OHDSI Home | Forums | Wiki | Github

CPT4 jar

started cpt4, but java program has not ended after a couple of hours. What is see is

java -jar cpt4.jar 5
Updated CPT4 records: 15446, records to update: 0

But do not see ‘CPT successfully updated’.

should I just be patient or is something wrong?

Has anyone else had this problem?

I have the same problem.

Same here. CONCEPT.csv is 0 bytes according to windows explorer. I’m probably an hour in so far–looking at the same exact message that @DTorok lists.

Does this resolve eventually, or should I restart, or…?

Thanks!

-Roy

@rpardee, @DTorok, @nay2006 - hello, I wil check and uniform you about results.

BR

1 Like

Unfortunately I can’t reproduce this behavior - so can you provide more information about your steps and environment please?
BR

1 Like

Today, I was able to run it with no issues.

1 Like

Thanks all–it’s running fine for me today. Took maybe 5 minutes total.

java -jar cpt4.jar 5 command produces an java.lang.OutOfMemory error.
Seems like it can not complete the file rewrite.

I have tried over a 2 day period to run this. With the same error. The csv file starts out with 5,386,839 rows and ends up with around 4,665,800 records. Each time i run it, it ends up with a slightly different count. I may have missed a step if not maybe there is another way to accomplish this.

Thanks
Mark

Hello, thank you for your reporting.
Can you answer what vocabulary set did you download before running cpt4.jar?
I will try to reproduce your error and will inform your about solution.
As a hotfix you can try to run jar command with “max heap size” parameter: java -Xmx1024M -jar cpt4.jar 5.
For checking default heap size please execute command java -XX:+PrintFlagsFinal -version | findstr HeapSize (for windows) or java -XX:+PrintFlagsFinal -version | grep HeapSize (for Unix/Linux). Please sent me console output after running this command.

BR

There are a total of 89 vocabularies. I am not sure what i needed so i downloaded what i could.
Here is the java output.

Here are the download files.

Thanks

Just an update here. I downloaded a different set of vocabularies and the process completed successfully.
Thanks

Ok, anyway I understand your trouble and created issue in Athena backlog.

BR

t