3DNA Forum

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

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:
Quote
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,
Eugene
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,

Xiang-Jun
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
Xiang-Jun
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.

Eugene