Hi Albert, Here's some information about our installation of 2013 AA (taken from an email to a user with a similar question last year). I hope this helps, and I hope things are working out ok. Please let us know how things go. We'll also keep you posted when we get to a 2014 version of UMLS.
================= I have the UMLS version 2013AA installed. The index using the following configuration contains 13,520,173 rows. The size is approximately 2.5 G when I look specifically at the size of the tables for that configuration. I don't think that would be a direct comparison though. I have a number of index files created so I can only give what I think is the estimate -- total I am using 575G. Here is the configuration: SAB :: include SNOMEDCT REL :: include PAR, CHD Just in case this is different from yours. I do not remember how long it took exactly. I started it on a Friday and went away for the weekend. SNOMEDCT is the largest source so it normally takes a couple days to process all of the nodes to create the index. ================== Cordially, Ted On Tue, Jul 22, 2014 at 11:50 AM, Albert Max Lai [email protected] [umls-similarity] <[email protected]> wrote: > > > Here's what's in our my.cnf file: > > key_buffer = 600M > > table_cache = 300 > > sort_buffer_size = 500M > > read_buffer_size = 200M > > query_cache_limit = 3M > > query_cache_size = 100M > > myisam_sort_buffer_size = 200M > > bulk_insert_buffer_size = 100M > > join_buffer_size = 100M > > They're the same as in the INSTALL document other than the fact that our > sort_buffer_size is larger, which I think came from the UMLS installation > guide. I don't know if we got an error message. The terminal that started > up the process may have gotten disconnected. We knew it was done because > the associated Perl exited and mysql CPU utilization went to 0. > > We've now installed 2013AA and trying to index again. Hopefully we'll know > soon whether or not we are able to successfully index that version. > > > > On Tue, Jul 22, 2014 at 7:42 AM, Ted Pedersen [email protected] > [umls-similarity] <[email protected]> wrote: > >> >> >> I'm afraid I won't be able to install a newer version of the UMLS just >> yet, but I'm sure we will do this within the next month or so, and we'll >> try and index SNOMEDCT_US. >> >> In the meantime, could you let us know what changes you made to your >> my.cnf file? (The recommended changes are described here : >> https://metacpan.org/source/BTMCINNES/UMLS-Interface-1.41/INSTALL) >> >> The fact that your install stopped makes me wonder if there is some issue >> with your my.cnf values. Can you let us know what those are set to? Also, >> when it stopped, did you get any error message? And/or, how did you >> know/realize that it had stopped? >> >> Thanks! >> Ted >> >> >> On Mon, Jul 21, 2014 at 6:45 PM, [email protected] >> [umls-similarity] <[email protected]> wrote: >> >>> >>> >>> Hi >>> >>> We tried creating index on SNOMEDCT_US and it stopped. However when we >>> tried testing theindex, it threw an error saying index was incomplete. >>> >>> Can you try indexing it at your end and let us know ? >>> >>> Thanks ! >>> Chaitanya. >>> >>> >> >> >> -- >> Ted Pedersen >> http://www.d.umn.edu/~tpederse >> >> > > -- Ted Pedersen http://www.d.umn.edu/~tpederse
