> adj = as.dist(adj)
Error: cannot allocate vector of size 3.0 Gb
> system("free -h")
total used free shared buff/cache available
Mem: 14G 2.2G 12G 88M 420M 12G
Swap: 0B 0B 0B
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 7799796 416.6 16746142 894.4 16746142 894.4
Vcells 41146681 314.0 520945812 3974.6 1665927139 12710.1
Why can't I allocate a vector of 3.0GB if I have 12GB free? I'm working on Linux CentOS, so I don't have access to memory.limit() and memorize.size().
This general question has been asked a lot. I don't see an answer that addresses my specific question, though. These questions are kind of the same, but the only answers I see are related to reducing the size of the object, using memory.limit() and memory.size(), or using bsub -q server_name -R. I don't know how to use the latter inside a script, and it doesn't address my question of why I can't allocate a vector when (it appears) I have the memory to do so. I've also tried including Sys.setenv('R_MAX_VSIZE'=32000000000) but that did not fix it.
Edit: I added gc() output. Does it matter that the available 12GB are virtual memory??
