If the Atomicity tests are passing, but the run has such errors, the likely cause is that the database was loaded at a lower rate than required by SPECvirt.
SPECvirt requires DB to be loaded at IR 500.
For loading, set txRate=500 in:
/opt/SPECjAppServer2004/config/run.properties
After loading, for run, switch it back to txRate=100.
Please see User Guide section 2.5 for details.