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kosta777 / parallel-genomeseq

Parallelization of popular genome sequencing algorithms
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Build on Leonhard cluster #22

Open huanglangwen opened 4 years ago

huanglangwen commented 4 years ago

I have successfully built our program on the Leonhard cluster, here’s some note on how to successfully build it:

  1. setup environment 
    module load gcc
module load openmpi
module load cmake
  2. configure and make: DISABLE the -flto flag in CMakeLists.txt because gcc 8 can’t recognize it 
    mkdir build
cd build
cmake .. -DUSEMPI=ON -DUSEOMP=ON
make

    @hanyao8 @spaceben @kosta777

spaceben commented 4 years ago

dont we have to use this: https://scicomp.ethz.ch/wiki/Using_the_batch_system

huanglangwen commented 4 years ago

Yes, but before we submit jobs to the batch system, we need to compile the program :)

huanglangwen commented 4 years ago

I found a good way to manage dependencies on clusters (including euler!): spack. With spack, it would be a piece of cake to handle our dependencies including C++17 compiler, openmpi, cmake and possibly HDF5 (with the chosen mpi). All we have to do is:

#module load python/3.6.0 #maybe have to update python
git clone https://github.com/spack/spack.git
cd spack/bin
./spack env activate myproject #bring installed packages into context, or manually load them using `./spack load <package>`
./spack install gcc@9.2.0
./spack install openmpi%gcc
./spack install hdf5%gcc

Spack will take a lot of time for compiling, but it should be all automatic.