'cannot allocate more memory!' error

[andrewSharo]

Hi Filipe,

Thanks for creating ngsLD! I have used ngsLD in the past successfully, but recently began using it for a larger dataset. My input line is:

/usr/local/src/ngsLD/ngsLD --geno ./full.beagle.forNgsld.gz --pos ./full.mafs.forNgsld.gz --probs --n_ind 95 --n_sites 19574912 --max_kb_dist 5 --n_threads 1 --out ./full_ngsld.ld

And ngsLD gives the following output and error message:

==> Input Arguments:
geno: ./full.beagle.forNgsld.gz
probs: true
log_scale: false
n_ind: 95
n_sites: 19574912
pos: ./full.mafs.forNgsld.gz (WITHOUT header)
max_kb_dist (kb): 5
max_snp_dist: 0
min_maf: 0.001000
ignore_miss_data: false
call_geno: false
N_thresh: 0.000000
call_thresh: 0.000000
rnd_sample: 1.000000
seed: 1645655030
extend_out: false
out: ./full_ngsld.ld (WITHOUT header)
n_threads: 1
verbose: 1
version: 1.1.1 (Feb 19 2022 @ 13:20:08)

==> GZIP input file (not BINARY)

=====
ERROR: [init_ptr] cannot allocate more memory!

Is there an easy way to calculate memory usage? I am using a machine with a ton of ram (512Gb). Can I increase the memory limit somehow? Should I try breaking my geno and pos files into separate chromosomes?

Thank you for any tips,
Andrew

[andrewSharo]

I've realized that the error was on my end. Despite having a ton of ram, it was all being used by another process. But I thought it might be helpful to leave this issue, rather than delete it, in case someone else has the same problem. Check your /proc/meminfo file! I'll close this issue.