[ensembl-dev] skip lock tables for ensembl-compara
Mateus Patricio
mateus at ebi.ac.uk
Wed Nov 15 10:07:31 GMT 2017
Hi Francesco,
Could you please confirm which checkout version of the compara code you have?
Cheers,
Mateus.
> On 13 Nov 2017, at 10:50, Francesco Lamanna <francesco.lamanna at gmail.com> wrote:
>
> Hi Mateus and Brandon,
>
> many thanks for your patch, it solved the issue.
>
> Unfortunately, I got stuck at the successive step with the following error message:
>
> mysql> SELECT * FROM msg;
> +-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
> | analysis_id | logic_name | log_message_id | job_id | role_id | worker_id | when_logged | retry | status | msg | is_error |
> +-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
> | 9 | copy_ncbi_table | 1 | 5 | 3 | 3 | 2017-11-13 11:16:31 | 0 | WRITE_OUTPUT | Successfully copied 1609518 'ncbi_taxa_node' rows | 0 |
> | 9 | copy_ncbi_table | 2 | 6 | 4 | 4 | 2017-11-13 11:20:15 | 0 | WRITE_OUTPUT | Successfully copied 2438889 'ncbi_taxa_name' rows | 0 |
> | 18 | make_treebest_species_tree | 3 | 10 | 9 | 9 | 2017-11-13 11:25:29 | 0 | FETCH_INPUT | Can't call method "get_all_subnodes" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. | 1 |
> | 18 | make_treebest_species_tree | 4 | 10 | 11 | 11 | 2017-11-13 11:26:29 | 1 | FETCH_INPUT | Can't call method "get_all_subnodes" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. | 1 |
> | 18 | make_treebest_species_tree | 5 | 10 | 13 | 13 | 2017-11-13 11:27:31 | 2 | FETCH_INPUT | Can't call method "get_all_subnodes" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. | 1 |
> | 18 | make_treebest_species_tree | 6 | 10 | 16 | 16 | 2017-11-13 11:28:32 | 3 | FETCH_INPUT | Can't call method "get_all_subnodes" on an undefined value at /home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/Utils/SpeciesTree.pm line 150. | 1 |
> +-------------+----------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
> 6 rows in set (0.00 sec)
>
> Do you have any suggestion?
>
> Thanks,
> Francesco
>
> 2017-11-09 17:25 GMT+01:00 Brandon Walts <bwalts at ebi.ac.uk <mailto:bwalts at ebi.ac.uk>>:
> Hi Francesco
>
> We have just pushed a fix to the MySQLTransfer.pm runnable, so that it no longer locks tables by default. If you go to your eHive checkout and perform a git pull, you should get this fix.
> Users who wish to retain the table locking behavior can switch it on by passing a parameter 'lock_tables=1' to MySQLTransfer.pm
>
> Best
> -Brandon
>
>
> On 09/11/2017 16:20, Mateus Patricio wrote:
>> Hi Francesco,
>>
>> So what’s happening here is that you are trying to lock a table in one of our servers.
>>
>> That can be fixed by telling mysqldump to avoid locking the table. (Like you initially suspected)
>>
>> You could do that directly on the eHive runnable "ehive/master/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm”
>>
>> The dump command is constructed at:
>> https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117 <https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117>
>>
>> I would suggest you to create a new entry to “mode_options”:
>> https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112 <https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112>
>>
>> So that you could access directly from your pipeline config file, by setting something like:
>>
>>> { -logic_name => 'copy_ncbi_table',
>>> -module => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer',
>>> -parameters => {
>>> 'src_db_conn' => '#ncbi_db#',
>>> 'mode' => ’SKIP_LOCK',
>>> 'filter_cmd' => 'sed "s/ENGINE=MyISAM/ENGINE=InnoDB/"',
>>> },
>>> },
>>
>> Please let me know if that doesn’t work.
>>
>> Cheers,
>>
>> Mateus.
>>
>>
>>
>>
>>> On 9 Nov 2017, at 15:44, Francesco Lamanna <francesco.lamanna at gmail.com <mailto:francesco.lamanna at gmail.com>> wrote:
>>>
>>> Hi Mateus,
>>>
>>> thank you for your answer.
>>>
>>> I am using 'ncbi_db' => 'mysql://anonymous@ensembldb.ensembl.org/ensembl_compara_90 <http://anonymous@ensembldb.ensembl.org/ensembl_compara_90>' to conncect to ncbi_db (I used the same value as in the NoMasterProteinTrees_conf.pm example).
>>>
>>> The failing analysis is copy_ncbi_table(9).
>>>
>>> Cheers,
>>> Francesco.
>>>
>>> 2017-11-09 16:29 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk <mailto:mateus at ebi.ac.uk>>:
>>> Hi Francesco,
>>>
>>> Looks like your pipeline is using the user anonymous to connect to the database.
>>>
>>> I would suggest that you add the skip option within your runnable.
>>>
>>> Which analysis is actually failing?
>>>
>>> Cheers,
>>>
>>> Mateus.
>>>
>>>
>>>> On 8 Nov 2017, at 17:36, Francesco Lamanna <francesco.lamanna at gmail.com <mailto:francesco.lamanna at gmail.com>> wrote:
>>>>
>>>> Hello,
>>>>
>>>> I am trying to apply the ProteinTrees pipeline to a set of Ensembl and non-Ensembl genomes.
>>>>
>>>> When running the pipeline without a master database (via beekeeper.pl <http://beekeeper.pl/>) I get the following error:
>>>>
>>>> ensembl_compara_90 ncbi_taxa_node | sed "s/ENGINE=MyISAM/ENGINE=InnoDB/" | mysql -h127.0.0.1 -P3306 -uroot -p$EHIVE_TMP_PASSWORD_0 hd_cc141_test_protein_trees_no_master_90' resulted in an error code=2
>>>> stderr is: mysql: [Warning] Using a password on the command line interface can be insecure.
>>>> mysqldump: Got error: 1044: Access denied for user 'anonymous'@'%' to database 'ensembl_compara_90' when doing LOCK TABLES
>>>>
>>>>
>>>> Is there a way to pass --skip-lock-tables to the pipeline (e.g. in the conf file) in order to be able to dump the database?
>>>>
>>>> Thanks,
>>>> Francesco.
>>>>
>>>>
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>>>
>>>
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>>
>>
>>
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