Failed to start thread "GC Thread#0" from cbioportal-container and cbioportal-session-container

[Raktim Sinha]

Trying to do docker-compose up, database seems to be setup correctly but 

cbioportal-container and cbioportal-session-container is throwing this error.

Linux Machine resources:

- nproc: 32

- free -h: 246G

- df -h /scratch/apps/cba_cbio/cbioportal-docker-compose
Filesystem                      Size  Used Avail Use% Mounted on
/dev/mapper/vg_root-lv_scratch  336G  9.4G  310G   3% /scratch

Can some help with this error please?

cbioportal-container           | Running Migrate DB Script
cbioportal-container           | Using database config:
cbioportal-container           | spring_datasource_username=cbio_user
cbioportal-container           | spring_datasource_password=xxxx
cbioportal-container           | spring_datasource_url=jdbc:mysql://cbioportal-database:3306/cbioportal
cbioportal-container           | mysqladmin: [Warning] Using a password on the command line interface can be insecure.
cbioportal-container           | mysqld is alive
cbioportal-container           | Database connection success
cbioportal-container           | Migrating database if necessary...
cbioportal-container           | Everything up to date, nothing to migrate.
cbioportal-container           | Finished.
cbioportal-container           | Running: /bin/sh -c rm -rf /cbioportal-webapp/lib/servlet-api-2.5.jar && java -Xms2g -Xmx4g -cp '/cbioportal-webapp:/cbioportal-webapp/lib/*' org.cbioportal.PortalApplication --spring.config.location=cbioportal-webapp/application.properties --authenticate=false --session.service.url=http://cbioportal-session:5000/api/sessions/my_portal/
cbioportal-container           | [0.010s][warning][os,thread] Failed to start thread "GC Thread#0" - pthread_create failed (EPERM) for attributes: stacksize: 1024k, guardsize: 4k, detached.
cbioportal-container           | [0.012s][error  ][gc,task  ] Failed to create worker thread
cbioportal-container exited with code 1

[de Bruijn, Ino]

Hi Raktim,

 

Thanks fo reaching out! Unfortunately I haven’t seen that error before so not sure what to recommend here. Seems like some issue with starting threads on your os

 

Do you have a different machine at your disposal to try this? Or e.g. a cloud instance?

 

Best wishes,

Ino

 

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[Raktim Sinha]

Hi Ino -

Thanks for your reply.

Unfortunately I do not have access to other machine.

Wondering if this is related to docker version .. mine is Docker version 18.09.9, build 039a7df9ba

Is there a specific Linux version of docker that cbioportal/cbioportal:6.0.9 requires?

[Raktim Sinha]

I am unable to get past this issue. Any thoughts or suggestions anyone?