Achilles eating my hard drive

Implementers
1

I’ve got the large synpuf dataset running on my Mac in Postgres. I dumped the data from the big ohdsi-in-a-box VM from the Vocabulary Tutorial at the Symposium. I’m just now trying to run Achilles on it. This is how far it’s gotten:

> exportToJson(connectionDetails, cdmDatabaseSchema = "public", resultsDatabaseSchema = "results", outputPath = "/Users/sigfried/Sites/OHDSI/Achilles/data/ohdsi_tutorial", cdmVersion = "5", vocabDatabaseSchema = "public")
Connecting using PostgreSQL driver
Generating condition treemap
  |=======================================================================| 100%
Generating condition reports
  |=======================================================================| 100%
Generating condition era treemap
  |=======================================================================| 100%
Generating condition era reports
  |=======================================================================| 100%
Generating data density reports
  |=======================================================================| 100%
Generating death reports
  |=======================================================================| 100%
Generating drug era treemap
  |=======================================================================| 100%
Generating drug era reports
  |=======================================================================| 100%
Generating drug treemap
  |=======================================================================| 100%
Generating drug reports
  |=======================================================================| 100%
Generating achilles heel report
Generating measurement treemap
  |                                                                       |   0%

Right now it’s gobbled up 140GB of hard drive in /Users/sigfried/Library/Application Support/Postgres/var-9.4/base/pgsql_tmp and getting bigger fast. I’m down to 9.75 GB on my hard drive. Any advice?

2

Oh well…

Generating measurement treemap
 |                                                                 |   0%
Error 
executing SQL: Error in rJava::.jcall(s, "Ljava/sql/ResultSet;", "executeQuery", as.character(query)[1]): org.postgresql.util.PSQLException: ERROR: could not write block 2657547 of temporary file: 
            No space left on device

An error report has been created at  /Users/sigfried/errorReport.txt
Error in value[[3L]](cond) : no loop for break/next, jumping to top level

I can free up a little more disk, but this is my second time through and I already freed up 50GB last time… I must be doing something wrong.

3

We have seen similar behavior when the database is not optimized. Have you created the recommended indexes?

4

Whoops, that might be the problem. Although I thought when I did the pg_dump it would have included indexes… I’ll go check. Thanks.

5

Yeah, I have indexes… hmm…

6

We experienced similar behavior when running achilles against the latest vocabulary/postgreSQL/Linux.

7

How can the poor innocent sweet vocabulary be guilty of such a behavior? Get off those girly Macs. :smile: