3
export FFTW_HOME=/share/apps/CENTOS7/fftw/3.3.8
export PATH=/share/apps/CENTOS7/fftw/3.3.8/bin:$PATH

# for gpu we have a c++ galario libraries
export LD_LIBRARY_PATH=/share/apps/CENTOS7/galario/1.2.2/usr/local/lib:$LD_LIBRARY_PATH

# attempt at linking those libraries
CPATH=/share/apps/CENTOS7/galario/1.2.2/usr/local/include \
LIBRARY_PATH=/share/apps/CENTOS7/galario/1.2.2/usr/local/lib    \
python  bin/nuitka --follow-imports

It compiled but when invoked it does not find any cuda routines. That may be because I can not find any cuda python code in the git repository either.

sample job

rm -f err-mpi-7c out-mpi-7c

# need conda initialization code block in ~/.bashrc, or next lines

# queues mwgpu, amber128 and exx96
#BSUB -q exx96
#BSUB -o out-mpi-7c
#BSUB -e err-mpi-7c
#BSUB -J test
#BSUB -R "span[hosts=1]"
#BSUB -n 8

# miniconda3
source /share/apps/CENTOS7/amber/miniconda3/etc/profile.d/
export PATH=/share/apps/CENTOS7/amber/miniconda3/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/lib:$LD_LIBRARY_PATH
which mpirun python conda

# wrapper handles  mpirun invocation
openmpi-mpirun \
./galario_SS-7.bin 'Sz_46.txt' \
1.28e-3 36.7 0.339 -1.0 1.0 10.9 61.7 0.46 -0.47 5 12 \
--outdir "output"


cluster/206.txt · Last modified: 2021/07/08 10:18 by hmeij07