Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#50911 closed defect (fixed)

netcdf +gcc5 Segmentation fault: 11 on El Capitan

Reported by: gnw3 Owned by: tenomoto (Takeshi Enomoto)
Priority: Normal Milestone:
Component: ports Version: 2.3.4
Keywords: Cc: petrrr
Port: netcdf

Description

The default build works, but ncarg requires a +gcc5 build which does not work:

$ port installed netcdf
The following ports are currently installed:
  netcdf @4.3.3.1_4+dap+gcc5+netcdf4
  netcdf @4.3.3.1_4+dap+netcdf4 (active)
$ /opt/local/bin/ncdump -h /opt/local/lib/ncarg/data/cdf/ocean.nc
netcdf ocean {
dimensions:
	z_t = 25 ;
	lat_t = 66 ;
variables:
	float T(z_t, lat_t) ;
		T:lon_t = 199.8f ;
		T:time = 69715. ;
		T:long_name = "Potential Temperature" ;
		T:units = "Celsius" ;
		T:time_rep = "averaged" ;
		T:missing_value = 9.999999e+29f ;
		T:_FillValue = 9.999999e+29f ;
	float z_t(z_t) ;
		z_t:long_name = "Depth (T grid)" ;
		z_t:units = "centimeters" ;
		z_t:minimum = 600.f ;
		z_t:maximum = 477529.f ;
		z_t:positive = "down" ;
	float lat_t(lat_t) ;
		lat_t:long_name = "Latitude (T grid)" ;
		lat_t:units = "degrees_north" ;
		lat_t:minimum = -78.92963f ;
		lat_t:maximum = 90.f ;
}

After activating the +gcc5 version, ncdump fails:

$ /opt/local/bin/ncdump -h /opt/local/lib/ncarg/data/cdf/ocean.nc
netcdf ocean {
dimensions:
	z_t = 25 ;
	lat_t = 66 ;
variables:
Segmentation fault: 11

Other programs (e.g., ncl) also give the Segmentation fault: 11. Upstream has a report of problems on 10.11 at https://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg13497.html

Change History (5)

comment:1 Changed 4 years ago by ryandesign (Ryan Schmidt)

Cc: takeshi removed
Keywords: gcc5 segfault removed
Owner: changed from macports-tickets@… to takeshi@…

The Cc field requires complete email addresses.

comment:2 Changed 4 years ago by petrrr

Cc: petr@… added

Cc Me!

comment:3 Changed 4 years ago by tenomoto (Takeshi Enomoto)

ncdump indeed fails with gcc5 (but not with gcc49). I'll see what I can.

comment:4 in reply to:  3 Changed 4 years ago by gnw3

Replying to takeshi@…:

ncdump indeed fails with gcc5 (but not with gcc49). I'll see what I can.

I just built netcdf-4.4.0 (stable release of Jan 2016) with gcc5 on El Capitan and ncdump is working, so one option could be to move up 4.4.0. The ports used here that broke were:

     gdal @2.0.2 +expat+hdf4+hdf5+netcdf
     vis5d @1.3.0-beta 
     wgrib2 @2.0.0 
     netcdf-fortran @4.4.2 +gcc5
     esmf @6_3_0rp1 +accelerate+gcc5
     nco @4.5.5 +accelerate
     ncarg @6.3.0 +gcc5
Last edited 4 years ago by ryandesign (Ryan Schmidt) (previous) (diff)

comment:5 Changed 4 years ago by tenomoto (Takeshi Enomoto)

Resolution: fixed
Status: newclosed

Committed in r147086 and r147087. Rev bumps in r147088. Thank you for reporting and testing.

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