add darshan views (for rocky and ubuntu)

.github/workflows/docker-builds.yaml

@@ -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"],

darshan-view-rocky/Dockerfile

@@ -0,0 +1,50 @@
+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" ]

darshan-view-rocky/package.py

@@ -0,0 +1,214 @@
+# 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()

darshan-view/Dockerfile

@@ -0,0 +1,51 @@
+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" ]
+