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jglaser / rdkit_rhea.txt
Last active August 5, 2020 15:04
Installing RDKit in a virtual environment on Linux
# assuming a python venv is active
# pixman
https://github.com/freedesktop/pixman
./autogen.sh --enable-shared --prefix=$VIRTUAL_ENV
make -j32 installl
# cairo
https://github.com/freedesktop/cairo
pixman_CFLAGS=-I$VIRTUAL_ENV/include/pixman-1 pixman_LIBS="-L$VIRTUAL_ENV/lib -lpixman-1" ./autogen.sh --enable-shared --prefix=$VIRTUAL_ENV
@jglaser
jglaser / blazingsql_on_summit.txt
Last active January 11, 2021 16:29
Build RAPIDS + BlazingSQL on Summit
# Build BlazingSQL + RAPIDS on Summit
# Jens Glaser <glaserj@ornl.gov> July 28 2020
# wherever bif128 occurs below, this refers to the project ID
# replace with yours, e.g. abc123
# est. "pure compile time" 3-4h
$ module list
@jglaser
jglaser / profile-nsight-systems
Created May 26, 2020 15:57
Run nsight-systems on summit
module load nsight-systems
jsrun -n30 -g 3 --smpiargs="-disable_gpu_hooks" nsys profile -c cudaProfilerApi -o profile_3.%q{OMPI_COMM_WORLD_RANK} -f true python profile_mpi.py
@jglaser
jglaser / gist:f7e40202b166383e086c1bae9022c7e4
Last active May 29, 2020 18:33
Run nsight-compute on Summit
module load nsight-compute
# profile the first two invocations of <kernel_name>
jsrun <jsrun args> --smpiargs "-disable_gpu_hooks" nv-nsight-cu-cli -k <kernel_name> -c 2 --profile-from-start=off --section=".*(Stats|Counters|Analysis|Occpuancy|SpeedOfLight)" -f -o output <process_to_profile>
@jglaser
jglaser / hoomd_on_summit.txt
Last active May 22, 2020 17:03
How to (properly) install HOOMD-blue into a virtual environment on Summit
# Jens Glaser <glaserj@ornl.gov> 05/21/2020
# The goal is to avoid installing *any* precompiled binaries that are not
# supported by OLCF. This is very important, as these usually come with their
# own versions of libstdc++, which pollute your environment and make it hard to
# track down ABI conflicts in your builds later on.
# we will therefore *avoid* conda, and use pip virtual environments
# for packages that support source compilation through pip, we will use that (pip install --no-binary <pkg> <pkg>)