align.seqs commend unable to spawn

mothur bugs
#1

Hi,
Because I need to analysis the fungi and Archaea, so I downloaded the alignment template file from Silva 111.
Recently I use 1.30 and 1.31 of mothur. when I doing align.seqs, it always has error that unable to spawn the necessary processes.
I have 64GB RAM. It is enough to load Silva 111, and I gave 1GB Swap. But still have problem. How can I fix it.

#2

When I set the swap to 100GB, the align.seqs commend is working. is it the problem of swap size?

#3

The unable to spawn error message is given when the OS is unable to complete the fork() command for multiple processes. Are you able to run the command with processors=1?

#4

I have a similar problem with Mothur v1.33.3 and Silva V119 (Ubuntu 14.04): “unable to spawn the necessary processes”. I’m using AWS instances where there is no SWAP. I was previously working with Silva V111 and I did not encounter that problem. Could you confirm that this is a RAM problem. I saw in version 1.34.2 that with the align.seqs command the number of processors was reduced to 1 when the problem occured.
BTW it works all the time if I only use 1 processor.

Thanks in advance for your response.

#5

It is a RAM issue. The error message is given when mothur tries to create another process but can’t due to lack of system resources. For mac and linux flavors, this means the fork() system command failed. en.wikipedia.org/wiki/Fork_(system_call)

#6

I confirm. I manage to get it working adding some more RAM (using a 30 GB RAM machine instead of a 15 GB RAM). Isn’t it any smart way to set the processors wrt to the available RAM?

#7

Thanks for the suggestion. The align.seqs command does this already. It tries to use the number of processors requested by the user, but if it is unable to do so it will reduce the number to as many as possible. We have intentions of adding this feature to mothur’s other multiple processors commands.