I've seen similar seg fault problems back in Feb on yellowstone
with compressed netcdf-4 files. For example, addfile with "w"
and getvaratts() didn't work properly. I came up with workarounds
to do what I needed to do.
After reading Dave's email, I re-did some tests.
Now with 6.1.2, addfile with "w" and getvaratts() seem working,
but I encountered a new problem with getfilevarnames().
There is an extra / in the beginning of the variable name.
A = addfile("netcdf4file.nc", "r")
varnames = getfilevarnames(A)
print(varnames)
Variable: varnames
Type: string
Total Size: 1112 bytes
139 values
Number of Dimensions: 1
Dimensions and sizes: [139]
Coordinates:
(0) /Times
(1) /LU_INDEX
(2) /ZNU
(3) /ZNW
Hui-Chuan
On 4/2/13 1:28 PM, Wei Huang wrote:
> For tracking purpose, I have created a JIRA ticket 1692.
>
> Wei
>
> huangwei@ucar.edu
> VETS/CISL
> National Center for Atmospheric Research
> P.O. Box 3000 (1850 Table Mesa Dr.)
> Boulder, CO 80307-3000 USA
> (303) 497-8924
>
>
>
>
>
>
> On Apr 2, 2013, at 12:04 PM, Dave Allured - NOAA Affiliate <dave.allured@noaa.gov> wrote:
>
>> Wei,
>>
>> Thanks for checking this out. There is definitely a problem
>> somewhere. Now I am finding the same seg fault on Linux systems as
>> well as different Mac OS machines, with both NCL 6.0.0 and 6.1.2. In
>> fact I can not find a local system that does NOT get this seg fault.
>>
>> Might this be related to supplemental libraries? Following are simple
>> dependency lists for both Linux and Mac. Let me know if there are any
>> other diagnostics that I can provide. This is not a high priority for
>> me, I have a workaround.
>>
>> Dave
>>
>> inta:~/temp/3-atts/402a 1045> date
>> Tue Apr 2 11:49:25 MDT 2013
>>
>> inta:~/temp/3-atts/402a 1046> uname -a
>> Linux inta.psd.esrl.noaa.gov 2.6.18-348.3.1.el5 #1 SMP Tue Mar 5
>> 13:19:32 EST 2013 x86_64 GNU/Linux
>>
>> inta:~/temp/3-atts/402a 1047> echo $NCARG_ROOT
>> /usr/local/ncl6.1.2
>>
>> inta:~/temp/3-atts/402a 1048> ls -go $NCARG_ROOT/bin/ncl
>> -rwxr-xr-x 1 32917555 Feb 6 21:30 /usr/local/ncl6.1.2/bin/ncl
>>
>> inta:~/temp/3-atts/402a 1049> ls -go
>> -rw-r--r-- 1 501 Apr 2 10:55 demo.wei-huang.0401a.ncl
>> -r--r--r-- 1 11294147 Apr 1 17:14 ozone.master.nc
>>
>> inta:~/temp/3-atts/402a 1050> cat demo.wei-huang.0401a.ncl
>> begin
>> outfile = "out.nc"
>> ; system ("cp ozone.master.nc " + outfile) ; create fresh writable copy
>> system ("cat ozone.master.nc > " + outfile) ; create fresh writable copy
>> system ("chmod +w " + outfile) ; create fresh writable copy
>>
>> out = addfile (outfile, "w")
>>
>> out@last_update = systemfunc ("date")
>> out@last_update_program = "demo.global-atts.ncl version 2013-apr-01"
>> out@last_update_source_file = "ei.ozone.1979010106.nc"
>> print ("Update complete.")
>> end
>>
>> inta:~/temp/3-atts/402a 1051> $NCARG_ROOT/bin/ncl demo.wei-huang.0401a.ncl
>> Copyright (C) 1995-2013 - All Rights Reserved
>> University Corporation for Atmospheric Research
>> NCAR Command Language Version 6.1.2
>> The use of this software is governed by a License Agreement.
>> See http://www.ncl.ucar.edu/ for more details.
>> (0) Update complete.
>> Segmentation fault
>>
>> inta:~/temp/3-atts/402a 1052> ldd $NCARG_ROOT/bin/ncl
>> linux-vdso.so.1 => (0x00007fff7dbfd000)
>> libcurl.so.3 => /usr/lib64/libcurl.so.3 (0x0000003288400000)
>> libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003278600000)
>> libbz2.so.1 => /usr/lib64/libbz2.so.1 (0x000000328c000000)
>> libXrender.so.1 => /usr/lib64/libXrender.so.1 (0x000000327aa00000)
>> libX11.so.6 => /usr/lib64/libX11.so.6 (0x0000003278e00000)
>> libXext.so.6 => /usr/lib64/libXext.so.6 (0x0000003279a00000)
>> libm.so.6 => /lib64/libm.so.6 (0x0000003277a00000)
>> libdl.so.2 => /lib64/libdl.so.2 (0x0000003277e00000)
>> libstdc++.so.6 => /usr/local/gcc-4.7/lib/libstdc++.so.6 (0x00002b9f6bc6c000)
>> libgcc_s.so.1 => /usr/local/gcc-4.7/lib/libgcc_s.so.1 (0x00002b9f6bf76000)
>> libc.so.6 => /lib64/libc.so.6 (0x0000003277600000)
>> /lib64/ld-linux-x86-64.so.2 (0x0000003277200000)
>> libgssapi_krb5.so.2 => /usr/lib64/libgssapi_krb5.so.2 (0x0000003282c00000)
>> libkrb5.so.3 => /usr/lib64/libkrb5.so.3 (0x0000003282400000)
>> libk5crypto.so.3 => /usr/lib64/libk5crypto.so.3 (0x0000003282000000)
>> libcom_err.so.2 => /lib64/libcom_err.so.2 (0x0000003281c00000)
>> libidn.so.11 => /usr/lib64/libidn.so.11 (0x0000003284000000)
>> libssl.so.6 => /lib64/libssl.so.6 (0x0000003288c00000)
>> libcrypto.so.6 => /lib64/libcrypto.so.6 (0x0000003288800000)
>> libz.so.1 => /lib64/libz.so.1 (0x0000003278200000)
>> libXau.so.6 => /usr/lib64/libXau.so.6 (0x0000003279600000)
>> libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x0000003278a00000)
>> libkrb5support.so.0 => /usr/lib64/libkrb5support.so.0 (0x0000003282800000)
>> libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x0000003281400000)
>> libresolv.so.2 => /lib64/libresolv.so.2 (0x0000003280c00000)
>> libselinux.so.1 => /lib64/libselinux.so.1 (0x000000327d200000)
>> libsepol.so.1 => /lib64/libsepol.so.1 (0x000000327ce00000)
>>
>> ========================================================
>>
>> mac56:~/ncl/bugs/3-atts/402a 35> uname -a
>> Darwin mac56 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10
>> PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64
>>
>> mac56:~/ncl/bugs/3-atts/402a 36> echo $NCARG_ROOT
>> /usr/local/ncl6.1.2
>>
>> mac56:~/ncl/bugs/3-atts/402a 37> ls -dgo $NCARG_ROOT/bin/ncl
>> -rwxr-xr-x 1 33112624 Feb 6 21:38 /usr/local/ncl6.1.2/bin/ncl
>>
>> mac56:~/ncl/bugs/3-atts/402a 38> ldd $NCARG_ROOT/bin/ncl
>> /usr/local/ncl6.1.2/bin/ncl:
>> /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 7.0.0)
>> /usr/lib/libiconv.2.dylib (compatibility version 7.0.0, current version 7.0.0)
>> /usr/X11/lib/libXrender.1.dylib (compatibility version 5.0.0, current
>> version 5.0.0)
>> /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)
>> /usr/X11/lib/libXpm.4.dylib (compatibility version 16.0.0, current
>> version 16.0.0)
>> /usr/X11/lib/libX11.6.dylib (compatibility version 10.0.0, current
>> version 10.0.0)
>> /usr/X11/lib/libXext.6.dylib (compatibility version 11.0.0, current
>> version 11.0.0)
>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
>> version 159.1.0)
>> /usr/local/lib/libstdc++.6.dylib (compatibility version 7.0.0,
>> current version 7.14.0)
>> /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
>> version 1.0.0)
>>
>> On Mon, Apr 1, 2013 at 9:35 PM, Wei Huang <huangwei@ucar.edu> wrote:
>>> Dave,
>>>
>>> I can not reproduce your problem.
>>>
>>> I only added:
>>> system ("chmod +w " + outfile)
>>> after system call in your script (as the original file is write protected).
>>>
>>> and it runs fine.
>>>
>>> I tested on Mac, with osx 10.8.3.
>>>
>>> Here is the full script I tested:
>>>
>>> ; 2013-apr-01 Test program reduced from era-update.ncl.
>>> ; Demonstrates seg fault when trying to overwrite global
>>> ; attributes in a Netcdf-4 classic file.
>>> ; By Dave Allured, NOAA/PSD/CIRES Climate Analysis Branch.
>>>
>>> begin
>>> outfile = "out.nc"
>>> ; system ("cp ozone.master.nc " + outfile) ; create fresh writable copy
>>> system ("cat ozone.master.nc > " + outfile) ; create fresh writable copy
>>> system ("chmod +w " + outfile) ; create fresh writable copy
>>>
>>> out = addfile (outfile, "w")
>>>
>>> out@last_update = systemfunc ("date")
>>> out@last_update_program = "demo.global-atts.ncl version 2013-apr-01"
>>> out@last_update_source_file = "ei.ozone.1979010106.nc"
>>> print ("Update complete.")
>>> end
>>>
>>>
>>> and part of ncdump -h out.nc:
>>>
>>> // global attributes:
>>> :title = "ERA-Interim Ozone mass mixing ratio, 4 times daily" ;
>>> :history = "Mon Apr 1 17:14:49 MDT 2013:\n",
>>> "Initial file made by era-create.ncl version 2013-apr-01 TEST" ;
>>> :dataset = "ERA-Interim" ;
>>> :version = "2.0" ;
>>> :references = "http://www.ecmwf.int/research/era/do/get/era-interim;\n",
>>> "D. P. Dee et al (2011), The ERA-Interim reanalysis:\n",
>>> " configuration and performance of the data assimilation system,\n",
>>> " Q.J.R. Meteorol. Soc., Vol. 137: 553-597, DOI: 10.1002/qj.828" ;
>>> :center = "European Center for Medium-Range Weather Forecasts (RSMC)" ;
>>> :metadata_source_file = "../ei.oper.an.pl.regn128sc.1979010100" ;
>>> :Conventions = "CF-1.6" ;
>>> :last_update = "Mon Apr 1 21:28:20 MDT 2013" ;
>>> :last_update_program = "demo.global-atts.ncl version 2013-apr-01" ;
>>> :last_update_source_file = "ei.ozone.1979010106.nc" ;
>>> }
>>>
>>>
>>> Wei
>>>
>>> huangwei@ucar.edu
>>> VETS/CISL
>>> National Center for Atmospheric Research
>>> P.O. Box 3000 (1850 Table Mesa Dr.)
>>> Boulder, CO 80307-3000 USA
>>> (303) 497-8924
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Apr 1, 2013, at 8:41 PM, Dave Allured - NOAA Affiliate <dave.allured@noaa.gov> wrote:
>>>
>>>> NCL support team,
>>>>
>>>> This program results in a seg fault error on program exit, after
>>>> attempting to overwrite some global attributes in a Netcdf-4 classic
>>>> file with HDF5 compression. Note that all three global attributes
>>>> exist previously in the target file, before running the test program.
>>>>
>>>> After the error, the target file is corrupted. This error is
>>>> strangely sensitive to the number and string lengths of the attributes
>>>> to be written. Can you please tell me what the problem is? Thank
>>>> you.
>>>>
>>>> begin
>>>> outfile = "out.nc"
>>>> system ("cat ozone.master.nc > " + outfile) ; create fresh writable copy
>>>>
>>>> out = addfile (outfile, "w")
>>>> out@last_update = systemfunc ("date")
>>>> out@last_update_program = "demo.global-atts.ncl version 2013-apr-01"
>>>> out@last_update_source_file = "ei.ozone.1979010106.nc"
>>>> print ("Update complete.")
>>>> end
>>>>
>>>> I get the same results with NCL versions 6.0.0 and 6.1.2. My system
>>>> is Mac OS 10.8.3 on a 64-bit Intel Mac desktop. Here is the console
>>>> output:
>>>>
>>>> mac56:~/ncl/bugs/3-atts/401i 491> ncl demo.global-atts.ncl
>>>> Copyright (C) 1995-2013 - All Rights Reserved
>>>> University Corporation for Atmospheric Research
>>>> NCAR Command Language Version 6.1.2
>>>> The use of this software is governed by a License Agreement.
>>>> See http://www.ncl.ucar.edu/ for more details.
>>>> (0) Update complete.
>>>> Segmentation fault
>>>>
>>>> mac56:~/ncl/bugs/3-atts/401i 492> ls -trgo
>>>> total 44136
>>>> -r--r--r-- 1 11294147 Apr 1 17:14 ozone.master.nc
>>>> -rw-r--r-- 1 570 Apr 1 19:51 demo.global-atts.ncl
>>>> -rw-r--r-- 1 11294201 Apr 1 20:16 out.nc
>>>>
>>>> mac56:~/ncl/bugs/3-atts/401i 493> ncdump -k ozone.master.nc
>>>> netCDF-4 classic model
>>>>
>>>> mac56:~/ncl/bugs/3-atts/401i 494> ncdump -k out.nc
>>>> ncdump: out.nc: NetCDF: Can't open HDF5 attribute
>>>>
>>>> mac56:~/ncl/bugs/3-atts/401i 495> uname -a
>>>> Darwin mac56 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10
>>>> PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64
>>>>
>>>> I uploaded the program and original Netcdf file (11 Mbytes) to
>>>> ftp.cgd.ucar.edu/incoming, as
>>>> "demo.global-atts.dave_allured.0401.zip". The original Netcdf file
>>>> was also made by NCL 6.1.2 and a different script. I can also send a
>>>> copy of the generating script and its input file, if you need it.
>>>> Please let me know. Thanks for taking a look at this.
>>>>
>>>> --Dave A.
>>>> NOAA/PSD/CIRES Climate Analysis Branch
>
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Received on Tue Apr 2 14:58:30 2013
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