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HiCOPS

Computational framework for scalable acceleration of database peptide search on supercomputers

Optional Packages

Install the following optional packages, preferably using Spack.

Packages  
papi timemory

Timemory and PAPI Install

Install timemory with at least Python, MPI, MPIP, OMPT and PAPI support using the following instructions:

# install timemory dependencies via Spack
$ spack install --only dependencies timemory@develop%gcc@<version> +ompt +tools \\
  +ompt_library ~dyninst +gotcha +python +papi \\
  ~caliper +mpi +mpip_library

# load dependencies
$ spack load --only dependencies timemory

# clone timemory
$ git clone https://github.com/NERSC/timemory.git && cd timemory && mkdir build && cd build

# configure using CMake
$ cmake .. -DTIMEMORY_USE_MPI=ON -DTIMEMORY_BUILD_MPIP_LIBRARY=ON -DTIMEMORY_USE_OMPT=ON -DTIMEMORY_USE_GOTCHA=ON -DCMAKE_INSTALL_PREFIX=../install -DCMAKE_CXX_STANDARD=14 -DTIMEMORY_USE_PYTHON=ON -DTIMEMORY_BUILD_TOOLS=ON -DUSE_MPI=ON -DUSE_OPENMP=ON -DTIMEMORY_USE_PAPI=ON

# build timemory
$ make install

# export required environment variables
$ export CMAKE_PREFIX_PATH=$PWD/../install:$CMAKE_PREFIX_PATH
$ export PYTHONPATH=$PWD:$PYTHONPATH
$ export MPLCONFIGDIR=$HOME/mplconfigdir

NOTE: Timemory and its dependencies can take upto 2-3 hours to install depending on the system so please be patient.

Ensure that the timemory installation path has correctly been appended to CMAKE_PREFIX_PATH. Also make sure that the Timemory’s python package (PyTimemory) is in PYTHONPATH. Set MPLCONFIGDIR to a writeable directory. e.g. $HOME/mplconfigdir

More Information

See Timemory installation instructions here. More Timemory installation examples can be found here.