[BioC] Rsubread crashes in 32bit linux
Wei Shi
shi at wehi.EDU.AU
Wed Jun 6 06:56:58 CEST 2012
Dear Dan,
It is probably because including genome sequences into the index slowed down your laptop. But I believe it should be alleviated if you give smaller values to the 'memory ' parameter of the buildindex() function. Also, the index building is an one-off operation, you do not need to redo it even when new releases come.
For your 32-bit opensuse box, I guess the problem will be solved if you change the amount of memory requested to be 1000MB.
Cheers,
Wei
On Jun 5, 2012, at 11:43 PM, Dan Du wrote:
> Hi Robert,
>
> I have been experiencing something else, possibly related to yours,
> on a 64bit ubuntu laptop with 6g of ram.
>
> As I recall, when bumping to Bioc 2.10, the Rsubread installation kind
> of ate all the memory, basically froze the system so I had to call it
> off, yet building it on the server side turned out fine. So I think I
> just accepted that the new version may be 'computationally heavy' thus
> not suitable for a normal pc, though I did not find any mentioning of
> this increased memory requirement in the NEWS file.
>
> So currently Rsubread stays at 1.4.4 on that pc, all subsequent versions
> of Rsubread drain the memory in the same way when compiling Rsubread.so.
>
> Now I think I can confirm this on a 32-bit opensuse box, it did
> successfully built, but when running the example code in the manual,
> same segfault happens.
>
>
>> library(Rsubread)
>> ref <- system.file("extdata","reference.fa",package="Rsubread")
>> path <- system.file("extdata",package="Rsubread")
>> buildindex(basename=file.path(path,"reference_index"),reference=ref)
>
> Building a base-space index.
> Size of memory used=3700 MB
> Base name of the built index
> = /home/opensuse/R-patched/library/Rsubread/extdata/reference_index
>
> *** caught segfault ***
> address 0xdf03ee80, cause 'memory not mapped'
>
> Traceback:
> 1: .C("R_buildindex_wrapper", argc = as.integer(n), argv =
> as.character(cmd), PACKAGE = "Rsubread")
> 2: buildindex(basename = file.path(path, "reference_index"), reference
> = ref)
>
>> sessionInfo()
> R version 2.15.0 Patched (2012-06-04 r59517)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] Rsubread_1.6.3
>
>
> Regards,
> Dan
>
> On Tue, 2012-06-05 at 09:45 +0200, Robert Castelo wrote:
>> hi,
>>
>> the computer room at my university where we do practicals on R & Bioconductor runs a 32bit linux distribution and when i tried to run the latest version of the Rsubread package (1.6.3) it crashes when calling the buildindex() function on a multifasta file with the yeast genome. this does *not* happen under a 64bit linux distribution.
>>
>> i have verified that installing the version before (1.4.4) on the current R 2.15 it also crashes (on the 32bit), but two versions before, the 1.1.1, it does *not* and it works smoothly on this 32bit linux distribution.
>>
>> i'm pasting below the output of using the 1.6.3 and 1.1.1 on R 2.15 where allChr.fa is the multifasta file with the yeast genome.
>>
>> so i can manage by now the problem by using the 1.1.1 version on R 2.15 for my teaching but i wonder whether there would be some easy solution for this, or even if it could be a symptom of something else that the Rsubread developers should worry about. i know that using a 32bit system nowadays is quite obsolete but this is what i got for teaching :( and i would be happy to let my students play with the latest version of Rsubread in the future.
>>
>>
>> thanks!!!
>> robert.
>>
>> ======================Rsubread 1.6.3 on R 2.15=======================
>>
>>> library(Rsubread)
>>> sessionInfo()
>> R version 2.15.0 (2012-03-30)
>> Platform: i686-pc-linux-gnu (32-bit)
>>
>> locale:
>> [1] LC_CTYPE=ca_ES.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=ca_ES.UTF-8 LC_COLLATE=ca_ES.UTF-8
>> [5] LC_MONETARY=ca_ES.UTF-8 LC_MESSAGES=ca_ES.UTF-8
>> [7] LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=ca_ES.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] Rsubread_1.6.3
>>
>>> buildindex(basename="subreadindex", reference="allChr.fa", memory=2500)
>>
>> Building a base-space index.
>> Size of memory used=2500 MB
>> Base name of the built index = subreadindex
>>
>> *** caught segfault ***
>> address 0xdf670cc0, cause 'memory not mapped'
>>
>> Traceback:
>> 1: .C("R_buildindex_wrapper", argc = as.integer(n), argv = as.character(cmd), PACKAGE = "Rsubread")
>> 2: buildindex(basename = "subreadindex", reference = "allChr.fa", memory = 2500)
>>
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> Selection:
>>
>>
>> ======================Rsubread 1.1.1 on R 2.15=======================
>>
>>> library(Rsubread)
>>> buildindex(basename="subreadindex", reference="allChr.fa", memory=2500)
>>
>> Building the index in the base space.
>> Size of memory requested=2500 MB
>> Index base name = subreadindex
>> INDEX ITEMS PER PARTITION = 275940352
>>
>> completed=40.88%; time used=1.7s; rate=2955.1k bps/s; total=12m bps completed=81.76%; time used=2.4s; rate=4111.8k bps/s; total=12m bps
>> All the chromosome files are processed.
>> | Dumping index [===========================================================>]
>> Index subreadindex is successfully built.
>>> sessionInfo()
>> R version 2.15.0 (2012-03-30)
>> Platform: i686-pc-linux-gnu (32-bit)
>>
>> locale:
>> [1] LC_CTYPE=ca_ES.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=ca_ES.UTF-8 LC_COLLATE=ca_ES.UTF-8
>> [5] LC_MONETARY=ca_ES.UTF-8 LC_MESSAGES=ca_ES.UTF-8
>> [7] LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=ca_ES.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] Rsubread_1.1.1
>>
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>
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