I have just retried the above long-time query and checked the virtuoso.log.
I see that after 45 minutes I get the following log entries (I executed the
query around 10.00):
10:24:23 * Monitor: High disk read (2)
10:41:23 * Monitor: High disk read (2)
10:43:24 * Monitor: High disk read (2)
10:43:41 mmap failed with 12
10:43:45 mmap failed with 12
10:43:45 mmap failed with 12
10:43:45 mmap failed with 12
10:43:46 mmap failed with 12
10:43:46 mmap failed with 12
10:43:46 GPF: Dkpool.c:1634 could not allocate memory with mmap
The same messages (more or less) had in the previous "lost connection"
incident.
Could somebody provide some hints?
Kind regards,
Pantelis Natsiavas
2016-08-09 9:58 GMT+03:00 Pantelis Natsiavas <natsia...@gmail.com>:
> Hi.
>
> I am trying to execute a SPARQL INSERT-WHERE taking a lot time to
> complete.
>
> INSERT {
> GRAPH <a
> <http://bio2rdf.org/clinicaltrials_resource:bio2rdf.dataset.clinicaltrials.R4>>
> {
> ?s <hasLabelAfterManualConversion> ?newLabel
> }
> }
> WHERE {
> GRAPH <a
> <http://bio2rdf.org/clinicaltrials_resource:bio2rdf.dataset.clinicaltrials.R4>>
> {
> ?s ?p ?o .
> FILTER (REGEX(STR(?o),"abc","i")) .
> BIND(REPLACE(?o, "abc", "", "i") AS ?newLabel)
> }
> };
>
> Trying to execute it through the web environment, I get a timeout. I
> thought that the most appropriate way to do it would be through the isql-v
> command line environment. When I try to do it, after some hours I get
>
> **** Error 08S01: [Virtuoso Driver]CL065: Lost connection to server*
>
> This is rather peculiar as the isql-v runs on the same VM as the virtuoso.
> It should also be noted that the virtuoso instance responds and has not
> collapsed.
>
> I have three questions:
> 1. Is this "lost connection" behavior in the isql-v environment normal?
> 2. Does this "lost connection" message mean that the transaction has
> rolled-back or is the command still running?
> 3. Is there a better way to run long-time queries against virtuoso?
>
> Kind regards,
> Pantelis Natsiavas
>
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