ncarg @6.6.2_7: setfileoption segmentation fault

[cmstuber (Chris Stuberg)]

setfileoption gives segmentation fault with default ncarg build. Building ncarg and hdf5 with variant +gcc10 resolves segmentation fault.

I'm getting similar segmentation fault errors as reported in ​https://trac.macports.org/ticket/53031.

Here's a list of selected deps that are installed:

hdf4 @4.2.15_1 (active)
hdf5 @1.12.1_0+cxx+hl (active)
hdfeos @2.20_0 (active)
hdfeos5 @1.16_6 (active)
netcdf @4.8.1_0+cdf5+dap+netcdf4 (active)
netcdf-cxx @4.2_17 (active)
netcdf-fortran @4.5.3_0+gcc11 (active)
gcc10 @10.3.0_0 (active)
gcc11 @11.2.0_2 (active)

ncarg is being built with defaults

root@mac66 Build # port install ncarg            
--->  Computing dependencies for ncarg
--->  Fetching archive for ncarg
--->  Attempting to fetch ncarg-6.6.2_7+accelerate+gfortran.darwin_19.x86_64.tbz2 from https://packages.macports.org/ncarg
--->  Attempting to fetch ncarg-6.6.2_7+accelerate+gfortran.darwin_19.x86_64.tbz2 from https://ywg.ca.packages.macports.org/mirror/macports/packages/ncarg
--->  Attempting to fetch ncarg-6.6.2_7+accelerate+gfortran.darwin_19.x86_64.tbz2 from https://mse.uk.packages.macports.org/ncarg
--->  Fetching distfiles for ncarg
--->  Verifying checksums for ncarg
--->  Extracting ncarg
--->  Applying patches to ncarg
--->  Configuring ncarg
--->  Building ncarg
--->  Staging ncarg into destroot                        
--->  Installing ncarg @6.6.2_7+accelerate+gfortran      
--->  Activating ncarg @6.6.2_7+accelerate+gfortran
--->  Cleaning ncarg
--->  Scanning binaries for linking errors
--->  No broken files found.                             
--->  No broken ports found.

Build is successful. However when using setfileoption in ncl I get a seg fault.

root@mac66 Build # echo $NCARG_ROOT
/opt/local
root@mac66 Build # ncl
 Copyright (C) 1995-2019 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.6.2
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
ncl 0> setfileoption("nc","Format","NetCDF4")
Segmentation fault: 11
root@mac66 Build #

Using the test3 script posted in ticket #53031, it errors with the seg fault as well

root@mac66 Desktop # ncl test3.ncl
 Copyright (C) 1995-2019 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.6.2
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
zsh: segmentation fault  ncl test3.ncl
root@mac66 Desktop # 

Rebuilding ncarg against gcc10 seems to have resolved the issue for me, although it requires rebuilding hdf5 against gcc10 as well.

root@mac66 Desktop # port uninstall ncarg
--->  Deactivating ncarg @6.6.2_7+accelerate+gfortran
--->  Cleaning ncarg
--->  Uninstalling ncarg @6.6.2_7+accelerate+gfortran
--->  Cleaning ncarg
root@mac66 Desktop # port -f clean ncarg
--->  Cleaning ncarg
root@mac66 Desktop # port install ncarg +accelerate+gcc10
--->  Computing dependencies for ncarg
--->  Fetching archive for ncarg
--->  Attempting to fetch ncarg-6.6.2_7+accelerate+gcc10.darwin_19.x86_64.tbz2 from https://packages.macports.org/ncarg
--->  Attempting to fetch ncarg-6.6.2_7+accelerate+gcc10.darwin_19.x86_64.tbz2 from https://ywg.ca.packages.macports.org/mirror/macports/packages/ncarg
--->  Attempting to fetch ncarg-6.6.2_7+accelerate+gcc10.darwin_19.x86_64.tbz2 from https://mse.uk.packages.macports.org/ncarg
--->  Configuring ncarg
Error: Install hdf5 +gcc10
Error: Failed to configure ncarg: hdf5 +gcc10 not installed
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_ncarg/ncarg/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug.
Error: Processing of port ncarg failed
root@mac66 Desktop # port uninstall hdf5
Note: It is not recommended to uninstall/deactivate a port that has dependents as it breaks the dependents.
The following ports will break:
 netcdf @4.8.1_0
 hdfeos5 @1.16_6
 wgrib2 @3.0.2_0
 nco @5.0.3_2
 grads @2.2.1_11
 cdo @2.0.0_0
Continue? [y/N]: y
Warning: Uninstall forced.  Proceeding despite dependencies.
--->  Deactivating hdf5 @1.12.1_0+cxx+hl
--->  Cleaning hdf5
--->  Uninstalling hdf5 @1.12.1_0+cxx+hl
--->  Cleaning hdf5
root@mac66 Desktop # port -f clean hdf5
--->  Cleaning hdf5
root@mac66 Desktop # port install hdf5 +cxx+hl+gcc10
--->  Computing dependencies for hdf5
--->  Fetching archive for hdf5
--->  Attempting to fetch hdf5-1.12.1_0+cxx+gcc10+hl.darwin_19.x86_64.tbz2 from https://packages.macports.org/hdf5
--->  Attempting to fetch hdf5-1.12.1_0+cxx+gcc10+hl.darwin_19.x86_64.tbz2 from https://ywg.ca.packages.macports.org/mirror/macports/packages/hdf5
--->  Attempting to fetch hdf5-1.12.1_0+cxx+gcc10+hl.darwin_19.x86_64.tbz2 from https://mse.uk.packages.macports.org/hdf5
--->  Fetching distfiles for hdf5
--->  Verifying checksums for hdf5
--->  Extracting hdf5
--->  Applying patches to hdf5
--->  Configuring hdf5
--->  Building hdf5                                      
--->  Staging hdf5 into destroot                         
--->  Installing hdf5 @1.12.1_0+cxx+gcc10+hl             
--->  Activating hdf5 @1.12.1_0+cxx+gcc10+hl
--->  Cleaning hdf5
--->  Scanning binaries for linking errors
--->  No broken files found.                             
--->  No broken ports found.
root@mac66 Desktop # port install ncarg +accelerate+gcc10
--->  Computing dependencies for ncarg
--->  Fetching archive for ncarg
--->  Attempting to fetch ncarg-6.6.2_7+accelerate+gcc10.darwin_19.x86_64.tbz2 from https://packages.macports.org/ncarg
--->  Attempting to fetch ncarg-6.6.2_7+accelerate+gcc10.darwin_19.x86_64.tbz2 from https://ywg.ca.packages.macports.org/mirror/macports/packages/ncarg
--->  Attempting to fetch ncarg-6.6.2_7+accelerate+gcc10.darwin_19.x86_64.tbz2 from https://mse.uk.packages.macports.org/ncarg
--->  Configuring ncarg
--->  Building ncarg
--->  Staging ncarg into destroot                        
--->  Installing ncarg @6.6.2_7+accelerate+gcc10         
--->  Activating ncarg @6.6.2_7+accelerate+gcc10
--->  Cleaning ncarg
--->  Scanning binaries for linking errors
--->  No broken files found.                             
--->  No broken ports found.

Running the test3.ncl script finishes successfully now.

root@mac66 Desktop # ncl test3.ncl 
 Copyright (C) 1995-2019 - All Rights Reserved
 University Corporation for Atmospheric Research
 NCAR Command Language Version 6.6.2
 The use of this software is governed by a License Agreement.
 See http://www.ncl.ucar.edu/ for more details.
(0)	99
root@mac66 Desktop # 

[tenomoto (Takeshi Enomoto)]

The following combination seems to circumvent segmentation faults.

hdf5 @1.12.2_1+gcc12+hl (active)
ncarg @6.6.2_15+accelerate+gcc12 (active)

hdf5 1.12.x is a major update breaking API. However, -DH5_USE_110_API ​API Compatibility Macros did not help.

[Dave-Allured (Dave Allured)]

This might have little or nothing to do with HDF5. The basic setfileoption function seems to be broken. This is with my own ncarg built from source, including -DH5_USE_110_API (hence the fake rev 16 on the portfile).

  hdf5 @1.12.2_1+cxx+hl (active)
  ncarg @6.6.2_16+accelerate+gfortran (active)

> ncl -Q
ncl 0> setfileoption ("bin", "ReadByteOrder", "LittleEndian")
Segmentation fault

I got the same result with the original rev 15 portfile, also with -DH5_USE_18_API.

Changing the first arg to "bin" should result in no calls at all to HDF5, unless someone is doing something too clever under the hood.