FAQ - Frequently Asked Questions¶
[CRITICAL] Unhandled exception on Autosubmit: attempt to write a readonly database¶
[CRITICAL] Unhandled exception on Autosubmit: attempt to write a readonly database
Traceback (most recent call last):
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit
.py", line 389, in parse_args
return Autosubmit.create(args.expid, args.noplot, args.hide, args.output, args.group_by, args.expand, args.expand_status)
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit
.py", line 1953, in create
"job_packages_" + expid).reset_table()
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/job/job_pa
ckage_persistence.py", line 65, in reset_table
self.db_manager.drop_table(self.JOB_PACKAGES_TABLE)
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/database/d
b_manager.py", line 65, in drop_table
cursor.execute(drop_command)
OperationalError: attempt to write a readonly database
Solution¶
This usually happens when trying to run autosubmit create with an expid of another user, please double check the expid you are using.
[ERROR] Command sbatch -D … failed with error message: sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified¶
Solution¶
This can be due to an invalid configuration in your ~/.ssh/config file, so check if you are able to run a ssh command using the account displayed in the error message. If so, once you are in the remote platform, type bsc_acct and see if the information for your username/account is displayed:
USER CONSUMED CPU:
User: Machine: Used [khours]:
If not, contact support referring to the problem and specifying your account.
[ERROR] Cannot send file to remote platform¶
[ERROR] marenostrum4 submission failed
[CRITICAL] Unhandled exception on Autosubmit: size mismatch in put! 0 != 38998
Traceback (most recent call last):
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 368, in parse_args
return Autosubmit.run_experiment(args.expid)
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 776, in run_experiment
if Autosubmit.submit_ready_jobs(as_conf, job_list, platforms_to_test, packages_persistence):
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 819, in submit_ready_jobs
package.submit(as_conf, job_list.parameters)
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/job/job_packages.py", line 87, in submit
self._send_files()
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/job/job_packages.py", line 115, in _send_files
self.platform.send_file(self._job_scripts[job.name])
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/platforms/paramiko_platform.py", line 129, in send_file
ftp.put(os.path.join(self.tmp_path, filename), os.path.join(self.get_files_path(), filename))
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/paramiko-1.15.0-py2.7.egg/paramiko/sftp_client.py", line 669, in put
return self.putfo(fl, remotepath, file_size, callback, confirm)
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/paramiko-1.15.0-py2.7.egg/paramiko/sftp_client.py", line 635, in putfo
raise IOError('size mismatch in put! %d != %d' % (s.st_size, size))
IOError: size mismatch in put! 0 != 38998
This happens when the quota has been reached and the machine is full
[CRITICAL] Unhandled exception on Autosubmit: database is locked¶
[CRITICAL] Unhandled exception on Autosubmit: database is locked
Traceback (most recent call last):
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 377, in parse_args
args.operational) != ''
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/autosubmit.py", line 532, in expid
exp_id = copy_experiment(copy_id, description, Autosubmit.autosubmit_version, test, operational)
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/experiment/experiment_common.py", line 93, in copy_experiment
new_name = new_experiment(description, version, test, operational)
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/experiment/experiment_common.py", line 68, in new_experiment
if not db_common.save_experiment(new_name, description, version):
File "/shared/earth/software/autosubmit/3.11.0b-foss-2015a-Python-2.7.9/lib/python2.7/site-packages/autosubmit-3.10.0-py2.7.egg/autosubmit/database/db_common.py", line 151, in save_experiment
{'name': name, 'description': description, 'version': version})
OperationalError: database is locked
Solution¶
If you were trying to copy an experiment, make sure you put the -y immediately after expid: autosubmit expid -y
bash: sbatch: command not found¶
Solution¶
First, check your jobs_expid.conf and platforms_expid.conf files and make sure the platform assigned to the running job is defined correctly and is a SLURM platform. If this is ok, check that the hostname of the platform you are using is also correctly defined in your ~/.ssh/config file.