Re: [Virtuoso-devel] sparql query error crashes the store

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Hi Salari,

It would appear the "isql" program being picked up is one from another tool and not virtuoso, run the following command to determine where it resides:

	which isql

To ensure you are running the Virtuoso "isql" command specify its full path explicitly which be default would be:

	/usr/local/virtuoso-opensource/bin/isql 1111 dba dba

Or change to the location of your installation, and run the query to see if the same crash occurs.

With regards to core file creation you need to check if the system will allow core file creation with the command:

	ulimit -c

If this returns "0" then set to unlimited before starting the Virtuoso server with the command:

	ulimit -c unlimited

Then the core file will be created in the database directory if a crash occurs due to a bus error etc.

If the crash does not occur with "isql" would you be able to provide a standalone Java program we can compile and run to attempt a recreation locally ?

Best Regards
Hugh Williams
Professional Services
OpenLink Software
Web: http://www.openlinksw.com
Support: http://support.openlinksw.com
Forums: http://boards.openlinksw.com/support
Twitter: http://twitter.com/OpenLink

On 11 Feb 2011, at 15:45, sa...@eb... wrote:

> Hi Hugh,
> 
> There is no error written at the end of the virtuoso.log file.
> 
> I'm sorry I'm not sure what you are referring to by "is a core file
> created whose stack trace can be analysed to determine point of the crash
> ( shall  "ulimit -c" needs to be greater then 0 for core file creation) ?"
> Which file is this and how can I get virtuoso to create this?
> 
> isql 1111 dba dba gives me
> [ISQL]ERROR: Could not SQLConnect
> 
> I can only get this to work on windows. Would you please let me know how I
> can get this to work.
> 
> Cheers,
> Sarala
> 
> 
>> Hi Sarala,
>> 
>> Is there any error written at the end of the virtuoso.log file at the
>> point of the crash and is a core file created whose stack trace can be
>> analysed to determine point of the crash ( shall  "ulimit -c" needs to be
>> greater then 0 for core file creation) ?
>> 
>> What happens if you execute the same query against the Virtuoso SQL
>> interface (port 1111 by default), which is the interface used by the Jena
>> Provider as opposed to the HTTP (8890 default) used by the sparql
>> endpoint, using the Virtuoso command line "isql" tool ?
>> 
>> Best Regards
>> Hugh Williams
>> Professional Services
>> OpenLink Software
>> Web: http://www.openlinksw.com
>> Support: http://support.openlinksw.com
>> Forums: http://boards.openlinksw.com/support
>> Twitter: http://twitter.com/OpenLink
>> 
>> On 10 Feb 2011, at 11:09, Sarala Wimalaratne wrote:
>> 
>>> Hi Hugh,
>>> 
>>> Thanks for the quick reply. Unfortunately with
>>> virtuoso-opensource-6-20110105, I get the same error and the server
>>> crashes.
>>> 
>>> I just tried the trial version glibc 2.5 x86 (32-bit) and it works. It
>>> would be great if I could get the virtuoso opensource linux version
>>> working.
>>> 
>>> Cheers,
>>> Sarala
>>> 
>>> On 10/02/2011 00:10, Hugh Williams wrote:
>>>> 
>>>> Hi Sarala,
>>>> 
>>>> A later 6.1.3 release candidate build can be downloaded from:
>>>> 
>>>> 	ftp://download.openlinksw.com/support/vos/virtuoso-opensource-6-20110105.tar.gz
>>>> 
>>>> Can you please download, recompile and test the query again to see if
>>>> the problem still occurs ...
>>>> 
>>>> Note a Windows 64bit equivalent build is also available from:
>>>> 
>>>> 	ftp://download.openlinksw.com/support/vos/virtuoso-opensource-win64-20101220.zip
>>>> 
>>>> Best Regards
>>>> Hugh Williams
>>>> Professional Services
>>>> OpenLink Software
>>>> Web: http://www.openlinksw.com
>>>> Support: http://support.openlinksw.com
>>>> Forums: http://boards.openlinksw.com/support
>>>> Twitter: http://twitter.com/OpenLink
>>>> 
>>>> On 9 Feb 2011, at 11:29, Sarala Wimalaratne wrote:
>>>> 
>>>> 
>>>>> Hi,
>>>>> 
>>>>> I have the virtuoso windows version
>>>>> (virtuoso-opensource-win64-6.1.2.zip
>>>>> - 2010-07-09) installed in my local machine and the linux version
>>>>> (virtuoso-opensource-6.1.2.tar.gz - 2010-07-09) installed in a remote
>>>>> server. Everything works fine on the local windows version (using the
>>>>> web interface and jena). However, some queries does not work on the
>>>>> virtuoso which is in the remote linux server when using Jena. Again
>>>>> everything works fine if I use the virtuoso web interface. Here is one
>>>>> of the queries that doesn't work. It throws an error and the server
>>>>> crashes.
>>>>> 
>>>>> private void select(){
>>>>>        String query = "define input:inference \"ricordo_rule\" " +
>>>>>                "PREFIX rcmd: <http://www.ebi.ac.uk/ricordo/model#> "
>>>>> +
>>>>>                "SELECT DISTINCT ?m COUNT (?s) FROM
>>>>> <http://ricordotest.com> WHERE { ?s rcmd:elementOf ?m . ?s ?p
>>>>> <urn:miriam:obo.fma:FMA%3A9557> } GROUP BY ?m";
>>>>> 
>>>>>        VirtuosoQueryExecution vqe =
>>>>> VirtuosoQueryExecutionFactory.create (query, graph);
>>>>> 
>>>>>        ResultSet results = vqe.execSelect();
>>>>> 
>>>>>        while (results.hasNext()) {
>>>>>            QuerySolution rs = results.nextSolution();
>>>>>            RDFNode s = rs.get("m");
>>>>>            RDFNode p = rs.get("?callret-1");
>>>>>            System.out.println(" { " + s + " " +
>>>>> p.asLiteral().getInt()
>>>>> + " }");
>>>>>        }
>>>>> }
>>>>> 
>>>>> Exception in thread "main" com.hp.hpl.jena.shared.JenaException: Can
>>>>> not
>>>>> create ResultSet.:virtuoso.jdbc3.VirtuosoException: Virtuoso
>>>>> Communications Link Failure (timeout) : Connection to the server lost
>>>>>    at virtuoso.jena.driver.VirtuosoQueryExecution.execSelect(Unknown
>>>>> Source)
>>>>> 
>>>>> It would be great if you could please let me know how I could resolve
>>>>> this issue.
>>>>> 
>>>>> Many thanks in advance
>>>>> Sarala
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio
>>>>> XE:
>>>>> Pinpoint memory and threading errors before they happen.
>>>>> Find and fix more than 250 security defects in the development cycle.
>>>>> Locate bottlenecks in serial and parallel code that limit performance.
>>>>> http://p.sf.net/sfu/intel-dev2devfeb
>>>>> _______________________________________________
>>>>> Virtuoso-devel mailing list
>>>>> Vir...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/virtuoso-devel
>>>>> 
>>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio
>>> XE:
>>> Pinpoint memory and threading errors before they happen.
>>> Find and fix more than 250 security defects in the development cycle.
>>> Locate bottlenecks in serial and parallel code that limit performance.
>>> http://p.sf.net/sfu/intel-dev2devfeb_______________________________________________
>>> Virtuoso-devel mailing list
>>> Vir...@li...
>>> https://lists.sourceforge.net/lists/listinfo/virtuoso-devel
>> 
>> 
> 
> 