Merge pull request #1 from gvallee/initial_code

Initial code

.gitignore

@@ -0,0 +1,70 @@
+# Prerequisites
+*.d
+
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+# Linker output
+*.ilk
+*.map
+*.exp
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+# Debug files
+*.dSYM/
+*.su
+*.idb
+*.pdb
+
+# Kernel Module Compile Results
+*.cmd
+.tmp_versions/
+modules.order
+Module.symvers
+Mkfile.old
+dkms.conf
+
+# Generated binaries
+tools/cmd/openhpca_setup/openhpca_setup
+tools/cmd/openhpca_run/openhpca_run
+tools/cmd/webui/webui
+src/overlap/overlap_iallreduce
+src/overlap/overlap_ialltoall
+src/overlap/overlap_ialltoallv
+src/overlap/overlap_ibarrier
+src/overlap/overlap_ibcast
+src/overlap/overlap_igather
+src/overlap/overlap_igatherv
+src/overlap/overlap_iallgather
+src/overlap/overlap_iallgatherv
+src/overlap/overlap_ireduce
+
+
+# Generated logs
+*.log

.gitmodules

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+[submodule "SMB"]
+	path = SMB
+	url = https://github.com/sandialabs/SMB
+[submodule "osu_noncontig_mem"]
+	path = osu_noncontig_mem
+	url = https://github.com/yqin/osu-micro-benchmarks

Makefile

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+.PHONY: check update tools init install
+
+.SILENT:
+all: check tools
+	@echo "Done"
+
+GOCMD := $(shell command -v go 2>/dev/null)
+ifndef GOCMD
+tools:
+	@echo "Go not installed; skipping tools' compilation"
+else
+tools:
+	cd tools && make;
+endif
+
+check:
+
+init:
+	./tools/cmd/openhpca_setup/openhpca_setup
+
+install: check update tools init
+
+update:
+	git submodule init
+	git submodule update --remote
+
+clean:
+	cd SMB/src/mpi_overhead; make clean
+	cd SMB/src/msgrate; make clean
+	cd tools; make clean
+	cd src/overlap; make clean

README.md

@@ -1 +1,138 @@
 # openhpca
+
+OpenHPCA is an implementation of the benchmarks defined by the High performance
+compute availability (HPCA) group.
+HPCA aims at providing a comprehensive set of benchmarks to evaluate the 
+overall compute resource performance in the presence of in-network computing 
+technologies​. These benchmarks are a mix of existing benchmarks as well as new
+benchmarks that are defined and implemented by the group.
+
+The benchmarks included in OpenHPCA are:
+- Sandia micro-benchmarks (SMB): https://cs.sandia.gov/smb/
+- the OSU micro-benchmarks: http://mvapich.cse.ohio-state.edu/benchmarks/
+- a modified version of the OSU mico-benchmarks for non-contiguous data
+- a OpenHPCA benchmark suite evaluating the overlap capabilities in the
+context of non-blocking MPI operations (overlap).
+
+The currently rely on the following versions of the different external
+bemchmarks:
+- OSU 5.7
+- SMB from `https://github.com/sandialabs/SMB`
+
+# Installation
+
+Since OpebHPCA is composed of already existing benchmarks and new benchmarks.
+an entire infrastructure has been developed to integrate them together and
+make it easier to install and run. While users are encouraged to use the
+integrated infrastructure, it is also possible to manually install all the
+different benchmarks.
+
+## Pre-requirements
+
+The OpenHPCA software requires the following components to be installed prior
+setting it up:
+- Go, version 1.14 or newer,
+- an MPI implementation.
+
+## Using the integrated infrastructure
+
+OpenHPCA relies on a workspace so before installing OpenHPCA for the first
+time, users
+are required to define the configuration of the workspace. A new workspace can
+be specified by creating the `~/.openhpcx/workspace.conf` file. only one
+workspace is supported at any given time at the moment, multiple workspaces
+can only be currently used by creating a symlink to the target configuration
+file that needs to be used at a given time. Future versions of the suite will
+support multiple workspace so multiple MPI installation could be evaluated
+in parallel. The content of the file should look like:
+
+```
+dir = <PATH/TO/DIRECTORY>
+mpi = <PATH/TO/THE/MPI/INSTALLATION/TO/USE/WITH/OPENHPCA>
+```
+Only two configuration parameters are required:
+- `dir`, which specifies where the workspace will be practically deployed, i.e.,
+where all the data, source codes, compiled data is stored. Note that it must be
+on a location that is accessible from compute nodes when installed on a cluster.
+- `mpi`, which points to the MPI installation to use to run the MPI benchmarks
+(e.g., SMB, OSU, overlap).
+Once the workspace configuration created, execute the following command:
+    `make init`
+
+Once the workspace defined, users can install the benchmarks simply by running
+`make install`. This configures, builds and installs all the benchmarks
+in the workspace.
+
+## Manual installation
+
+### OSU
+
+While the intergated infrastructure will automatically download and install the
+OSU mico-benchmarks, a manual installation requires users to manually download,
+configure and install it. Please refer to the OSU documentation for details.
+
+### SMB
+
+While the intergated infrastructure will automatically download and install the
+SMB micro-benchmarks, a manual installation requires users to manually download,
+configure and install it. Please refer to the documentation available from the
+github project: https://github.com/sandialabs/SMB.
+
+### overlap
+
+Please refer to the `src/overlap/README.md` file for instructions.
+
+# Execution
+
+## Using the integrated framework
+
+OpenHPCA provides the `openhpca_run` tool that automatically run all the
+benchmarks following best practices for such benchmarks. This tool can
+interface with Slurm and other job management systems. Note that the
+current implementation focuses on Slurm and already provide some support
+for SSH based configuration. If support for other job managers is required,
+please contact the development team. The infrastructure has been designed
+to be easily extensible and support for additional job managers should be
+doable with minimum effort.
+
+To run the benchmarks, the full command line looks like:
+```
+./tools/cmd/openhpca_run/openhpca_run -d mlx5_0:1 -p cluster_partition
+```
+Where `mlx5_0:1` is the device to use for the execution of the device and
+`cluster_partition` the partition to use, for instance, on a Slurm cluster.
+For a full description of the supported parameters, please execute
+`./tools/cmd/openhpca_run/openhpca_run -h` from the top directory of the
+OpenHPCA source code.
+
+## Manual execution
+
+For a manual execution, users are asked to run the various benchmarks as they
+would usually do. All the benchmarks are available from the `install` directory
+in the workspace that they defined.
+
+# Data visualization
+
+Since OpenHPCA generates a fairly large of data, the recommanded way to
+visualize all the results is to use the OpenHPCA viewer.
+
+To start the viewer, simply execute the following command from the top
+directory of the OpenHPCA source code:
+```
+./tools/cmd/webui/webui -port 8082
+```
+In this example, the viewer starts on the 8082 port (8080 is used by default).
+
+For details about all the supported parameters, please refer to the
+`./tools/cmd/webui/webui -h` command output.
+
+As a note, to connect to a remmote server through SSH where the webui is meant
+to be executed, use a SSH port fowarding command such as:
+```
+ssh -L 8080:127.0.0.1:8080 remote-server
+```
+You can the connect to the remote server and access the webui using your
+preferred web browser on your local machine by using the following URL:
+```
+http://127.0.0.1:8080
+```

etc/examples/workspace.conf

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+workspace_dir = /tmp/workspace_dir

openhpca.conf

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+# This is the configuration file used by OpenHPCA to store configuration
+# data. This configuration file is not meant to be modified by users.
+# To customize the openHPCA environment, please create/update the
+# ~/.openhpca/workspace.conf file.
+# An example of openhpca_workspace.conf file is provided in:
+#   etc/examples/openhpca_workspace.conf
+
+[OSU]
+    URL=http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.7.tar.gz
+
+[osu_noncontig_mem]
+    URL=file://OPENHPCA_DIR/osu_noncontig_mem
+
+[SMB]
+    URL=file://OPENHPCA_DIR/SMB
+
+[overlap]
+    URL=file://OPENHPCA_DIR/src/overlap

src/overlap/Makefile

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+#
+# Copyright (c) 2021, NVIDIA CORPORATION. All rights reserved.
+#
+# See LICENSE.txt for license information
+#
+
+CFLAGS=-Wall -std=c99
+
+all: overlap_ialltoall \
+	overlap_ialltoallv \
+	overlap_ireduce \
+	overlap_iallreduce \
+	overlap_ibcast \
+	overlap_ibarrier \
+	overlap_igather \
+	overlap_igatherv \
+	overlap_iallgather \
+	overlap_iallgatherv
+
+overlap_igather: overlap_igather.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_igather overlap_igather.c -lm
+
+overlap_igatherv: overlap_igatherv.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_igatherv overlap_igatherv.c -lm
+
+overlap_iallgather: overlap_iallgather.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_iallgather overlap_iallgather.c -lm
+
+overlap_iallgatherv: overlap_iallgatherv.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_iallgatherv overlap_iallgatherv.c -lm
+
+overlap_ialltoall: overlap_ialltoall.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_ialltoall overlap_ialltoall.c -lm
+
+overlap_ialltoallv: overlap_ialltoallv.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_ialltoallv overlap_ialltoallv.c -lm
+
+overlap_ireduce: overlap_ireduce.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_ireduce overlap_ireduce.c -lm
+
+overlap_iallreduce: overlap_iallreduce.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_iallreduce overlap_iallreduce.c -lm
+
+overlap_ibcast: overlap_ibcast.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_ibcast overlap_ibcast.c -lm
+
+overlap_ibarrier: overlap_ibarrier.c overlap.h overlap_tdm.h overlap_ddm.h
+	mpicc -Wno-format-zero-length ${CFLAGS} -o overlap_ibarrier overlap_ibarrier.c -lm
+
+clean:
+	@rm -f overlap_ireduce
+	@rm -f overlap_iallreduce
+	@rm -f overlap_ialltoall
+	@rm -f overlap_ialltoallv
+	@rm -f overlap_igather
+	@rm -f overlap_igatherv
+	@rm -f overlap_iallgather
+	@rm -f overlap_iallgatherv
+	@rm -f overlap_ibcast
+	@rm -f overlap_ibarrier