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Re: [netcdfgroup] Using NetCDF with OPeNDAP on MacOS Sierra (homebrew- and netCDF-dependant software)

In looking at the occurlflags.c code, I think I was being
too clever by half. I am going to rewrite it to be less clever.
That may fix te proximate bug that started this thread.

However, it is true that the certificate entries in .dodsrc
will not be used if you are not using standard libcurl.
Apple broke things by moving to SecureTransport.
I can add suport for this is I can get
some help in telling me where/how SecureTransport gets its certificates
and keys. Also, does anyone know if the Apple libcurl still uses .netrc?
If not, then I need to know if there is a replacement.

=Dennis Heimbigner
 Unidata


On 5/4/2017 12:10 AM, Larry Baker 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/ncdumphttp://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 -hhttp://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 -vhttp://test.opendap.org/opendap/data/nc/3fnoc.nc.das
*   Trying 52.44.0.41...
* TCP_NODELAY set
* Connected totest.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 -vhttp://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 accesshttp://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


_______________________________________________
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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
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do not want to be made public.
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For list information or to unsubscribe, visit:http://www.unidata.ucar.edu/mailing_lists/ 

_______________________________________________
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