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Created September 11, 2015 22:21
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repro.c
#include <stdio.h>
#include <stdlib.h>
#include <netcdf.h>
// Fails similarly on ubuntu 14.04.02 LTS's HDF5/netcdf libraries and
// on the latest github version.
//
// Config on Ubuntu:
// $ dpkg -l '*netcdf*'
// /Desired=Unknown/Install/Remove/Purge/Hold
// | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
// |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
// ||/ Name Version Architecture Description
// +++-==================================-======================-======================-=========================================================================
// ii libnetcdf-dev 1:4.1.3-7ubuntu2 amd64 Development kit for NetCDF
// un libnetcdf4 <none> <none> (no description available)
// un libnetcdf6 <none> <none> (no description available)
// ii libnetcdfc++4 1:4.1.3-7ubuntu2 amd64 Interface for scientific data access to large binary data
// un libnetcdfc++5 <none> <none> (no description available)
// ii libnetcdfc7 1:4.1.3-7ubuntu2 amd64 Interface for scientific data access to large binary data
// ii libnetcdff5 1:4.1.3-7ubuntu2 amd64 Interface for scientific data access to large binary data
// ii netcdf-bin 1:4.1.3-7ubuntu2 amd64 Programs for reading and writing NetCDF files
// un netcdf-doc <none> <none> (no description available)
// $ dpkg -l '*hdf5*'
// Desired=Unknown/Install/Remove/Purge/Hold
// | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
// |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
// ||/ Name Version Architecture Description
// +++-==================================-======================-======================-=========================================================================
// ii hdf5-helpers 1.8.11-5ubuntu7 amd64 Hierarchical Data Format 5 (HDF5) - Helper tools
// un hdf5-tools <none> <none> (no description available)
// un libhdf5-1.8 <none> <none> (no description available)
// un libhdf5-1.8.4 <none> <none> (no description available)
// un libhdf5-1.8.6 <none> <none> (no description available)
// un libhdf5-1.8.7 <none> <none> (no description available)
// rc libhdf5-7:amd64 1.8.11-5ubuntu7 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
// un libhdf5-dev <none> <none> (no description available)
// un libhdf5-doc <none> <none> (no description available)
// un libhdf5-mpich2-1.8.4 <none> <none> (no description available)
// un libhdf5-mpich2-1.8.6 <none> <none> (no description available)
// un libhdf5-mpich2-1.8.7 <none> <none> (no description available)
// ii libhdf5-mpich2-7:amd64 1.8.11-5ubuntu7 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - MPICH2 version
// ii libhdf5-mpich2-dev 1.8.11-5ubuntu7 amd64 Hierarchical Data Format 5 (HDF5) - development files - MPICH2 version
// un libhdf5-serial-1.8.4 <none> <none> (no description available)
// un libhdf5-serial-1.8.6 <none> <none> (no description available)
// un libhdf5-serial-1.8.7 <none> <none> (no description available)
//
//
//
// Just compiled with:
// g++ repro.c -o repro -lnetcdf
// using the netcdf-c from github (commit
// 219a873f8d42245b190dd5ee19ed99812dcbbc90), compiled as below and
// verified it still crashed
// g++ repro.c ~/src/netcdf/vc/netcdf-c/liblib/.libs/libnetcdf.a -lhdf5 -lhdf5_hl -lmpi -lcurl -o repro
//
// By default, runs all seven tests. Accepts a single optional
// integer argument MASK (which may be hex) that selects which of the
// seven tests to run.
//
void
check_err(const int stat, const int line, const char *file) {
if (stat != NC_NOERR) {
(void)fprintf(stderr,"line %d of %s: %s\n", line, file, nc_strerror(stat));
fflush(stderr);
exit(1);
}
}
void
run_test(const char *testname,
bool v1unicode,
bool v2unicode,
bool deletefirst
) {
int stat; /* return status */
int ncid; /* netCDF id */
/* group ids */
int root_grp;
/* dimension ids */
int dim_dim;
/* dimension lengths */
size_t dim_len = 10;
/* variable ids */
int var_id;
/* rank (number of dimensions) for each variable */
# define RANK_var 1
/* variable shapes */
int var_dims[RANK_var];
printf("Beginning test %s\n", testname);
/* enter define mode */
stat = nc_create("test.nc", NC_CLOBBER|NC_NETCDF4, &ncid);
check_err(stat,__LINE__,__FILE__);
root_grp = ncid;
/* define dimensions */
stat = nc_def_dim(root_grp, "dim", dim_len, &dim_dim);
check_err(stat,__LINE__,__FILE__);
/* define variables */
var_dims[0] = dim_dim;
stat = nc_def_var(root_grp, "var", NC_DOUBLE, RANK_var, var_dims, &var_id);
check_err(stat,__LINE__,__FILE__);
/* assign per-variable attributes */
{ /* _FillValue */
static const double var_FillValue_att[1] = {-1} ;
stat = nc_put_att_double(root_grp, var_id, "_FillValue", NC_DOUBLE, 1, var_FillValue_att);
check_err(stat,__LINE__,__FILE__);
}
printf("1st pass: calling ");
if (v1unicode) {
printf("nc_put_att_string");
{ /* att */
static const char* var_att_att[1] = {"foo"} ;
stat = nc_put_att_string(root_grp, var_id, "att", 1, var_att_att); check_err(stat,__LINE__,__FILE__);
}
} else {
printf("nc_put_att_text");
{ /* att */
stat = nc_put_att_text(root_grp, var_id, "att", 3, "foo");
check_err(stat,__LINE__,__FILE__);
}
}
printf("\n");
if (deletefirst) {
printf("Deleting attribute\n");
stat = nc_del_att(root_grp, var_id, "att");
check_err(stat,__LINE__,__FILE__);
}
printf("2nd pass: calling ");
if (v2unicode) {
printf("nc_put_att_string");
{ /* att */
static const char* var_att_att[1] = {"foo"} ;
stat = nc_put_att_string(root_grp, var_id, "att", 1, var_att_att); check_err(stat,__LINE__,__FILE__);
}
} else {
printf("nc_put_att_text");
{ /* att */
stat = nc_put_att_text(root_grp, var_id, "att", 3, "foo");
check_err(stat,__LINE__,__FILE__);
}
}
printf("\n");
/* leave define mode */
stat = nc_enddef (root_grp);
check_err(stat,__LINE__,__FILE__);
/* assign variable data */
stat = nc_close(root_grp);
check_err(stat,__LINE__,__FILE__);
printf("\n");
}
int
main(int argc, char *argv[]) {
int count = -1;
if (argc > 1) {
count = strtol(argv[1], NULL, 0);
printf("TEST MASK %x\n", count);
}
for (int pass = 0; pass < 3; ++pass) {
if (count < 0 || (count & (1 << 0)))
run_test("0 SSF", false, false, false); // OKAY
if (count < 0 || (count & (1 << 1)))
run_test("1 UUF", true, true, false); // OKAY
if (count < 0 || (count & (1 << 2)))
run_test("2 SST", false, false, true); // OKAY
if (count < 0 || (count & (1 << 3)))
run_test("3 UUT", true, true, true); // OKAY
if (count < 0 || (count & (1 << 4)))
run_test("4 UST", true, false, true); // OKAY
if (count < 0 || (count & (1 << 5)))
run_test("5 SUT", false, true, true); // OKAY
if (count < 0 || (count & (1 << 6)))
run_test("6 USF", true, false, false);
if (count < 0 || (count & (1 << 7)))
run_test("7 SUT", false, true, false); // CRASH
}
return 0;
}
/*
Test 6, ubuntu netcdf
Crashes reliably.
Fixed in latest, maybe?
TEST MASK ff
Beginning test 0 SSF
1st pass: calling nc_put_att_text
2nd pass: calling nc_put_att_text
Beginning test 1 UUF
1st pass: calling nc_put_att_string
2nd pass: calling nc_put_att_string
Beginning test 2 SST
1st pass: calling nc_put_att_text
Deleting attribute
2nd pass: calling nc_put_att_text
Beginning test 3 UUT
1st pass: calling nc_put_att_string
Deleting attribute
2nd pass: calling nc_put_att_string
Beginning test 4 UST
1st pass: calling nc_put_att_string
Deleting attribute
2nd pass: calling nc_put_att_text
Beginning test 5 SUT
1st pass: calling nc_put_att_text
Deleting attribute
2nd pass: calling nc_put_att_string
Beginning test 6 USF
1st pass: calling nc_put_att_string
2nd pass: calling nc_put_att_text
*** Error in `repro_ubuntu': munmap_chunk(): invalid pointer: 0x0000000000641890 ***
Program received signal SIGABRT, Aborted.
0x00007ffff770ecc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
56 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0 0x00007ffff770ecc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
#1 0x00007ffff77120d8 in __GI_abort () at abort.c:89
#2 0x00007ffff774b394 in __libc_message (do_abort=do_abort@entry=1, fmt=fmt@entry=0x7ffff7859b28 "*** Error in `%s': %s: 0x%s ***\n")
at ../sysdeps/posix/libc_fatal.c:175
#3 0x00007ffff77560f7 in malloc_printerr (action=<optimized out>, str=0x7ffff7859ea8 "munmap_chunk(): invalid pointer", ptr=<optimized out>) at malloc.c:4996
#4 0x00007ffff7b258b0 in nc4_att_list_del () from /usr/lib/libnetcdf.so.7
#5 0x00007ffff7b259f4 in nc4_rec_grp_del () from /usr/lib/libnetcdf.so.7
#6 0x00007ffff7b1f461 in ?? () from /usr/lib/libnetcdf.so.7
#7 0x00007ffff7b2062c in NC4_close () from /usr/lib/libnetcdf.so.7
#8 0x00007ffff7ad6da3 in nc_close () from /usr/lib/libnetcdf.so.7
#9 0x0000000000400ec9 in run_test(char const*, bool, bool, bool) ()
#10 0x000000000040105b in main ()
*/
/*
Test 7, latest netcdf
Doesn't crash reliably. Seems to work okay if just test 7 was run (MASK = 0x80),
ubuntu: I've seen a crash in this location, but not while connected
to GDB to provide a stack trace.
TEST MASK c0
Beginning test 6 USF
1st pass: calling nc_put_att_string
2nd pass: calling nc_put_att_text
Beginning test 7 SUT
1st pass: calling nc_put_att_text
2nd pass: calling nc_put_att_string
Program received signal SIGSEGV, Segmentation fault.
strlen () at ../sysdeps/x86_64/strlen.S:106
106 ../sysdeps/x86_64/strlen.S: No such file or directory.
(gdb) bt
#0 strlen () at ../sysdeps/x86_64/strlen.S:106
#1 0x00007ffff7ae0838 in H5T__conv_vlen () from /usr/lib/x86_64-linux-gnu/libhdf5.so.7
#2 0x00007ffff7ad520c in H5T_convert () from /usr/lib/x86_64-linux-gnu/libhdf5.so.7
#3 0x00007ffff795fb47 in H5Awrite () from /usr/lib/x86_64-linux-gnu/libhdf5.so.7
#4 0x000000000043105d in put_att_grpa (att=0x374aae0, varid=0, grp=0x3755310) at nc4hdf.c:1332
#5 write_attlist (attlist=<optimized out>, varid=0, grp=grp@entry=0x3755310) at nc4hdf.c:1360
#6 0x00000000004352ac in var_create_dataset (grp=grp@entry=0x3755310, var=var@entry=0x374a9e0, write_dimid=write_dimid@entry=NC_FALSE) at nc4hdf.c:1701
#7 0x0000000000435b24 in write_var (write_dimid=NC_FALSE, grp=<optimized out>, var=0x374a9e0) at nc4hdf.c:2272
#8 nc4_rec_write_metadata (grp=<optimized out>, bad_coord_order=NC_FALSE) at nc4hdf.c:2577
#9 0x000000000042b927 in sync_netcdf4_file (h5=0x374a850) at nc4file.c:3000
#10 0x000000000042f22e in nc4_enddef_netcdf4_file (h5=<optimized out>) at nc4file.c:3315
#11 0x000000000042f282 in NC4_enddef (ncid=<optimized out>) at nc4file.c:2958
#12 0x0000000000406e82 in nc_enddef (ncid=65536) at dfile.c:907
#13 0x0000000000405fa8 in run_test(char const*, bool, bool, bool) ()
#14 0x0000000000406186 in main ()
*/
Raw
repro.py
import netCDF4 as nc
def run_test(testname, v1, v2, delfirst=False):
ds = nc.Dataset("test.nc", 'w')
ds.createDimension('dim', 10)
v = ds.createVariable('var', 'd',
dimensions=('dim',),
fill_value=-1)
attname = 'att'
v.setncattr(attname, v1)
att = v.getncattr(attname)
print testname, "AFTER FIRST", type(att), att
if delfirst:
v.delncattr(attname)
v.setncattr(attname, v2)
att = v.getncattr(attname)
print testname, "AFTER SECOND", type(att), att
ds.close()
print
run_test('0 SSF', 'foo', 'bar') # OKAY
# run_test('1 UUF', u'foo', u'bar') # OKAY
# run_test('2 SST', 'foo', 'bar', True) # OKAY
# run_test('3 UUT', u'foo', u'bar', True) # OKAY
# run_test('4 UST', u'foo', 'bar', True) # OKAY
# run_test('5 SUT', 'foo', u'bar', True) # OKAY
#run_test('6 USF', u'foo', 'bar') # CRASH, always, at getncattr(attname) the second time
#run_test('7 SUT', 'foo', u'bar') # CRASH, sometimes, at close, not at fetch
# 6 callstack
# 6 USF AFTER FIRST <type 'unicode'> foo
# 6 USF AFTER SECOND <type 'unicode'>
# *** Error in `/usr/bin/python': free(): invalid pointer: 0x00007ffff7bb57b8 ***
#
# Program received signal SIGABRT, Aborted.
# 0x00007ffff782dcc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
# 56 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
# (gdb) bt
# #0 0x00007ffff782dcc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
# #1 0x00007ffff78310d8 in __GI_abort () at abort.c:89
# #2 0x00007ffff786a394 in __libc_message (do_abort=do_abort@entry=1, fmt=fmt@entry=0x7ffff7978b28 "*** Error in `%s': %s: 0x%s ***\n")
# at ../sysdeps/posix/libc_fatal.c:175
# #3 0x00007ffff787666e in malloc_printerr (ptr=<optimized out>, str=0x7ffff7974c19 "free(): invalid pointer", action=1) at malloc.c:4996
# #4 _int_free (av=<optimized out>, p=<optimized out>, have_lock=0) at malloc.c:3840
# #5 0x00007ffff660b8b0 in nc4_att_list_del () from /usr/lib/libnetcdf.so.7
# #6 0x00007ffff660b9f4 in nc4_rec_grp_del () from /usr/lib/libnetcdf.so.7
# #7 0x00007ffff6605461 in ?? () from /usr/lib/libnetcdf.so.7
# #8 0x00007ffff660662c in NC4_close () from /usr/lib/libnetcdf.so.7
# #9 0x00007ffff65bcda3 in nc_close () from /usr/lib/libnetcdf.so.7
# #10 0x00007ffff68dba35 in __pyx_pf_7netCDF4_8_netCDF4_7Dataset_14close (__pyx_v_self=0x7fffecd34910, __pyx_v_self=0x7fffecd34910)
# at netCDF4/_netCDF4.c:11843
# #11 __pyx_pw_7netCDF4_8_netCDF4_7Dataset_15close (__pyx_v_self=0x7fffecd34910, unused=<optimized out>) at netCDF4/_netCDF4.c:11816
# #12 0x000000000049a3b5 in PyEval_EvalFrameEx ()
# #13 0x00000000004a090c in PyEval_EvalCodeEx ()
# #14 0x0000000000499a52 in PyEval_EvalFrameEx ()
# #15 0x00000000004a1634 in ?? ()
# #16 0x000000000044e4a5 in PyRun_FileExFlags ()
# #17 0x000000000044ec9f in PyRun_SimpleFileExFlags ()
# #18 0x000000000044f904 in Py_Main ()
# #19 0x00007ffff7818ec5 in __libc_start_main (main=0x44f9c2 <main>, argc=2, argv=0x7fffffffd898, init=<optimized out>, fini=<optimized out>,
# rtld_fini=<optimized out>, stack_end=0x7fffffffd888) at libc-start.c:287
# #20 0x0000000000578c4e in _start ()
# (gdb)
# 7 callstack
#
# 7 SUT AFTER FIRST <type 'unicode'> foo
# 7 SUT AFTER SECOND <type 'unicode'> bar
#
# Program received signal SIGSEGV, Segmentation fault.
# strlen () at ../sysdeps/x86_64/strlen.S:106
# 106 ../sysdeps/x86_64/strlen.S: No such file or directory.
# (gdb) bt
# #0 strlen () at ../sysdeps/x86_64/strlen.S:106
# #1 0x00007ffff6059838 in H5T__conv_vlen () from /usr/lib/x86_64-linux-gnu/libhdf5.so.7
# #2 0x00007ffff604e20c in H5T_convert () from /usr/lib/x86_64-linux-gnu/libhdf5.so.7
# #3 0x00007ffff5ed8b47 in H5Awrite () from /usr/lib/x86_64-linux-gnu/libhdf5.so.7
# #4 0x00007ffff660d03e in ?? () from /usr/lib/libnetcdf.so.7
# #5 0x00007ffff66101ee in nc4_rec_write_metadata () from /usr/lib/libnetcdf.so.7
# #6 0x00007ffff66053d9 in ?? () from /usr/lib/libnetcdf.so.7
# #7 0x00007ffff660544d in ?? () from /usr/lib/libnetcdf.so.7
# #8 0x00007ffff660662c in NC4_close () from /usr/lib/libnetcdf.so.7
# #9 0x00007ffff65bcda3 in nc_close () from /usr/lib/libnetcdf.so.7
# #10 0x00007ffff68dba35 in __pyx_pf_7netCDF4_8_netCDF4_7Dataset_14close (__pyx_v_self=0x7fffecd34910, __pyx_v_self=0x7fffecd34910) at netCDF4/_netCDF4.c:11843
# #11 __pyx_pw_7netCDF4_8_netCDF4_7Dataset_15close (__pyx_v_self=0x7fffecd34910, unused=<optimized out>) at netCDF4/_netCDF4.c:11816
# #12 0x000000000049a3b5 in PyEval_EvalFrameEx ()
# #13 0x00000000004a090c in PyEval_EvalCodeEx ()
# #14 0x0000000000499a52 in PyEval_EvalFrameEx ()
# #15 0x00000000004a1634 in ?? ()
# #16 0x000000000044e4a5 in PyRun_FileExFlags ()
# #17 0x000000000044ec9f in PyRun_SimpleFileExFlags ()
# #18 0x000000000044f904 in Py_Main ()
# #19 0x00007ffff7818ec5 in __libc_start_main (main=0x44f9c2 <main>, argc=2, argv=0x7fffffffd898, init=<optimized out>, fini=<optimized out>,
# rtld_fini=<optimized out>, stack_end=0x7fffffffd888) at libc-start.c:287
# #20 0x0000000000578c4e in _start ()
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