From ca5180f7a24d08d49f046a4efa8ef5b48201211d Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Tue, 14 Jun 2016 17:03:00 -0400
Subject: [PATCH] Correct Blosc install on Darwin
---
.../repos/builtin/packages/c-blosc/package.py | 4 +
.../builtin/packages/hdf5-blosc/package.py | 177 +++++++++++++++---
2 files changed, 153 insertions(+), 28 deletions(-)
diff --git a/var/spack/repos/builtin/packages/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py
index 16e8c89811..dee332be14 100644
--- a/var/spack/repos/builtin/packages/c-blosc/package.py
+++ b/var/spack/repos/builtin/packages/c-blosc/package.py
@@ -23,6 +23,8 @@
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
+import sys
+
from spack import *
class CBlosc(Package):
@@ -45,3 +47,5 @@ def install(self, spec, prefix):
make()
make("install")
+ if sys.platform == 'darwin':
+ fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
index 897c079e4e..680bc41c41 100644
--- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py
+++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
@@ -43,35 +43,156 @@ class Hdf5Blosc(Package):
parallel = False
def install(self, spec, prefix):
- cmake('.', *std_cmake_args)
+ # The included cmake recipe doesn"t work for Darwin
+ # cmake(".", *std_cmake_args)
+ #
+ # make()
+ # make("install")
+ # if sys.platform == "darwin":
+ # fix_darwin_install_name(prefix.lib)
- make()
- make("install")
- if sys.platform == 'darwin':
- fix_darwin_install_name(prefix.lib)
+ libtool = Executable(join_path(spec["libtool"].prefix.bin, "libtool"))
+ if "+mpi" in spec["hdf5"]:
+ cc = "mpicc"
+ else:
+ cc = "cc"
+ shlibext = "so" if sys.platform!="darwin" else "dylib"
+ mkdirp(prefix.include)
+ mkdirp(prefix.lib)
- # Build and install plugin manually
- # The plugin requires at least HDF5 1.8.11:
- if spec['hdf5'].satisfies('@1.8.11:'):
- # The plugin does not yet work with Windows:
- if sys.platform not in ('win32', 'cygwin'):
- # cc = which('cc')
- libtool = Executable(join_path(spec['libtool'].prefix.bin,
- 'libtool'))
- with working_dir('src'):
- libtool('--mode=compile', '--tag=CC',
- 'cc', '-g', '-O', '-c', 'blosc_plugin.c')
- libtool('--mode=link', '--tag=CC',
- 'cc', '-g', '-O',
- '-rpath', prefix.lib,
- '-o', 'libblosc_plugin.la', 'blosc_plugin.lo')
- shlibext = 'so' if sys.platform!='darwin' else 'dylib'
- shlib0 = 'libblosc_plugin.0.%s' % shlibext
- shutil.copyfile(join_path('.libs', shlib0),
- join_path(prefix.lib, shlib0))
- shlib = 'libblosc_plugin.%s' % shlibext
- os.symlink(shlib0, join_path(prefix.lib, shlib))
+ # Build and install filter
+ with working_dir("src"):
+ libtool("--mode=compile", "--tag=CC",
+ "cc", "-g", "-O",
+ "-c", "blosc_filter.c")
+ libtool("--mode=link", "--tag=CC",
+ "cc", "-g", "-O",
+ "-rpath", prefix.lib,
+ "-o", "libblosc_filter.la",
+ "blosc_filter.lo",
+ "-L%s" % spec["c-blosc"].prefix.lib, "-lblosc",
+ "-L%s" % spec["hdf5"].prefix.lib, "-lhdf5")
+ shlib0 = "libblosc_filter.0.%s" % shlibext
+ shlib = "libblosc_filter.%s" % shlibext
+ shutil.copyfile(join_path(".libs", shlib0),
+ join_path(prefix.lib, shlib0))
+ os.symlink(shlib0, join_path(prefix.lib, shlib))
+
+ # Build and install plugin
+ # The plugin requires at least HDF5 1.8.11:
+ if spec["hdf5"].satisfies("@1.8.11:"):
+ libtool("--mode=compile", "--tag=CC",
+ "cc", "-g", "-O",
+ "-c", "blosc_plugin.c")
+ libtool("--mode=link", "--tag=CC",
+ "cc", "-g", "-O",
+ "-rpath", prefix.lib,
+ "-o", "libblosc_plugin.la",
+ "blosc_plugin.lo",
+ "-L%s" % prefix.lib, "-lblosc_filter",
+ "-L%s" % spec["c-blosc"].prefix.lib, "-lblosc",
+ "-L%s" % spec["hdf5"].prefix.lib, "-lhdf5")
+ shlib0 = "libblosc_plugin.0.%s" % shlibext
+ shlib = "libblosc_plugin.%s" % shlibext
+ shutil.copyfile(join_path(".libs", shlib0),
+ join_path(prefix.lib, shlib0))
+ os.symlink(shlib0, join_path(prefix.lib, shlib))
+
+ self.check_install(spec)
+ def check_install(self, spec):
+ "Build and run a small program to test the installed HDF5 Blosc plugin"
+ print "Checking HDF5-Blosc plugin..."
+ checkdir = "spack-check"
+ with working_dir(checkdir, create=True):
+ source = r"""\
+#include <hdf5.h>
+#include <assert.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#define FILTER_BLOSC 32001 /* Blosc filter ID registered with the HDF group */
+
+int main(int argc, char **argv) {
+ herr_t herr;
+ hid_t file = H5Fcreate("file.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ assert(file >= 0);
+ hsize_t dims[3] = {10, 10, 10};
+ hid_t space = H5Screate_simple(3, dims, NULL);
+ assert(space >= 0);
+ hid_t create_proplist = H5Pcreate(H5P_DATASET_CREATE);
+ assert(create_proplist >= 0);
+ herr = H5Pset_chunk(create_proplist, 3, dims);
+ assert(herr >= 0);
+ herr = H5Pset_filter(create_proplist, FILTER_BLOSC, H5Z_FLAG_OPTIONAL, 0,
+ NULL);
+ assert(herr >= 0);
+ htri_t all_filters_avail = H5Pall_filters_avail(create_proplist);
+ assert(all_filters_avail > 0);
+ hid_t dataset = H5Dcreate(file, "dataset", H5T_NATIVE_DOUBLE, space,
+ H5P_DEFAULT, create_proplist, H5P_DEFAULT);
+ assert(dataset >= 0);
+ double data[10][10][10];
+ for (int k=0; k<10; ++k) {
+ for (int j=0; j<10; ++j) {
+ for (int i=0; i<10; ++i) {
+ data[k][j][i] = 1.0 / (1.0 + i + j + k);
+ }
+ }
+ }
+ herr = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, space, space, H5P_DEFAULT,
+ &data[0][0][0]);
+ assert(herr >= 0);
+ herr = H5Pclose(create_proplist);
+ assert(herr >= 0);
+ herr = H5Dclose(dataset);
+ assert(herr >= 0);
+ herr = H5Sclose(space);
+ assert(herr >= 0);
+ herr = H5Fclose(file);
+ assert(herr >= 0);
+ printf("Done.\n");
+ return 0;
+}
+"""
+ expected = """\
+Done.
+"""
+ with open("check.c", "w") as f:
+ f.write(source)
+ if "+mpi" in spec["hdf5"]:
+ cc = which("mpicc")
+ else:
+ cc = which("cc")
+ # TODO: Automate these path and library settings
+ cc("-c", "-I%s" % spec["hdf5"].prefix.include, "check.c")
+ cc("-o", "check", "check.o",
+ "-L%s" % spec["hdf5"].prefix.lib, "-lhdf5")
+ try:
+ check = Executable("./check")
+ output = check(return_output=True)
+ except:
+ output = ""
+ success = output == expected
+ if not success:
+ print "Produced output does not match expected output."
+ print "Expected output:"
+ print "-"*80
+ print expected
+ print "-"*80
+ print "Produced output:"
+ print "-"*80
+ print output
+ print "-"*80
+ print "Environment:"
+ env = which("env")
+ env()
+ raise RuntimeError("HDF5 Blosc plugin check failed")
+ shutil.rmtree(checkdir)
+
+ def setup_environment(self, spack_env, run_env):
+ spack_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib)
+ run_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib)
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
- spack_env.append_path('HDF5_PLUGIN_PATH', self.spec.prefix.lib)
- run_env.append_path('HDF5_PLUGIN_PATH', self.spec.prefix.lib)
+ spack_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib)
+ run_env.append_path("HDF5_PLUGIN_PATH", self.spec.prefix.lib)
--
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