Is this an issue then with something interesting Xcode?
Sent from my iPhone
On May 4, 2017, at 00:12, Larry Baker <baker@xxxxxxxx<mailto:baker@xxxxxxxx>>
wrote:
See https://github.com/Unidata/netcdf-c/issues/122 around July 10, 2015 for a
similar/the same bug? My previous inference about strcmp() being the culprit
is not quite right. The failing code in the thread I found (below) is just
before the strcmp() call. Looks like the same problem to me. The cause at
that time was "c" had a value of 67, while the nameindices[] array was declared
[26].
doutriaux1@maryam:[build]:[10587]> lldb ~/build//install/Externals/bin/ncdump
http://test.opendap.org/opendap/hyrax/netcdf/examples/ECMWF_ERA-40_subset.nc
(lldb) target create "/Users/doutriaux1/build//install/Externals/bin/ncdump"
Current executable set to
'/Users/doutriaux1/build//install/Externals/bin/ncdump' (x86_64).
(lldb) settings set -- target.run-args
"http://test.opendap.org/opendap/hyrax/netcdf/examples/ECMWF_ERA-40_subset.nc";
(lldb) r
Process 45302 launched: '/Users/doutriaux1/build//install/Externals/bin/ncdump'
(x86_64)
Process 45302 stopped
* thread #1: tid = 0xebf1, 0x00000001000b09c7
libnetcdf.7.dylib`occurlflagbyname(name=0x0000000100186749) + 327 at
occurlflags.c:301, queue = 'com.apple.main-thread', stop reason =
EXC_BAD_ACCESS (code=1, address=0x2)
frame #0: 0x00000001000b09c7
libnetcdf.7.dylib`occurlflagbyname(name=0x0000000100186749) + 327 at
occurlflags.c:301
298
299 if(nameindices[c] == NULL)
300 return NULL; /* no possible match */
-> 301 for(f=nameindices[c];f->name;f++) {
302 int cmp = strcmp(name,f->name);
303 if(cmp > 0) break; /* We assume sorted */
304 if(cmp == 0) return f;
Larry Baker
US Geological Survey
650-329-5608
baker@xxxxxxxx<mailto:baker@xxxxxxxx>
On May 3, 2017, at 10:57 PM, Larry Baker
<baker@xxxxxxxx<mailto:baker@xxxxxxxx>> wrote:
Looks to me like an illegal memory access in a strcmp() inside
libnetcdf.11.dylib. The "occurlflagbyname()" is the failing function inside
libnetcdf?
Larry Baker
US Geological Survey
650-329-5608
baker@xxxxxxxx<mailto:baker@xxxxxxxx>
On May 3, 2017, at 10:44 PM, Capehart, William J
<William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>> wrote:
OK. I am not familiar with how to use this but here is the output that I have
for lldb usng …
lldb --debug /usr/local/bin/ncdump
http://test.opendap.org/opendap/data/nc/3fnoc.nc
https://gist.github.com/wjcapehart/8cc8068a6b6951ee98a2a48dbae02520
And for my output for the fortran program that I wrote.
https://gist.github.com/9a46b7750bc5a9c3ebfdf1916941f490
For the command
% otool -L /usr/local/bin/ncdump
http://test.opendap.org/opendap/data/nc/3fnoc.nc
/usr/local/bin/ncdump:
@rpath/libnetcdf.11.dylib (compatibility version 11.0.0,
current version 11.4.0)
/usr/local/opt/hdf5/lib/libhdf5_hl.100.dylib (compatibility
version 101.0.0, current version 101.0.0)
/usr/local/opt/hdf5/lib/libhdf5.100.dylib (compatibility
version 101.0.0, current version 101.1.0)
/usr/local/opt/szip/lib/libsz.2.dylib (compatibility version
3.0.0, current version 3.0.0)
/usr/local/lib/libz.1.dylib (compatibility version 1.0.0,
current version 1.2.8)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
current version 1238.50.2)
/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current
version 9.0.0)
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/objdump:
'http://test.opendap.org/opendap/data/nc/3fnoc.nc': No such file or directory
------------------------------------------------
Bill Capehart <William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>>
Atmospheric and Environmental Sciences Program Coordinator
Civil and Environmental Engineering
201 Mineral Industries Building
South Dakota School of Mines and Technology
501 East St Joseph Street
Rapid City, SD 57701-3995
Ph: +1-605-394-1994 Mobile: +1-605-484-4692
From:
<netcdfgroup-bounces@xxxxxxxxxxxxxxxx<mailto:netcdfgroup-bounces@xxxxxxxxxxxxxxxx>>
on behalf of Larry Baker <baker@xxxxxxxx<mailto:baker@xxxxxxxx>>
Date: Wednesday, May 3, 2017 at 16:45 MDT
To: "dmh@xxxxxxxx<mailto:dmh@xxxxxxxx>" <dmh@xxxxxxxx<mailto:dmh@xxxxxxxx>>
Cc: "netcdfgroup@xxxxxxxxxxxxxxxx<mailto:netcdfgroup@xxxxxxxxxxxxxxxx>"
<netcdfgroup@xxxxxxxxxxxxxxxx<mailto:netcdfgroup@xxxxxxxxxxxxxxxx>>
Subject: Re: [netcdfgroup] Using NetCDF with OPeNDAP on MacOS Sierra (homebrew-
and netCDF-dependant software)
Good idea: lldb
Larry Baker
US Geological Survey
650-329-5608
baker@xxxxxxxx<mailto:baker@xxxxxxxx>
On 3 May 2017, at 3:35:19 PM, dmh@xxxxxxxx<mailto:dmh@xxxxxxxx> wrote:
Is there a osx equivalent of gdb? If so, you could
probably run the ncdump command using that debugger
and it will probably catch the seg fault. This would
allow some idea of where the failure is occurring.
=Dennis Heimbigner
Unidata
On 5/3/2017 4:25 PM, Capehart, William J wrote:
To be desperate ;-P is there a way to test things with just the libcurl to see
where the problem is? I am assuming that most people are getting satisfaction
with the resident version with Sierra. I'm really on my last leg here. I'm
not even getting core files with my seg faults on ncdump or my simple Fortran
program inbuilt to test it... both run just fine on Centos .
Sent from my iPhone
On May 3, 2017, at 15:04, "dmh@xxxxxxxx<mailto:dmh@xxxxxxxx>"
<dmh@xxxxxxxx<mailto:dmh@xxxxxxxx>> wrote:
To be pedantic, ncdump (via the netcdf-c library) uses libcurl.
=Dennis Heimbigner
Unidata
On 5/3/2017 2:31 PM, Roy Mendelssohn - NOAA Federal wrote:
Hmm - I may be wrong but i thought the ncdump for a remote file just uses curl
to get the .das and .dds and forms the .cdl response from those. Have you
tried a different server?
Say,
ncdump -h http://coastwatch.pfeg.noaa.gov/erddap/griddap/jplAquariusSSSMonthlyV4
-Roy
On May 3, 2017, at 1:25 PM, Capehart, William J
<William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>> wrote:
Roy for the curl I get the followingf
% curl -v http://test.opendap.org/opendap/data/nc/3fnoc.nc.das
* Trying 52.44.0.41...
* TCP_NODELAY set
* Connected to test.opendap.org<http://test.opendap.org/> (52.44.0.41) port 80
(#0)
GET /opendap/data/nc/3fnoc.nc.das HTTP/1.1
Host: test.opendap.org<http://test.opendap.org/>
User-Agent: curl/7.51.0
Accept: */*
< HTTP/1.1 200 OK
< Date: Wed, 03 May 2017 20:22:21 GMT
< X-FRAME-OPTIONS: DENY
< Last-Modified: Tue, 10 Jan 2006 18:32:26 GMT
< Set-Cookie: JSESSIONID=63E4296077ED5DBE9CFE2C49B169D4ED; Path=/opendap;
HttpOnly
< XDODS-Server: dods/3.2
< XOPeNDAP-Server: bes/3.17.4, csv_handler/1.1.6, dap-server/ascii/4.1.5,
dap-server/usage/4.2.6, dap-server/www/4.1.5, dapreader_module/0.0.1,
fileout_gdal/0.10.1, fileout_json/1.0.6, fileout_netcdf/1.4.3,
fits_handler/1.0.18, freeform_handler/3.9.6, functions/1.1.0,
gateway_module/1.1.9, gdal_handler/1.0.7, hdf4_handler/3.12.3,
hdf5_handler/2.3.5, libdap/3.18.3, ncml_moddule/1.4.4, netcdf_handler/3.11.6,
w10n_handler/1.0.6, xml_data_handler/1.1.2
< X-DAP: 3.2
< Content-Description: dods_das
< Content-Type: text/plain
< Connection: close
< Transfer-Encoding: chunked
<
Attributes {
u {
String units "meter per second";
String long_name "Vector wind eastward component";
String missing_value "-32767";
String scale_factor "0.005";
}
v {
String units "meter per second";
String long_name "Vector wind northward component";
String missing_value "-32767";
String scale_factor "0.005";
}
lat {
String units "degree North";
}
lon {
String units "degree East";
}
time {
String units "hours from base_time";
}
NC_GLOBAL {
String base_time "88-245-00:00:00";
String title " FNOC UV wind components from 1988-245 to 1988-247.";
}
DODS_EXTRA {
String Unlimited_Dimension "time_a";
}
}
* Curl_http_done: called premature == 0
* Closing connection 0
------------------------------------------------
Bill Capehart <William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>>
Atmospheric and Environmental Sciences Program Coordinator
Civil and Environmental Engineering
201 Mineral Industries Building
South Dakota School of Mines and Technology
501 East St Joseph Street
Rapid City, SD 57701-3995
Ph: +1-605-394-1994 Mobile: +1-605-484-4692
On 5/3/17, 14:19 MDT, "Roy Mendelssohn - NOAA Federal"
<roy.mendelssohn@xxxxxxxx<mailto:roy.mendelssohn@xxxxxxxx>> wrote:
More specifically, what do you get when you give:
curl -v http://test.opendap.org/opendap/data/nc/3fnoc.nc.das
-Roy
On May 3, 2017, at 1:01 PM, Roy Mendelssohn - NOAA Federal
<roy.mendelssohn@xxxxxxxx<mailto:roy.mendelssohn@xxxxxxxx>> wrote:
What happens if you just do a curl to get the address but ask for the .das
instead, and see if your curl and access the site.
-Roy
On May 3, 2017, at 12:57 PM, Capehart, William J
<William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>> wrote:
Did that with both fink and homebrew including compiling all from source each
time. Still no traction. :-(
------------------------------------------------
Bill Capehart <William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>>
Atmospheric and Environmental Sciences Program Coordinator
Civil and Environmental Engineering
201 Mineral Industries Building
South Dakota School of Mines and Technology
501 East St Joseph Street
Rapid City, SD 57701-3995
Ph: +1-605-394-1994 Mobile: +1-605-484-4692
On 5/3/17, 08:06 MDT, "Roy Mendelssohn - NOAA Federal"
<roy.mendelssohn@xxxxxxxx<mailto:roy.mendelssohn@xxxxxxxx>> wrote:
try installing the fink curl.
-roy
On May 3, 2017, at 6:47 AM, Capehart, William J
<William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>> wrote:
I am attaching my gist of the build
https://gist.github.com/anonymous/4db828fcd4384c7883a8687147ced1f7
The C tst is 3.make
The C++4 Test is 7.make
The Fortran Test is 11.make
The C++ test is 16.make
Hi Sean: And the output of my nc-config –alll
https://gist.github.com/733ad6330523a83cee204f9f7f34c061
The curl version on my mac (10.12.4) is the on-board version which I presume is
what I need
% curl --version
curl 7.51.0 (x86_64-apple-darwin16.0) libcurl/7.51.0 SecureTransport zlib/1.2.8
Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3
pop3s rtsp smb smbs smtp smtps telnet tftp
Features: AsynchDNS IPv6 Largefile GSS-API Kerberos SPNEGO NTLM NTLM_WB SSL
libz UnixSockets
And curl -Oing my the target file produces the following
https://gist.github.com/wjcapehart/6f49640a075f47b1040c48917ebd631b
Sorry Larry: valgrind is reporting from homebrew that is in compatible with
MacOS post El Capitan.
Roy: from the client side I’m not seeing any significant redflags in the
console logs
Really really out of clues at this point. Thanks to everyone or their input
though.
Bill
From: Sean Arms <sarms@xxxxxxxx<mailto:sarms@xxxxxxxx>>
Date: Tuesday, May 2, 2017 at 17:50 MDT
To: William Capehart
<William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>>
Cc: "netcdfgroup@xxxxxxxxxxxxxxxx<mailto:netcdfgroup@xxxxxxxxxxxxxxxx>"
<netcdfgroup@xxxxxxxxxxxxxxxx<mailto:netcdfgroup@xxxxxxxxxxxxxxxx>>
Subject: Re: [netcdfgroup] Using NetCDF with OPeNDAP on MacOS Sierra (homebrew-
and netCDF-dependant software)
Greetings Bill,
I have a suspicion this has to do with the way curl was built. What does
nc-config --libs
give you?
Sean
On Sun, Apr 30, 2017 at 10:42 AM, Capehart, William J
<William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>> wrote:
Hi All
I have been having a particularly time working with NetCDF with OPeNDAP on my
Macs (right now both are on MacOS 10.12.4). I’ve mostly been using homebrew
but this also happens with NCL 6.3 and 6.4 as downloaded from Earth System Grid.
When testing code using just the NetCDF fortran libraries as well as just using
ncdump I get segmentation faults when I try to access
http://test.opendap.org/opendap/data/nc/3fnoc.nc
Is anyone else having any luck with their MacOS Sierra NetCDF builds and the
software that leverages NetCDF?
------------------------------------------------
Bill Capehart <William.Capehart@xxxxxxxxx<mailto:William.Capehart@xxxxxxxxx>>
Atmospheric and Environmental Sciences Program Coordinator
Civil and Environmental Engineering
201 Mineral Industries Building
South Dakota School of Mines and Technology
501 East St Joseph Street
Rapid City, SD 57701-3995
Ph: +1-605-394-1994 Mobile: +1-605-484-4692
_______________________________________________
NOTE: All exchanges posted to Unidata maintained email lists are
recorded in the Unidata inquiry tracking system and made publicly
available through the web. Users who post to any of the lists we
maintain are reminded to remove any personal information that they
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For list information or to unsubscribe, visit:
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**********************
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn@xxxxxxxx<mailto:Roy.Mendelssohn@xxxxxxxx> www:
http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
**********************
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn@xxxxxxxx<mailto:Roy.Mendelssohn@xxxxxxxx> www:
http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
**********************
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn@xxxxxxxx<mailto:Roy.Mendelssohn@xxxxxxxx> www:
http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
**********************
"The contents of this message do not reflect any position of the U.S.
Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn@xxxxxxxx<mailto:Roy.Mendelssohn@xxxxxxxx> www:
http://www.pfeg.noaa.gov/
"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
_______________________________________________
NOTE: All exchanges posted to Unidata maintained email lists are
recorded in the Unidata inquiry tracking system and made publicly
available through the web. Users who post to any of the lists we
maintain are reminded to remove any personal information that they
do not want to be made public.
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For list information or to unsubscribe, visit:
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