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Use generic approach to decide what to patchelf
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@ocaisa
ocaisa committed Sep 5, 2023
1 parent 1db90be commit f23017f
Showing 1 changed file with 48 additions and 42 deletions.
90 changes: 48 additions & 42 deletions easybuild/easyblocks/j/java.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,58 +127,64 @@ def post_install_step(self):
if elf_interp is None:
raise EasyBuildError("Failed to isolate ELF interpreter!")

bindir = os.path.join(self.installdir, 'bin')
for path in os.listdir(bindir):
path = os.path.join(bindir, path)
out, _ = run_cmd("file %s" % path, trace=False)
if "dynamically linked" in out:
module_guesses = self.make_module_req_guess()

out, _ = run_cmd("patchelf --print-interpreter %s" % path, trace=False)
self.log.debug("ELF interpreter for %s: %s" % (path, out))
bindirs = [os.path.join(self.installdir, bindir) for bindir in module_guesses['PATH'] if
os.path.exists(os.path.join(self.installdir, bindir))]
for bindir in bindirs:
for path in os.listdir(bindir):
path = os.path.join(bindir, path)
out, _ = run_cmd("file %s" % path, trace=False)
if "dynamically linked" in out:

run_cmd("patchelf --set-interpreter %s %s" % (elf_interp, path), trace=False)
out, _ = run_cmd("patchelf --print-interpreter %s" % path, trace=False)
self.log.debug("ELF interpreter for %s: %s" % (path, out))

out, _ = run_cmd("patchelf --print-interpreter %s" % path, trace=False)
self.log.debug("ELF interpreter for %s: %s" % (path, out))
run_cmd("patchelf --set-interpreter %s %s" % (elf_interp, path), trace=False)

out, _ = run_cmd("patchelf --print-rpath %s" % path, simple=False, trace=False)
curr_rpath = out.strip()
self.log.debug("RPATH for %s: %s" % (path, curr_rpath))
out, _ = run_cmd("patchelf --print-interpreter %s" % path, trace=False)
self.log.debug("ELF interpreter for %s: %s" % (path, out))

new_rpath = ':'.join([curr_rpath] + sysroot_lib_paths)
# note: it's important to wrap the new RPATH value in single quotes,
# to avoid magic values like $ORIGIN being resolved by the shell
run_cmd("patchelf --set-rpath '%s' %s" % (new_rpath, path), trace=False)
out, _ = run_cmd("patchelf --print-rpath %s" % path, simple=False, trace=False)
curr_rpath = out.strip()
self.log.debug("RPATH for %s: %s" % (path, curr_rpath))

curr_rpath, _ = run_cmd("patchelf --print-rpath %s" % path, simple=False, trace=False)
self.log.debug("RPATH for %s (prior to shrinking): %s" % (path, curr_rpath))
new_rpath = ':'.join([curr_rpath] + sysroot_lib_paths)
# note: it's important to wrap the new RPATH value in single quotes,
# to avoid magic values like $ORIGIN being resolved by the shell
run_cmd("patchelf --set-rpath '%s' %s" % (new_rpath, path), trace=False)

run_cmd("patchelf --shrink-rpath %s" % path, trace=False)
curr_rpath, _ = run_cmd("patchelf --print-rpath %s" % path, simple=False, trace=False)
self.log.debug("RPATH for %s (prior to shrinking): %s" % (path, curr_rpath))

curr_rpath, _ = run_cmd("patchelf --print-rpath %s" % path, simple=False, trace=False)
self.log.debug("RPATH for %s (after shrinking): %s" % (path, curr_rpath))
run_cmd("patchelf --shrink-rpath %s" % path, trace=False)

libdir = os.path.join(self.installdir, 'lib')
shlib_ext = '.' + get_shared_lib_ext()
for path, _, filenames in os.walk(libdir):
shlibs = [os.path.join(path, x) for x in filenames if x.endswith(shlib_ext)]
for shlib in shlibs:
out, _ = run_cmd("patchelf --print-rpath %s" % shlib, simple=False, trace=False)
curr_rpath = out.strip()
self.log.debug("RPATH for %s: %s" % (shlib, curr_rpath))

new_rpath = ':'.join([curr_rpath] + sysroot_lib_paths)
# note: it's important to wrap the new RPATH value in single quotes,
# to avoid magic values like $ORIGIN being resolved by the shell
run_cmd("patchelf --set-rpath '%s' %s" % (new_rpath, shlib), trace=False)

curr_rpath, _ = run_cmd("patchelf --print-rpath %s" % shlib, simple=False, trace=False)
self.log.debug("RPATH for %s (prior to shrinking): %s" % (path, curr_rpath))
curr_rpath, _ = run_cmd("patchelf --print-rpath %s" % path, simple=False, trace=False)
self.log.debug("RPATH for %s (after shrinking): %s" % (path, curr_rpath))

run_cmd("patchelf --shrink-rpath %s" % shlib, trace=False)

curr_rpath, _ = run_cmd("patchelf --print-rpath %s" % shlib, simple=False, trace=False)
self.log.debug("RPATH for %s (after shrinking): %s" % (path, curr_rpath))
libdirs = [os.path.join(self.installdir, libdir) for libdir in module_guesses['LIBRARY_PATH'] if
os.path.exists(os.path.join(self.installdir, libdir))]
shlib_ext = '.' + get_shared_lib_ext()
for libdir in libdirs:
for path, _, filenames in os.walk(libdir):
shlibs = [os.path.join(path, x) for x in filenames if x.endswith(shlib_ext)]
for shlib in shlibs:
out, _ = run_cmd("patchelf --print-rpath %s" % shlib, simple=False, trace=False)
curr_rpath = out.strip()
self.log.debug("RPATH for %s: %s" % (shlib, curr_rpath))

new_rpath = ':'.join([curr_rpath] + sysroot_lib_paths)
# note: it's important to wrap the new RPATH value in single quotes,
# to avoid magic values like $ORIGIN being resolved by the shell
run_cmd("patchelf --set-rpath '%s' %s" % (new_rpath, shlib), trace=False)

curr_rpath, _ = run_cmd("patchelf --print-rpath %s" % shlib, simple=False, trace=False)
self.log.debug("RPATH for %s (prior to shrinking): %s" % (path, curr_rpath))

run_cmd("patchelf --shrink-rpath %s" % shlib, trace=False)

curr_rpath, _ = run_cmd("patchelf --print-rpath %s" % shlib, simple=False, trace=False)
self.log.debug("RPATH for %s (after shrinking): %s" % (path, curr_rpath))

except OSError as err:
raise EasyBuildError("Failed to patch RPATH section in binaries/libraries: %s", err)
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