Opened 5 years ago

Last modified 4 years ago

#49198 new defect

netcdf @4.3.3.1_2 +dap +netcdf4 +gcc49/+gcc5 test fails

Reported by: dstrubbe (David Strubbe) Owned by: tenomoto (Takeshi Enomoto)
Priority: Normal Milestone:
Component: ports Version: 2.3.4
Keywords: Cc: mats.bentsen@…, pgf, platipodium (Carsten Lemmen)
Port: netcdf

Description

Extracts from the log below. This is with XCode 6.4, OSX Yosemite 10.10.5.

With +gcc49, using hdf5 @1.8.15-patch1_0+cxx+gcc49:

:info:test PASS: t_nc
:info:test PASS: tst_small
:info:test ../test-driver: line 107: 33547 Segmentation fault: 11  "$@" > $log_file 2>&1
:info:test FAIL: nc_test
:info:test PASS: tst_misc
:info:test PASS: tst_norm
:info:test PASS: tst_names
:info:test PASS: tst_nofill
:info:test PASS: tst_nofill2
:info:test PASS: tst_nofill3
:info:test ../test-driver: line 107: 33684 Segmentation fault: 11  "$@" > $log_file 2>&1
:info:test FAIL: tst_atts3
:info:test PASS: tst_meta
:info:test PASS: tst_atts
:info:test PASS: run_diskless.sh
:info:test make[4]: Nothing to be done for `all'.
:info:test ============================================================================
:info:test Testsuite summary for netCDF 4.3.3.1
:info:test ============================================================================
:info:test # TOTAL: 13
:info:test # PASS:  11
:info:test # SKIP:  0
:info:test # XFAIL: 0
:info:test # FAIL:  2
:info:test # XPASS: 0
:info:test # ERROR: 0
:info:test ============================================================================
:info:test See nc_test/test-suite.log
:info:test Please report to support-netcdf@unidata.ucar.edu
:info:test ============================================================================
:info:test make[3]: *** [test-suite.log] Error 1

with +gcc5, using hdf5 @1.8.15-patch1_0+cxx+gcc5:

info:test Making check in ncgen3
:info:test /Applications/Xcode.app/Contents/Developer/usr/bin/make  check-TESTS
:info:test FAIL: run_tests.sh
:info:test FAIL: run_nc4_tests.sh
:info:test make[4]: Nothing to be done for `all'.
:info:test ============================================================================
:info:test Testsuite summary for netCDF 4.3.3.1
:info:test ============================================================================
:info:test # TOTAL: 2
:info:test # PASS:  0
:info:test # SKIP:  0
:info:test # XFAIL: 0
:info:test # FAIL:  2
:info:test # XPASS: 0
:info:test # ERROR: 0
:info:test ============================================================================
:info:test See ncgen3/test-suite.log
:info:test Please report to support-netcdf@unidata.ucar.edu
:info:test ============================================================================
:info:test make[3]: *** [test-suite.log] Error 1
:info:test make[2]: *** [check-TESTS] Error 2
:info:test make[1]: *** [check-am] Error 2
:info:test make: *** [check-recursive] Error 1
:info:test Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_netcdf/netcdf/work/netcdf-c-4.3.3.1" && /usr/bin/make check

===========================================
   netCDF 4.3.3.1: ncgen3/test-suite.log
===========================================

# TOTAL: 2
# PASS:  0
# SKIP:  0
# XFAIL: 0
# FAIL:  2
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: run_tests.sh
==================

*** Testing ncgen3.
*** creating classic file c0.nc from c0.cdl...
./run_tests.sh: line 8: 76145 Segmentation fault: 11  ./ncgen3 -b -o c0.nc $srcdir/c0.cdl

FAIL: run_nc4_tests.sh
======================

*** Testing ncgen3 for netCDF-4.
*** creating netCDF-4 file c0_4.nc from c0.cdl...
./run_nc4_tests.sh: line 8: 76166 Segmentation fault: 11  ./ncgen3 -k3 -b -o c0_4.nc $srcdir/c0.cdl

Change History (4)

comment:1 Changed 5 years ago by mats.bentsen@…

Cc: mats.bentsen@… added

Cc Me!

comment:2 Changed 5 years ago by pgf

I have a similar problem with netcdf @4.3.3.1_4+dap+gcc5+netcdf4 using MacPorts 2.3.4 on El Capitan (10.11.1). The installation process seems OK, but I have problems running ncdump or other software using the netcdf library (nco, cdo, ncview, ...).
gdb gives the following error:

sudo gdb --args ncdump -h foo.nc
Reading symbols from ncdump...(no debugging symbols found)...done.
(gdb) run
Starting program: /opt/local/bin/ncdump -h foo.nc
netcdf foo {
dimensions:
        time = UNLIMITED ; // (120 currently)
        latitude = 180 ;
        longitude = 360 ;
        nv = 2 ;
variables:

Program received signal SIGSEGV, Segmentation fault.
0x00007fff909c12da in stack_not_16_byte_aligned_error () from /usr/lib/system/libdyld.dylib
(gdb) where
#0  0x00007fff909c12da in stack_not_16_byte_aligned_error () from /usr/lib/system/libdyld.dylib
#1  0x000000000000001c in ?? ()
#2  0x00000001000b31e8 in ?? () from /opt/local/lib/libnetcdf.7.dylib
#3  0x0000000000000bbe in ?? ()
#4  0x0000000100020990 in utf8proc_reencode () from /opt/local/lib/libnetcdf.7.dylib
#5  0x0000000100020a2c in utf8proc_map () from /opt/local/lib/libnetcdf.7.dylib
#6  0x0000000100020a98 in utf8proc_NFC () from /opt/local/lib/libnetcdf.7.dylib
#7  0x000000010002fde2 in NC_finddim () from /opt/local/lib/libnetcdf.7.dylib
#8  0x000000010003027c in NC3_inq_dimid () from /opt/local/lib/libnetcdf.7.dylib
#9  0x000000010001a0e2 in nc_inq_dimid () from /opt/local/lib/libnetcdf.7.dylib
#10 0x0000000100004c25 in do_ncdump_rec.isra ()
#11 0x000000010000aecb in main ()

This problem does not happen if netcdf is compiled without the gcc5 variant or with the clang37 variant (I have not tested other versions).

Might the stack_not_16_byte_aligned_error error be related to the Libtool MACOSX_DEPLOYMENT_TARGET bug happening on El Capitan (10.11)?

comment:3 Changed 5 years ago by pgf

Cc: piergiuseppe.fogli@… added

Cc Me!

comment:4 Changed 4 years ago by platipodium (Carsten Lemmen)

Cc: carsten@… added

Cc Me!

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