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add darshan views (for rocky and ubuntu) (#32)
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* add darshan views (for rocky and ubuntu)

Signed-off-by: vsoch <[email protected]>

* fix build and package.py

Signed-off-by: vsoch <[email protected]>

---------

Signed-off-by: vsoch <[email protected]>
Co-authored-by: vsoch <[email protected]>
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vsoch and vsoch authored Nov 2, 2023
1 parent f764890 commit 505b08a
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2 changes: 2 additions & 0 deletions .github/workflows/docker-builds.yaml
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Expand Up @@ -28,6 +28,8 @@ jobs:
["ovis-hpc", "ghcr.io/converged-computing/metric-ovis-hpc:latest"],
["kripke", "ghcr.io/converged-computing/metric-kripke:latest"],
["mpitrace-rocky", "ghcr.io/converged-computing/metric-mpitrace:rocky"],
["darshan-view", "ghcr.io/converged-computing/metric-darshan-view:ubuntu"],
["darshan-view-rocky", "ghcr.io/converged-computing/metric-darshan-view:rocky"],
["hpctoolkit-viewer", "ghcr.io/converged-computing/metric-hpctoolkit-viewer:latest"],
["hpctoolkit-view", "ghcr.io/converged-computing/metric-hpctoolkit-view:ubuntu"],
["hpctoolkit-view-rocky", "ghcr.io/converged-computing/metric-hpctoolkit-view:rocky"],
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50 changes: 50 additions & 0 deletions darshan-view-rocky/Dockerfile
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FROM spack/rockylinux8:latest as builder

# What we want to install and how we want to install it
# is specified in a manifest file (spack.yaml)
RUN mkdir /opt/spack-environment \
&& (echo spack: \
&& echo ' specs: [darshan-runtime +hdf5, darshan-util, py-darshan]' \
&& echo ' view: /opt/views/view' \
&& echo ' concretizer:' \
&& echo ' unify: true' \
&& echo ' packages:' \
&& echo ' all:' \
&& echo ' require: ["target=:x86_64"]' \
&& echo ' config:' \
&& echo ' install_tree: /opt/software') > /opt/spack-environment/spack.yaml

# Install the software, remove unnecessary deps
COPY ./package.py /opt/spack/var/spack/repos/builtin/packages/darshan-runtime/package.py
RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y

# Strip all the binaries
RUN find -L /opt/views/view/* -type f -exec readlink -f '{}' \; | \
xargs file -i | \
grep 'charset=binary' | \
grep 'x-executable\|x-archive\|x-sharedlib' | \
awk -F: '{print $1}' | xargs strip

# Modifications to the environment that are necessary to run
RUN cd /opt/spack-environment && \
spack env activate --sh -d . > activate.sh

# Bare OS image to run the installed executables
FROM rockylinux:8

COPY --from=builder /opt/spack-environment /opt/spack-environment
COPY --from=builder /opt/software /opt/software

# paths.view is a symlink, so copy the parent to avoid dereferencing and duplicating it
COPY --from=builder /opt/views /opt/views

RUN { \
echo '#!/bin/sh' \
&& echo '.' /opt/spack-environment/activate.sh \
&& echo 'exec "$@"'; \
} > /entrypoint.sh \
&& chmod a+x /entrypoint.sh \
&& ln -s /opt/views/view /opt/view

ENTRYPOINT [ "/entrypoint.sh" ]
CMD [ "/bin/bash" ]
214 changes: 214 additions & 0 deletions darshan-view-rocky/package.py
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# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

import os

from spack.package import *


class DarshanRuntime(AutotoolsPackage):
"""Darshan (runtime) is a scalable HPC I/O characterization tool
designed to capture an accurate picture of application I/O behavior,
including properties such as patterns of access within files, with
minimum overhead. DarshanRuntime package should be installed on
systems where you intend to instrument MPI applications."""

homepage = "https://www.mcs.anl.gov/research/projects/darshan/"
url = "https://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
git = "https://github.com/darshan-hpc/darshan.git"

maintainers("shanedsnyder", "carns")

tags = ["e4s"]
test_requires_compiler = True

version("main", branch="main", submodules=True)
version("3.4.2", sha256="b095c3b7c059a8eba4beb03ec092b60708780a3cae3fc830424f6f9ada811c6b")
version("3.4.1", sha256="77c0a4675d94a0f9df5710e5b8658cc9ef0f0981a6dafb114d0389b1af64774c")
version("3.4.0", sha256="7cc88b7c130ec3b574f6b73c63c3c05deec67b1350245de6d39ca91d4cff0842")
version(
"3.4.0-pre1", sha256="57d0fd40329b9f8a51bdc9d7635b646692b341d80339115ab203357321706c09"
)
version("3.3.1", sha256="281d871335977d0592a49d053df93d68ce1840f6fdec27fea7a59586a84395f7")
version("3.3.0", sha256="2e8bccf28acfa9f9394f2084ec18122c66e45d966087fa2e533928e824fcb57a")
version(
"3.3.0-pre2", sha256="0fc09f86f935132b7b05df981b05cdb3796a1ea02c7acd1905323691df65e761"
)
version(
"3.3.0-pre1", sha256="1c655359455b5122921091bab9961491be58a5f0158f073d09fe8cc772bd0812"
)
version("3.2.1", sha256="d63048b7a3d1c4de939875943e3e7a2468a9034fcb68585edbc87f57f622e7f7")
version("3.2.0", sha256="4035435bdc0fa2a678247fbf8d5a31dfeb3a133baf06577786b1fe8d00a31b7e")
version("3.1.8", sha256="3ed51c8d5d93b4a8cbb7d53d13052140a9dffe0bc1a3e1ebfc44a36a184b5c82")
version("3.1.7", sha256="9ba535df292727ac1e8025bdf2dc42942715205cad8319d925723fd88709e8d6")
version("3.1.6", sha256="21cb24e2a971c45e04476e00441b7fbea63d2afa727a5cf8b7a4a9d9004dd856")
version("3.1.0", sha256="b847047c76759054577823fbe21075cfabb478cdafad341d480274fb1cef861c")
version("3.0.0", sha256="95232710f5631bbf665964c0650df729c48104494e887442596128d189da43e0")

depends_on("mpi", when="+mpi")
depends_on("zlib")
depends_on("hdf5", when="+hdf5")
depends_on("parallel-netcdf", when="+parallel-netcdf")
depends_on("papi", when="+apxc")
depends_on("autoconf", type="build", when="@main")
depends_on("automake", type="build", when="@main")
depends_on("libtool", type="build", when="@main")
depends_on("m4", type="build", when="@main")
depends_on("autoconf", type="build", when="@3.4.0:")
depends_on("automake", type="build", when="@3.4.0:")
depends_on("libtool", type="build", when="@3.4.0:")
depends_on("m4", type="build", when="@3.4.0:")

variant("mpi", default=True, description="Compile with MPI support")
variant("hdf5", default=False, description="Compile with HDF5 module", when="@3.2:")
variant(
"parallel-netcdf",
default=False,
description="Compile with Parallel NetCDF module",
when="@3.4.1:",
)
variant("apmpi", default=False, description="Compile with AutoPerf MPI module", when="@3.3:")
variant(
"apmpi_sync",
default=False,
description="Compile with AutoPerf MPI module (with collective synchronization timing)",
when="@3.3:",
)
variant("apxc", default=False, description="Compile with AutoPerf XC module", when="@3.3:")
variant(
"scheduler",
default="NONE",
description="queue system scheduler JOB ID",
values=("NONE", "cobalt", "pbs", "sge", "slurm"),
multi=False,
)

@property
def configure_directory(self):
return "darshan-runtime"

def configure_args(self):
spec = self.spec
extra_args = []

job_id = "NONE"
if "+slurm" in spec:
job_id = "SLURM_JOBID"
if "+cobalt" in spec:
job_id = "COBALT_JOBID"
if "+pbs" in spec:
job_id = "PBS_JOBID"
if "+sge" in spec:
job_id = "JOB_ID"

if "+hdf5" in spec:
if self.version < Version("3.3.2"):
extra_args.append("--enable-hdf5-mod=%s" % spec["hdf5"].prefix)
else:
extra_args.append("--enable-hdf5-mod")
if "+parallel-netcdf" in spec:
extra_args.append("--enable-pnetcdf-mod")
if "+apmpi" in spec:
extra_args.append("--enable-apmpi-mod")
if "+apmpi_sync" in spec:
[extra_args.append(x) for x in ["--enable-apmpi-mod", "--enable-apmpi-coll-sync"]]
if "+apxc" in spec:
extra_args.append("--enable-apxc-mod")

extra_args.append("--with-mem-align=8")
extra_args.append("--with-log-path-by-env=DARSHAN_LOG_DIR_PATH")
extra_args.append("--with-jobid-env=%s" % job_id)
extra_args.append("--with-zlib=%s" % spec["zlib"].prefix)

if "+mpi" in spec:
extra_args.append("CC=%s" % self.spec["mpi"].mpicc)
else:
extra_args.append("CC=%s" % self.compiler.cc)
extra_args.append("--without-mpi")

print(extra_args)
return extra_args

def setup_run_environment(self, env):
# default path for log file, could be user or site specific setting
darshan_log_dir = os.environ["HOME"]
env.set("DARSHAN_LOG_DIR_PATH", darshan_log_dir)

@property
def basepath(self):
return join_path("darshan-test", join_path("regression", join_path("test-cases", "src")))

@run_after("install")
def _copy_test_inputs(self):
test_inputs = [join_path(self.basepath, "mpi-io-test.c")]
self.cache_extra_test_sources(test_inputs)

def _test_intercept(self):
testdir = "intercept-test"
with working_dir(testdir, create=True):
if "+mpi" in self.spec:
# compile a test program
logname = join_path(os.getcwd(), "test.darshan")
fname = join_path(
self.test_suite.current_test_cache_dir,
join_path(self.basepath, "mpi-io-test.c"),
)
cc = Executable(self.spec["mpi"].mpicc)
compile_opt = ["-c", fname]
link_opt = ["-o", "mpi-io-test", "mpi-io-test.o"]
cc(*(compile_opt))
cc(*(link_opt))

# run test program and intercept
purpose = "Test running code built against darshan"
exe = "./mpi-io-test"
options = ["-f", "tmp.dat"]
status = [0]
installed = False
expected_output = [
r"Write bandwidth = \d+.\d+ Mbytes/sec",
r"Read bandwidth = \d+.\d+ Mbytes/sec",
]
env["LD_PRELOAD"] = "libdarshan.so"
env["DARSHAN_LOGFILE"] = logname
self.run_test(
exe,
options,
expected_output,
status,
installed,
purpose,
skip_missing=False,
work_dir=None,
)
env.pop("LD_PRELOAD")

import llnl.util.tty as tty

# verify existence of log and size is > 0
tty.msg("Test for existince of log:")
if os.path.exists(logname):
sr = os.stat(logname)
print("PASSED")
tty.msg("Test for size of log:")
if not sr.st_size > 0:
exc = BaseException("log size is 0")
m = None
if spack.config.get("config:fail_fast", False):
raise TestFailure([(exc, m)])
else:
self.test_failures.append((exc, m))
else:
print("PASSED")
else:
exc = BaseException("log does not exist")
m = None
if spack.config.get("config:fail_fast", False):
raise TestFailure([(exc, m)])
else:
self.test_failures.append((exc, m))

def test(self):
self._test_intercept()
51 changes: 51 additions & 0 deletions darshan-view/Dockerfile
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FROM spack/ubuntu-jammy:latest as builder

# What we want to install and how we want to install it
# is specified in a manifest file (spack.yaml)
RUN mkdir /opt/spack-environment \
&& (echo spack: \
&& echo ' specs: [darshan-runtime +hdf5, darshan-util, py-darshan]' \
&& echo ' view: /opt/views/view' \
&& echo ' concretizer:' \
&& echo ' unify: true' \
&& echo ' packages:' \
&& echo ' all:' \
&& echo ' require: ["target=:x86_64"]' \
&& echo ' config:' \
&& echo ' install_tree: /opt/software') > /opt/spack-environment/spack.yaml

# Install the software, remove unnecessary deps
COPY ./package.py /opt/spack/var/spack/repos/builtin/packages/darshan-runtime/package.py
RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y

# Strip all the binaries
RUN find -L /opt/views/view/* -type f -exec readlink -f '{}' \; | \
xargs file -i | \
grep 'charset=binary' | \
grep 'x-executable\|x-archive\|x-sharedlib' | \
awk -F: '{print $1}' | xargs strip

# Modifications to the environment that are necessary to run
RUN cd /opt/spack-environment && \
spack env activate --sh -d . > activate.sh

# Bare OS image to run the installed executables
FROM ubuntu:22.04

COPY --from=builder /opt/spack-environment /opt/spack-environment
COPY --from=builder /opt/software /opt/software

# paths.view is a symlink, so copy the parent to avoid dereferencing and duplicating it
COPY --from=builder /opt/views /opt/views

RUN { \
echo '#!/bin/sh' \
&& echo '.' /opt/spack-environment/activate.sh \
&& echo 'exec "$@"'; \
} > /entrypoint.sh \
&& chmod a+x /entrypoint.sh \
&& ln -s /opt/views/view /opt/view

ENTRYPOINT [ "/entrypoint.sh" ]
CMD [ "/bin/bash" ]

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