#127 ncks giving a seg fault

[Cathy Smith]

We are getting a seg fault for some netCDF files with ncks

ncks -O -d time,7,7 /Datasets/godas/pottmp.2021.nc file.nc
Segmentation fault

ncks -O -d time,0,7 https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc file.nc
NO ERROR

And if we use TDS, we get
ncks -O -d time,0,7 https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc file.nc
NO ERROR

We also tried this

ncks -O -d time,7,7 /Datasets/godas/Derived/pottmp.mon.ltm.nc file.nc

NO ERROR

for the pottmp 2021 file we have

time = 80719, 80750, 80778, 80809, 80839, 80870, 80900, 80931, 80962, 80992,
81023, 81053 ;

 time:units = "days since 1800-01-01 00:00:0.0" ;

and -tv

time = "2021-01-01", "2021-02-01", "2021-03-01", "2021-04-01", "2021-05-01",
"2021-06-01", "2021-07-01", "2021-08-01", "2021-09-01", "2021-10-01",
"2021-11-01", "2021-12-01" ;

And we have on linux

ncks -r
NCO netCDF Operators version 4.8.1

We also tried an updated version and got the same seg fault
NCO netCDF Operators version 5.0.5

We are using linux. As the dates look correct, we can subset different dates, and TDS works on the same file that local linux does not, we are stumped.

Cathy Smith

[Charlie Zender]

Thank you for reporting this. This is the type of issue that can probably only be solved by pointing me to the dataset. Unless it's too big, in which case please cut it down as much as possible while still retaining the buggy behavior.

[Cathy Smith]

It is large. You can download it from here

ftp ftp.cdc.noaa.gov

cd /Datasets/godas

get pottmp.2021.nc

If it's too large I can see if I can remove levels. Let me know.

Cathy

On 2/1/22 7:57 AM, Charlie Zender wrote:

Thank you for reporting this. This is the type of issue that can
probably only be solved by pointing me to the dataset. Unless it's too
big, in which case please cut it down as much as possible while still
retaining the buggy behavior.

---

[bugs:#127] https://sourceforge.net/p/nco/bugs/127/ ncks giving a
seg fault

Status: open
Group:
Created: Tue Feb 01, 2022 02:40 PM UTC by Cathy Smith
Last Updated: Tue Feb 01, 2022 02:41 PM UTC
Owner: nobody

We are getting a seg fault for some netCDF files with ncks

ncks -O -d time,7,7 /Datasets/godas/pottmp.2021.nc file.nc
Segmentation fault

ncks -O -d time,0,7
https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc file.nc
NO ERROR

And if we use TDS, we get
ncks -O -d time,0,7
https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc file.nc
NO ERROR

We also tried this

ncks -O -d time,7,7 /Datasets/godas/Derived/pottmp.mon.ltm.nc file.nc

NO ERROR

for the pottmp 2021 file we have

time = 80719, 80750, 80778, 80809, 80839, 80870, 80900, 80931, 80962,
80992,
81023, 81053 ;

time:units = "days since 1800-01-01 00:00:0.0" ;

and -tv

time = "2021-01-01", "2021-02-01", "2021-03-01", "2021-04-01",
"2021-05-01",
"2021-06-01", "2021-07-01", "2021-08-01", "2021-09-01", "2021-10-01",
"2021-11-01", "2021-12-01" ;

And we have on linux

ncks -r
NCO netCDF Operators version 4.8.1

We also tried an updated version and got the same seg fault
NCO netCDF Operators version 5.0.5

We are using linux. As the dates look correct, we can subset different
dates, and TDS works on the same file that local linux does not, we
are stumped.

Cathy Smith

---

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[Cathy Smith]

Charlie

Also, We have been experimenting here. We did try the upgraded NCO
version which didn't work but when we combined with upgraded netCDF, it did.

version 4.8.1

Unfortunately, different versions of other applications work with
different versions of netcdf (4.7 is what we are using) so it will be
complicated to fix everything here. But I think it's not a NCO issue and
you can close the ticket.

Cathy

On 2/1/22 8:08 AM, Cathy Smith wrote:

It is large. You can download it from here

ftp ftp.cdc.noaa.gov

cd /Datasets/godas

get pottmp.2021.nc

If it's too large I can see if I can remove levels. Let me know.

Cathy

On 2/1/22 7:57 AM, Charlie Zender wrote:

Thank you for reporting this. This is the type of issue that can
probably only be solved by pointing me to the dataset. Unless it's
too big, in which case please cut it down as much as possible while
still retaining the buggy behavior.

---

[bugs:#127] https://sourceforge.net/p/nco/bugs/127/ ncks giving a
seg fault

Status: open
Group:
Created: Tue Feb 01, 2022 02:40 PM UTC by Cathy Smith
Last Updated: Tue Feb 01, 2022 02:41 PM UTC
Owner: nobody

We are getting a seg fault for some netCDF files with ncks

ncks -O -d time,7,7 /Datasets/godas/pottmp.2021.nc file.nc
Segmentation fault

ncks -O -d time,0,7
https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc file.nc
NO ERROR

And if we use TDS, we get
ncks -O -d time,0,7
https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc file.nc
NO ERROR

We also tried this

ncks -O -d time,7,7 /Datasets/godas/Derived/pottmp.mon.ltm.nc file.nc

NO ERROR

for the pottmp 2021 file we have

time = 80719, 80750, 80778, 80809, 80839, 80870, 80900, 80931, 80962,
80992,
81023, 81053 ;

time:units = "days since 1800-01-01 00:00:0.0" ;

and -tv

time = "2021-01-01", "2021-02-01", "2021-03-01", "2021-04-01",
"2021-05-01",
"2021-06-01", "2021-07-01", "2021-08-01", "2021-09-01", "2021-10-01",
"2021-11-01", "2021-12-01" ;

And we have on linux

ncks -r
NCO netCDF Operators version 4.8.1

We also tried an updated version and got the same seg fault
NCO netCDF Operators version 5.0.5

We are using linux. As the dates look correct, we can subset
different dates, and TDS works on the same file that local linux does
not, we are stumped.

Cathy Smith

---

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https://sourceforge.net/p/nco/bugs/127/

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---

NOAA PSL and CU CIRES
https://psl.noaa.gov/people/cathy.smith/

Emails about data/webpages may get quicker responses by emailing
psl.data@noaa.gov

--

NOAA PSL and CU CIRES
https://psl.noaa.gov/people/cathy.smith/

Emails about data/webpages may get quicker responses by emailing
psl.data@noaa.gov

[Charlie Zender]

Cathy,

Thank you for figuring out the problem,
and taking ownership of it.

Charlie

On 2/1/22 10:04, Cathy Smith wrote:

Charlie

Also, We have been experimenting here. We did try the upgraded NCO
version which didn't work but when we combined with upgraded netCDF, it did.

version 4.8.1

Unfortunately, different versions of other applications work with
different versions of netcdf (4.7 is what we are using) so it will be
complicated to fix everything here. But I think it's not a NCO issue and
you can close the ticket.

Cathy

On 2/1/22 8:08 AM, Cathy Smith wrote:

It is large. You can download it from here

ftp ftp.cdc.noaa.gov

cd /Datasets/godas

get pottmp.2021.nc

If it's too large I can see if I can remove levels. Let me know.

Cathy

On 2/1/22 7:57 AM, Charlie Zender wrote:

    Thank you for reporting this. This is the type of issue that can
    probably only be solved by pointing me to the dataset. Unless it's
    too big, in which case please cut it down as much as possible while
    still retaining the buggy behavior.

    ------------------------------------------------------------------------

    /[bugs:#127] <https://sourceforge.net/p/nco/bugs/127/>
    https://sourceforge.net/p/nco/bugs/127/
    <https://sourceforge.net/p/nco/bugs/127/> ncks giving a
    seg fault/

    /Status:/ open
    /Group:/
    /Created:/ Tue Feb 01, 2022 02:40 PM UTC by Cathy Smith
    /Last Updated:/ Tue Feb 01, 2022 02:41 PM UTC
    /Owner:/ nobody

    We are getting a seg fault for some netCDF files with ncks

    ncks -O -d time,7,7 /Datasets/godas/pottmp.2021.nc file.nc
    Segmentation fault

    ncks -O -d time,0,7
    https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc
    <https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc>
    file.nc
    NO ERROR

    And if we use TDS, we get
    ncks -O -d time,0,7
    https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc
    <https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc>
    file.nc
    NO ERROR

    We also tried this

    ncks -O -d time,7,7 /Datasets/godas/Derived/pottmp.mon.ltm.nc
    file.nc

    NO ERROR

    for the pottmp 2021 file we have

    time = 80719, 80750, 80778, 80809, 80839, 80870, 80900, 80931,
    80962,
    80992,
    81023, 81053 ;

    time:units = "days since 1800-01-01 00:00:0.0" ;

    and -tv

    time = "2021-01-01", "2021-02-01", "2021-03-01", "2021-04-01",
    "2021-05-01",
    "2021-06-01", "2021-07-01", "2021-08-01", "2021-09-01",
    "2021-10-01",
    "2021-11-01", "2021-12-01" ;

    And we have on linux

    ncks -r
    NCO netCDF Operators version 4.8.1

    We also tried an updated version and got the same seg fault
    NCO netCDF Operators version 5.0.5

    We are using linux. As the dates look correct, we can subset
    different dates, and TDS works on the same file that local linux
    does
    not, we are stumped.

    Cathy Smith

    ------------------------------------------------------------------------

    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/nco/bugs/127/
    <https://sourceforge.net/p/nco/bugs/127/>

    To unsubscribe from further messages, please visit
    https://sourceforge.net/auth/subscriptions/
    <https://sourceforge.net/auth/subscriptions/>

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------------------------------------------------------------------------

NOAA PSL and CU CIRES
https://psl.noaa.gov/people/cathy.smith/
<https://psl.noaa.gov/people/cathy.smith/>

Emails about data/webpages may get quicker responses by emailing
psl.data@noaa.gov


--

NOAA PSL and CU CIRES
https://psl.noaa.gov/people/cathy.smith/
https://psl.noaa.gov/people/cathy.smith/

Emails about data/webpages may get quicker responses by emailing
psl.data@noaa.gov

---

[bugs:#127] https://sourceforge.net/p/nco/bugs/127/ ncks giving a seg
fault

Status: open
Group:
Created: Tue Feb 01, 2022 02:40 PM UTC by Cathy Smith
Last Updated: Tue Feb 01, 2022 02:57 PM UTC
Owner: nobody

We are getting a seg fault for some netCDF files with ncks

ncks -O -d time,7,7 /Datasets/godas/pottmp.2021.nc file.nc
Segmentation fault

ncks -O -d time,0,7
https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc
https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc file.nc
NO ERROR

And if we use TDS, we get
ncks -O -d time,0,7
https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc
https://psl.noaa.gov/thredds/dodsC/Datasets/godas/pottmp.2021.nc file.nc
NO ERROR

We also tried this

ncks -O -d time,7,7 /Datasets/godas/Derived/pottmp.mon.ltm.nc file.nc

NO ERROR

for the pottmp 2021 file we have

time = 80719, 80750, 80778, 80809, 80839, 80870, 80900, 80931, 80962, 80992,
81023, 81053 ;

time:units = "days since 1800-01-01 00:00:0.0" ;

and -tv

time = "2021-01-01", "2021-02-01", "2021-03-01", "2021-04-01", "2021-05-01",
"2021-06-01", "2021-07-01", "2021-08-01", "2021-09-01", "2021-10-01",
"2021-11-01", "2021-12-01" ;

And we have on linux

ncks -r
NCO netCDF Operators version 4.8.1

We also tried an updated version and got the same seg fault
NCO netCDF Operators version 5.0.5

We are using linux. As the dates look correct, we can subset different
dates, and TDS works on the same file that local linux does not, we are
stumped.

Cathy Smith

---

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/nco/bugs/127/
https://sourceforge.net/p/nco/bugs/127/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
https://sourceforge.net/auth/subscriptions/

--
Charlie Zender, Earth System Sci. & Computer Sci.
University of California, Irvine 949-891-2429 )'(