<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">You can try mpi = 3 and cpus=10. It might recuce memory usage.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 19, 2021, at 11:02 AM, Kyungyong Seong <<a href="mailto:s.kyungyong@berkeley.edu" class="">s.kyungyong@berkeley.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thank you for the tips! How about reducing the time for tblastx? My cluster has a 3 days run limit. I think what is happening is that MAKER is terminated because of out-of-memory issues or runtime cap, and when MAKER is restarted, tblastx needs to start from scratch. Do you think it would be better not to use MPI and set cpus=30? Or would it be okay to set up mpi = 3 and cpus=10 if I have 30 cores?<div class=""><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Dec 17, 2021 at 9:29 AM Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">1. Make sure your system is not configured with an in memory /tmp directory. If it is, every file written to temporary storage will use RAM.<br class="">
2. If running under MPI, cpu= in maker_opts.ctl must be set to 1.<br class="">
3. max_dna_len= should be 100000 (the default)<br class="">
4. In maker_bopts.ctl, set all the depth_blast= options to something like 10 or 20 (there are 3 depth values you will have to set). The default is to keep everything, and if you have really deep alignments that can use a lot of RAM with out any actual benefit for gene prediction.<br class="">
<br class="">
—Carson<br class="">
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> On Dec 16, 2021, at 11:03 AM, Kyungyong Seong <<a href="mailto:s.kyungyong@berkeley.edu" target="_blank" class="">s.kyungyong@berkeley.edu</a>> wrote:<br class="">
> <br class="">
> Hi!<br class="">
> <br class="">
> MAKER has been running fine on my genome (~1Gb; 800 contigs) but is now stuck with ~30 contigs that keep failing because of high memory consumption. I am using mpi, running 20-30 contigs for annotation in parallel, depending on the machine. I started with 64Gb memory machines but have moved up to 1.5 Tb machines as the job kept failing. Unfortunately, all memory of this machine is also saturated. It looks like tblastx is taking lots of time and resources. The databases I have are about 200 Mb for the proteins and 570 Mb for cDNAs. max_dna_len is set as 100000 in maker_opt.ctl. Would there be a way to improve this? Decreasing the number of jobs for MPI slowed down memory saturation but eventually the same happened. <br class="">
> <br class="">
> Thank you!<br class="">
> Kyungyong<br class="">
> <br class="">
> <br class="">
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