jglaser

Computational Scientist

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 / blazingsql_on_summit.txt

Last active January 11, 2021 16:29

Build RAPIDS + BlazingSQL on Summit

	# Build BlazingSQL + RAPIDS on Summit

	# Jens Glaser <[email protected]> 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 / 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 / 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 / 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 <[email protected]> 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>)