My apologies. I should have continued reading the documentation. I found a sample configuration file here:
http://crd-legacy.lbl.gov/~kewu/fastbit/doc/dataLoading.html#samplerc Unfortunately, even when I set the value to 1000000Mb (fileManager.maxBytes=1000000Mb), I still get the same error originally reported. On Mon, Jul 28, 2014 at 1:29 PM, Darryl Reeves <[email protected]> wrote: > Hi John, > > After reading your response on a different thread ("Out of memory without > MMAP"), I'm thinking that increasing the fileManager cache might help me > with this problem as well. From the online documentation, I was able to > determine that I can set the cache size in a file named "ibis.rc" that is > located in the same directory where I am running "buildIndex." What should > the format of the configuration parameter be? > > I tried: > > fileManager.maxBytes = 5GB > > But this doesn't seem to make a difference. Can you provide an example > configuration file? > > Thanks, > Darryl > > > On Fri, Jul 25, 2014 at 7:02 PM, Darryl Reeves <[email protected]> wrote: > >> Hi John, >> >> I just shared the file with you through my Google Drive account. Let me >> know if you have any problems accessing the file. >> >> The command that I have tried to run is: >> >> fastquery-0.8.2.8/examples/buildIndex -f sample.2.h5 -n k >> >> Thanks, >> Darryl >> >> >> On Thu, Jul 24, 2014 at 10:59 PM, John Wu <[email protected]> wrote: >> >>> Hi, Darryl, >>> >>> Are you able to share the test data with us? It would be useful for us >>> to reproduce the problem. >>> >>> If yes, please provide instructions on reproducing the problem. >>> >>> Thanks. >>> >>> K Wu >>> On Jul 24, 2014 1:25 AM, "Darryl Reeves" <[email protected]> wrote: >>> >>>> Hello, >>>> >>>> I am attempting to index a file consisting of unsigned integer data >>>> using the example program "buildIndex" included with fastquery. This >>>> program works fine for the test data included with the source code. >>>> >>>> However, when I try to index my data, I receive the following memory >>>> allocation error: >>>> >>>> Warning -- fileManager::storage::ctor unable to find 6,572,816,304 >>>> bytes of space in memory >>>> terminate called after throwing an instance of 'ibis::bad_alloc' >>>> what(): storage::ctor(memory) failed >>>> >>>> This error is revealed very early in the execution of the program. By >>>> monitoring the memory being used, I can tell that only 58756 Kb have been >>>> allocated by the program. The server where this is running has no shortage >>>> of RAM available. I am willing to share the dataset that I am using but it >>>> is 3.2 Gb, so it cannot be transferred as part of this message. >>>> >>>> Any help that can you can provide to figure out this issue is >>>> appreciated. >>>> >>>> Thanks, >>>> >>>> -- >>>> Darryl Reeves >>>> Ph.D. Candidate >>>> Mason Lab >>>> Weill Cornell Medical College of Cornell University >>>> Tri-Institutional Program in Computational Biology and Medicine >>>> >>>> _______________________________________________ >>>> FastBit-users mailing list >>>> [email protected] >>>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >>>> >>>> >>> _______________________________________________ >>> FastBit-users mailing list >>> [email protected] >>> https://hpcrdm.lbl.gov/cgi-bin/mailman/listinfo/fastbit-users >>> >>> >> >> >> -- >> Darryl Reeves >> Ph.D. Candidate >> Mason Lab >> Weill Cornell Medical College of Cornell University >> Tri-Institutional Program in Computational Biology and Medicine >> > > > > -- > Darryl Reeves > Ph.D. Candidate > Mason Lab > Weill Cornell Medical College of Cornell University > Tri-Institutional Program in Computational Biology and Medicine > -- Darryl Reeves Ph.D. Candidate Mason Lab Weill Cornell Medical College of Cornell University Tri-Institutional Program in Computational Biology and Medicine
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