Hi,
Whether you have enough RAM will be a function of lots of things -
which genome you are matching too (some are larger than others), how
careful you are about dropping sequences when they are not needed etc.
And as you have not provide those details it is not possible to give
more concrete advice.
You could try breaking the sequences down into smaller subsets, say
build a PDict on half of the data - match, then repeat on the other half
(or thirds or whatever size does work for your architecture). In
general, you may want to consider moving the analysis to a Linux box
with more RAM (we typically use machines with 32 or 64 GB of RAM - which
are surprisingly inexpensive these days).
best wishes
Robert
Stephen Henderson wrote:
Hi Joseph
You look like you should have enough RAM on your MacPro. Have you compiled a
64-bit version of R for the Mac? The CRAN binaries are 32-bit and will restrict
the available memory.
Stephen
________________________________
From: [EMAIL PROTECTED] on behalf of Joseph Dhahbi, P.h.D.
Sent: Tue 03/06/2008 16:21
To: [email protected]
Cc: [email protected]
Subject: [Bioc-sig-seq] PDict question
Hello
I need help on how to get around the memory error reported
below, especially when I can not add anymore RAM:
Here is the Hardware Overview:
Model Name: Mac Pro
Model Identifier: MacPro1,1
Processor Name: Dual-Core Intel Xeon
Processor Speed: 2.66 GHz
Number Of Processors: 2
Total Number Of Cores: 4
L2 Cache (per processor): 4 MB
Memory: 20 GB
Bus Speed: 1.33 GHz
Boot ROM Version: MP11.005C.B08
SMC Version: 1.7f10
Serial Number: G87052SGUPZ
NM_seq=readSolexaFastA(NM_fa)
NM_alf=alphabetFrequency(NM_seq, baseOnly=TRUE)
NM_seq_clean = NM_seq[NM_alf[,"other"]==0]
length(NM_seq)
[1] 4820218
length(NM_seq_clean)
[1] 4817537
NM_seq_clean
A DNAStringSet instance of length 4817537
width seq
[1] 36 GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGAT
[2] 36 GTGGTAATTCATCAGATCTCGGATGGCATTGGTCAT
[3] 36 GGGAGGTCACTAATGGAGACACACAGAAATGTAACA
[4] 36 GGGATTGGTTTTTTGTTACTGATTTGTTTGAGTTCA
[5] 36 GTGGTAATTTTGACTTTTTAGGTTAATTTATTTTTT
[6] 36 GATCGGAAGGAGCTCGTATGCCGTCTTCTGCTTAGA
[7] 36 GGTCAGTTGTGTTCTCCTGAGTAGGTTGTGTGAATG
[8] 36 GGGAGGTCACTAATGGAGACACACAGAAATGTAACA
[9] 36 GGGAGGCTGAGGCAGGAGAATGGCATGAACCTAGAT
... ... ...
[4817529] 36 TTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAG
[4817530] 36 CATCAATGTATCTTAAGGCGTAAATTGTAAGCGTTA
[4817531] 36 CGAGCAGCGACGCATCACCCAGCTAGATCGGAAGAG
[4817532] 36 GCAATGCCACTGGCGCGACAACCGGGACACCATAGG
[4817533] 36 CCTCGCCGGACACGCTGAACTTGTGGCCGTTTTCGT
[4817534] 36 CCATTGTACAACGTATCGACATATCCTCCACCCGCC
[4817535] 36 CCCCCTGAACCTGAAACATAAAATGAATGCAATTGT
[4817536] 36 ACCATGTTGTCCAAGGGCGAATTCTGCAGATATCCA
[4817537] 36 CAGGGGCCGGCGGCTGGCTAGGGCTGCAGCGTTAAA
NM_seq_pDict=PDict(NM_seq_clean)
Error in .PDict(dict, names(dict), tb.start, tb.end,
drop.head, drop.tail, :
alloc_actree_nodes_buf(): failed to alloc
actree_nodes_buf
R(433,0xa000d000) malloc: *** vm_allocate(size=4032987136)
failed (error code=3)
R(433,0xa000d000) malloc: *** error: can't allocate region
R(433,0xa000d000) malloc: *** set a breakpoint in
szone_error to debug
sessionInfo()
R version 2.7.0 (2008-04-22)
i386-apple-darwin8.10.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] tools stats graphics grDevices utils
datasets methods base
other attached packages:
[1] BiostringsCinterfaceDemo_0.1.2 Biostrings_2.8.9
Biobase_2.0.1
Regards,
Joseph
Joseph M. Dhahbi, PhD
Childrens Hospital Oakland Research Institute
5700 Martin Luther King Jr. Way
Oakland, CA 94609
USA
Ph.(510)428-3885 EXT.5743
Cell.(702)335-0795
Fax (510)450-7910
[EMAIL PROTECTED]
The email message (and any attachments) is for the sole...{{dropped:21}}
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--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
[EMAIL PROTECTED]
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