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[ferret_users] Segmentation fault with long global attrubute
- To: ferret_users@xxxxxxxx
- Subject: [ferret_users] Segmentation fault with long global attrubute
- From: "McCann, Mike" <mccann@xxxxxxxxx>
- Date: Thu, 23 Sep 2010 12:46:03 -0700
- Sender: owner-ferret_users@xxxxxxxx
- Thread-index: ActbV/RZUrB4aOYjFE6vftKZ73WPeQ==
- Thread-topic: Segmentation fault with long global attrubute
- User-agent: Microsoft-Entourage/12.26.0.100708
Title: Segmentation fault with long global attrubute
Hello,
While experimenting with adding some very long global attributes to my in situ netCDF files I encountered what I think might be a bug in Ferret:
> ferret
NOAA/PMEL TMAP
FERRET v6.62
Linux rh5 (gfortran) 2.6.18-164.11.1.el5 - 06/11/10
23-Sep-10 12:28
yes? use "http://dods.mbari.org/opendap/data/ssdsdata/deployments/m0/200406/m0_ctd0001_20040727_original.nc"
yes? show data/attributes
currently SET data sets:
1> http://dods.mbari.org/opendap/data/ssdsdata/deployments/m0/200406/m0_ctd0001_20040727_original.nc (default)
Variable VarType(in dset) AttributeName AttType Size OutFlag AttValue
------------------------------------------------------------------------------------------
. Unlimited_DimensCHAR 4 F time
naming_authorityCHAR 33 F org.mbari.ssds.DataContainer.Name
SIAM_metadata CHAR 175 F http://new-ssds.mbari.org:8080/servlet/GetOriginalDataServlet?deviceID=1338&startTimestampSeconds=1090952259&endTimestampSeconds=1097085600&recordTypeID=0&noHTMLHeader=1&isi=1
standard_name_voCHAR ry 6 F CF-1.0
keywords CHAR 16 F ocean; Moorings;
cdm_data_type CHAR 7 F Station
geospatial_vertiCHAR sitive4 F down
summary CHAR 144 F Observational oceanographic data obtained from a moored platform. Sensors placed on the mooring record environmental parameters as time passes.
keywords_vocabulCHAR 4 F GCMD
title CHAR 80 F Mooring M0 CTD data from MBARI instrument id 1338 at original sampling intervals
Conventions CHAR 6 F CF-1.0
creator_name CHAR 26 F DStoNetCDF.pl version 1.52
time_coverage_stCHAR 20 F 2004-07-27T18:17:45Z
time_coverage_enCHAR 20 F 2004-10-06T17:56:12Z
date_created CHAR 24 F Thu Sep 23 09:27:19 2010
id CHAR 31 F m0_ctd0001_20040727_original.nc
At line 239 of file tm_fmt.f
Fortran runtime error: Nonnegative width required in format
(1PG**.+8)
^
Segmentation fault
The full attributes are shown by our Hyrax server: http://dods.mbari.org/opendap/data/ssdsdata/deployments/m0/200406/m0_ctd0001_20040727_original.nc.info
It’s the ssds_provenance attribute at 3307 characters that apparently causes the problem.
Another dataset ( http://dods.mbari.org/opendap/data/ssdsdata/deployments/m0/200406/m0_ctd0001_20040604_original.nc.info) with 2187 characters properly reports an error message:
> ferret
NOAA/PMEL TMAP
FERRET v6.62
Linux rh5 (gfortran) 2.6.18-164.11.1.el5 - 06/11/10
23-Sep-10 12:34
yes? use "http://dods.mbari.org/opendap/data/ssdsdata/deployments/m0/200406/m0_ctd0001_20040604_original.nc"
yes? show data/attributes
currently SET data sets:
1> http://dods.mbari.org/opendap/data/ssdsdata/deployments/m0/200406/m0_ctd0001_20040604_original.nc (default)
Variable VarType(in dset) AttributeName AttType Size OutFlag AttValue
------------------------------------------------------------------------------------------
. Unlimited_DimensCHAR 4 F time
naming_authorityCHAR 33 F org.mbari.ssds.DataContainer.Name
SIAM_metadata CHAR 175 F http://new-ssds.mbari.org:8080/servlet/GetOriginalDataServlet?deviceID=1314&startTimestampSeconds=1086307200&endTimestampSeconds=1090951200&recordTypeID=0&noHTMLHeader=1&isi=1
standard_name_voCHAR ry 6 F CF-1.0
keywords CHAR 16 F ocean; Moorings;
cdm_data_type CHAR 7 F Station
geospatial_vertiCHAR sitive4 F down
summary CHAR 144 F Observational oceanographic data obtained from a moored platform. Sensors placed on the mooring record environmental parameters as time passes.
keywords_vocabulCHAR 4 F GCMD
title CHAR 80 F Mooring M0 CTD data from MBARI instrument id 1314 at original sampling intervals
Conventions CHAR 6 F CF-1.0
creator_name CHAR 26 F DStoNetCDF.pl version 1.52
time_coverage_stCHAR 20 F 2004-06-04T00:05:18Z
time_coverage_enCHAR 20 F 2004-07-27T15:18:10Z
date_created CHAR 24 F Thu Sep 23 09:22:08 2010
id CHAR 31 F m0_ctd0001_20040604_original.nc
*** NOTE: DC.name=m0_ctd0001_20040604_original.nc<br>DC.dataContainerType=File<br>DC.original=false<br>DC.uriString=http://dods.mbari.org/opendap/data/ssdsdata/deployments/m0/200406/m0_ctd0001_20040604_original.nc<br>DC.dodsAccessible=false<br>DC.dodsUrlString=http://dods.mbari.org/opendap/data/ssdsdata/deployments/m0/200406/m0_ctd0001_20040604_original.nc<br>DC.noNetCDF=true<br>+DP.name=DStoNetCDF.pl - ctd.pl run on 2010-09-23T16:22:01Z<br>+DP.description=DStoNetCDF.pl script executed with arguments: -mooring M0 -deployment M0 - June 2004 -ssdsServer new-ssds.mbari.org -ssdsDataServer new-ssds.mbari.org -outputDir /mbari/ssdsdata/deployments -procClosed -verbose<br>+DP.dataProducerType=ProcessRun<br>+DP.startDate=2010-09-23T16:22:01Z<br>+DP.endDate=2010-09-23T16:22:09Z<br>+DP.hostName=elvis<br>+Software.name=ctd.pl<br>+Software.description=Salinity is calculated from C, T, and P using conductivity ratio divisor of 4.29140.<br>+Software.uriString=http://moonjelly.shore.mbari.org/cgi-bin/cvsweb.cgi/DPforSSDS/cimt/ctd.pl?rev=1.52<br>+Software.softwareVersion=1.52<br>.+DC.name=1314_1_1_1299<br>.+DC.dataContainerType=File<br>.+DC.original=false<br>.+DC.uriString=http://new-ssds.mbari.org:8080/servlet/GetOriginalDataServlet?deviceID=1314&startParentID=1299&startPacketSubType=1&startDataDescriptionID=1&lastNumberOfPackets=10&isi=1<br>.+DC.dodsAccessible=false<br>.+DC.noNetCDF=true<br>..+DP.name=ID 1314 deployed on id 1299<br>..+DP.dataProducerType=Deployment<br>..+DP.startDate=2004-06-04T00:00:00Z<br>..+DP.endDate=2004-07-27T18:00:00Z<br>..+DP.role=instrument<br>..+DP.nominalDepth=1.0<br>...+Device.uuid=f671f7db-d50f-11d9-8c1e-00306e389969<br>...+Device.name=Serial CTD<br>...+Device.mfgName=Seabird<br>...+Device.mfgModel=SBE 37-SM V2.5<br>...+Device.mfgSerialNumber=3531<br>...+DP.dataProducerType=Deployment<br>...+DP.endDate=2007-01-26T19:56:21Z<br>...+DP.role=sensor<br>...+Device.uuid=76E60D98-77C4-45F5-AE00-3AF33F4FCA87<br>...+Device.name=Pressure Sensor<br>...+Device.mfgName=Seabird<br>...+Device.mfgModel=unknown<br>...+Devi:
*** NOTE: Maximum characters: 2048
ssds_provenance CHAR 2074 F Maximum characters: 2048
....
Is there some way I can tell ferret to not use this attribute? When I try and save variables from the former data set ferret just hangs.
BTW, there is a minor typo (missing a ‘T’) at http://ferret.pmel.noaa.gov/Ferret/documentation/users-guide/variables-xpressions/VARIABLES:
Chapter 3, Section 1.8.1
SHOW ATTRIBUTE commands
SHOW DATA/ATRIBUTE Expands the SHOW DATA output, listing dataset attributes and variable attributes
SHOW ATTRIBUTE varname.attname Lists the value(s) of an attribute. It gives the same information as LIST varname.attname
SHOW ATRIBUTE/ALL varname Lists all of the attributes for the variable
Thanks in advance,
Mike
--
Mike McCann
Software Engineer
Monterey Bay Aquarium Research Institute
7700 Sandholdt Road
Moss Landing, CA 95039-9644
Voice: 831.775.1769 Fax: 831.775.1736 http://www.mbari.org
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