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Questions and answers => RNA structures (DSSR) => Topic started by: febos on January 31, 2017, 08:33:37 am

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Title: "malloc failure"
Post by: febos on January 31, 2017, 08:33:37 am
Good afternoon, Dr. Lu

i have found a problem with some pdb entries (around 50 different entries).
For example:
entry 5tgm:
x3dna-dssr-170122 -i=5tgm.cif1 --idstr=long --more -o=5tgm0122.out1

Processing file '5tgm.cif1'
allocate_atoms_array(): malloc failure (411589)

Time used: 00:00:00:05

this problem holds within at least three last versions of DSSR (17jan22, 16nov19, 16oct19).

Could you please explain this issue?

thanks in advance,
Title: Re: "malloc failure"
Post by: xiangjun on January 31, 2017, 09:33:37 am
Hi Eugene,

Thanks for reporting this issue (presumably out of memory?). Just notice your message, and I'll get it fixed ASAP.

Best regards,

Title: Re: "malloc failure"
Post by: xiangjun on February 01, 2017, 12:13:59 pm
Hi Eugene,

I've run DSSR on 5TGM as below, and the program works as expected. Since this is huge ribosomal structure, I guess your computer is running out of memory. What're settings of your system? How many GB memory do you have?

Code: [Select]
Command: x3dna-dssr -i=5TGM.cif --format=mmcif --idstr=long --more -o=5tgm0122.out
Date and time: Wed Feb  1 11:29:17 2017
File name: 5TGM.cif
    no. of DNA/RNA chains: 10 [1=3151,2=1781,3=121,4=158,5=3152,6=1795,7=121,8=158,P=3,p=3]
    no. of nucleotides:    10439
    no. of atoms:          411545
    no. of waters:         0
    no. of metals:         2302 [Mg=1191,Zn=16,Os=1095]

# excerpt output on screen
    total number of base pairs: 5079
    total number of multiplets: 607
    total number of helices: 304
    total number of stems: 646
    total number of isolated WC/wobble pairs: 264
    total number of atom-base capping interactions: 619
    total number of splayed-apart dinucleotides: 1322
    total number of hairpin loops: 232
    total number of bulges: 153
    total number of internal loops: 329
    total number of junctions: 128
    total number of A-minor (type I and II) motifs: 199
    total number of ribose zippers: 104
    total number of kink turns: 13
    total number of non-loop single-stranded segments: 101
    total number of kissing loops: 10

Title: Re: "malloc failure"
Post by: febos on February 01, 2017, 12:45:47 pm
Good afternoon, Dr. Lu

At first i have not thought about memory since problematic entries were not the largest ones. Now I understand that when i run DSSR i have had some other heavy processes running. I tried to stop them and run DSSR on 5tgm again. It worked just fine.
Thank you and please sorry for bothering.


Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.