Hi Pantelis, What is the memory consumption of Virtuoso whilst running the insert query and what is the size of the graph the insert is being performed against ? As note for SPARUL operation against graph with large amounts of data it is recommended queries are performed in row-wise auto commit mode to reduce memory consumption which case otherwise be depleted causing hangs or the server crash if memory cannot be allocated, with the Virtuoso log_enable function as detailed at:
http://docs.openlinksw.com/virtuoso/fn_log_enable.html
http://virtuoso.openlinksw.com/dataspace/doc/dav/wiki/Main/VirtTipsAndTricksGuideDeleteLargeGraphs
Best Regards
Hugh Williams
Professional Services
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> On 9 Aug 2016, at 12:11, Pantelis Natsiavas <natsia...@gmail.com> wrote:
>
> 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
> <mailto: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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