Cipres Science Gateway

Two Current RAxML Issues

Issue 1. Cloned jobs fail:

Recently we upgraded RAxML to version 7.3.0. We did this because the version in use (7.2.8) did not respect uploaded constraint files used with the -q option. While the upgrade corrected this issue, it created a second issue. Unlike RAxML 7.2.8, v 7.3.0 requires the user to specify the parsimony seed for tree inference. The new interface is configured to provide this seed by default. However, if you clone and resubmit an old job, this option will not be set by default.

If you use the RAxML BlackBox interface, if you wish to clone a job created using RAxML 7.2.8, you will need to open the parameter pane, click the reset button on the bottom of the page, reconfigure the job, and resubmit.

If you use the full featured RAxML interface to create a job from RAxML 7.2.8, in order to clone it, you must open the parameter pane and check the -p option, and provide a seed (12345 by default) before submitting. If you don't do this, the job will fail, and there will be an error message in the stdout.txt file citing the failure to provide a parsomony seed. Please contact us if you have an issue with this.

Issue 2. Partitioned Jobs Fail:

A number of users report that sometimes RAxML 7.3.0 fails on partitioned jobs run under default parameters. The message that appears on job failure is:

raxmlHPC-HYBRID: parsePartitions.c:596: parsePartitions: Assertion `0' failed.
MPI process (rank: 8) terminated unexpectedly on trestles-3-18.local

Alexis is working on this issue. In the mean time, we find that the runs that fail with this error under the GAMMA model (the default choice) will succeed using the CAT model.