I only have the fink libcurl, which it lists as 7.54.0-1. But it looks like
when he built the netcdf libs, either the Fink libcurl wasn't installed, or
paths were such that it found the Apple one first. Sometime with Fink you need
to remove things temporarily from /usr that might conflict.
-Roy
> On May 4, 2017, at 8:50 AM, Sean Arms <sarms@xxxxxxxx> wrote:
>
> Just to reitterate - even if we find the line that is causing the issue, you
> will not be able to use the homebrew netcdf-c lib/tools against any remote
> site that requries authorization/authentication.
>
> Roy - what does the fink curl give you for "curl --version"?
>
> On Thu, May 4, 2017 at 9:45 AM, Capehart, William J
> <William.Capehart@xxxxxxxxx> wrote:
> At Sean’s request I moved my .dodsrc I was able to get it to work.
>
>
>
> (I think the only question I now have is what is wrong with that particular
> .dodsrc file..)
>
>
>
> USE_CACHE=0
>
> MAX_CACHE_SIZE=20
>
> MAX_CACHED_OBJ=5
>
> IGNORE_EXPIRES=0
>
> CACHE_ROOT=/Users/wjc/.dods_cache/
>
> DEFAULT_EXPIRES=86400
>
> ALWAYS_VALIDATE=0
>
> DEFLATE=0
>
> VALIDATE_SSL=1
>
> CURL.COOKIEJAR=.dods_cookies
>
> CURL.SSL.VALIDATE=1
>
> CURL.SSL.CERTIFICATE=/Users/wjc/.esg/credentials.pem
>
> CURL.SSL.KEY=/Users/wjc/.esg/credentials.pem
>
> CURL.SSL.CAPATH=/Users/wjc/.esg/certificates
>
> HTTP.COOKIEJAR=/Users/wjc/.cookies
>
> HTTP.NETRC=/Users/wjc/.netrc
>
>
>
> Wjhich specific lines need to be edited or removed?
>
>
>
> I’ll then close a second item that we have on github and close things there.
>
>
>
> Thanks much all!
>
>
>
>
>
> ------------------------------------------------
> Bill Capehart <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: Larry Baker <baker@xxxxxxxx>
> Date: Thursday, May 4, 2017 at 00:10 MDT
> To: William Capehart <William.Capehart@xxxxxxxxx>
> Cc: "dmh@xxxxxxxx" <dmh@xxxxxxxx>, "netcdfgroup@xxxxxxxxxxxxxxxx"
> <netcdfgroup@xxxxxxxxxxxxxxxx>
>
>
> Subject: Re: [netcdfgroup] Using NetCDF with OPeNDAP on MacOS Sierra
> (homebrew- and netCDF-dependant software)
>
>
>
> 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
>
>
>
>
>
>
>
> On May 3, 2017, at 10:57 PM, Larry Baker <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
>
>
>
>
>
>
>
> On May 3, 2017, at 10:44 PM, Capehart, William J <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>
> 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> on behalf of Larry Baker
> <baker@xxxxxxxx>
> Date: Wednesday, May 3, 2017 at 16:45 MDT
> To: "dmh@xxxxxxxx" <dmh@xxxxxxxx>
> Cc: "netcdfgroup@xxxxxxxxxxxxxxxx" <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
>
>
>
>
>
>
>
> On 3 May 2017, at 3:35:19 PM, 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" <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>
> 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 (52.44.0.41) port 80 (#0)
>
>
>
> GET /opendap/data/nc/3fnoc.nc.das HTTP/1.1
> Host: 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>
> 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> 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> 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>
> wrote:
>
> Did that with both fink and homebrew including compiling all from source each
> time. Still no traction. :-(
>
> ------------------------------------------------
> Bill Capehart <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> wrote:
>
> try installing the fink curl.
>
> -roy
>
>
>
>
> On May 3, 2017, at 6:47 AM, Capehart, William J <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>
> Date: Tuesday, May 2, 2017 at 17:50 MDT
> To: William Capehart <William.Capehart@xxxxxxxxx>
> Cc: "netcdfgroup@xxxxxxxxxxxxxxxx" <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> 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>
> 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
> do not want to be made public.
>
>
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit:
> http://www.unidata.ucar.edu/mailing_lists/
>
>
>
>
> **********************
> "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 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 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 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 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.
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit:
> http://www.unidata.ucar.edu/mailing_lists/
>
>
> _______________________________________________
> 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.
>
>
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit:
> http://www.unidata.ucar.edu/mailing_lists/
>
>
> _______________________________________________
> 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.
>
>
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit:
> http://www.unidata.ucar.edu/mailing_lists/
>
>
>
>
>
>
>
>
> _______________________________________________
> 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.
>
>
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit:
> http://www.unidata.ucar.edu/mailing_lists/
>
> _______________________________________________
> 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.
>
>
> netcdfgroup mailing list
> netcdfgroup@xxxxxxxxxxxxxxxx
> For list information or to unsubscribe, visit:
> http://www.unidata.ucar.edu/mailing_lists/
**********************
"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 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.
