[MacPorts] #64361: ncarg @6.6.2_7: setfileoption segmentation fault
MacPorts
noreply at macports.org
Tue Jan 4 19:54:11 UTC 2022
#64361: ncarg @6.6.2_7: setfileoption segmentation fault
----------------------+--------------------
Reporter: cmstuber | Owner: (none)
Type: defect | Status: new
Priority: Normal | Milestone:
Component: ports | Version: 2.7.1
Keywords: | Port: ncarg
----------------------+--------------------
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 at 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 at mac66 Build # echo $NCARG_ROOT
/opt/local
root at 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 at mac66 Build #
}}}
Using the test3 script posted in ticket #53031, it errors with the seg
fault as well
{{{
root at 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 at mac66 Desktop #
}}}
Rebuilding ncarg against gcc10 seems to have resolved the issue for me,
although it requires rebuilding hdf5 against gcc10 as well.
{{{
root at 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 at mac66 Desktop # port -f clean ncarg
---> Cleaning ncarg
root at 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 at 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 at mac66 Desktop # port -f clean hdf5
---> Cleaning hdf5
root at 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 at 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 at 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 at mac66 Desktop #
}}}
--
Ticket URL: <https://trac.macports.org/ticket/64361>
MacPorts <https://www.macports.org/>
Ports system for macOS
More information about the macports-tickets
mailing list