Comments (12)
trel
commented on July 19, 2024
Were you able to successfully build the externals yourself? irods/externals#151
If not, are you using packaged externals? If so, you have sudo rights?
Does /home/syslab/workspace_chc/install_irods/usr/sbin/hostname_resolves_to_local_address exist?
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xkdzml
commented on July 19, 2024
It succeeded in changing the version and building it.
/home/syslab/workspace_chc/install_irods/sbin/hostname_resolves_to_local_address exists.
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xkdzml
commented on July 19, 2024
I tried to create and run the /usr directory, but this time I got another error.
syslab@syslab:~/workspace_chc/irods/var/lib/irods$ sudo python ./scripts/setup_irods.py
Warning: Hostname `syslab` should be a fully qualified domain name.
Error encountered running setup_irods:
Traceback (most recent call last):
File "./scripts/setup_irods.py", line 447, in main
test_mode=options.test_mode)
File "./scripts/setup_irods.py", line 68, in setup_server
check_hostname()
File "./scripts/setup_irods.py", line 168, in check_hostname
if not irods.lib.hostname_resolves_to_local_address(hostname):
File "/home/syslab/workspace_chc/irods/var/lib/irods/scripts/irods/lib.py", line 391, in hostname_resolves_to_local_address
raise IrodsError('Error encountered in hostname_resolves_to_local_address for hostname [{0}]:\n{1}'.format(hostname, err))
IrodsError: Error encountered in hostname_resolves_to_local_address for hostname [syslab]:
/home/syslab/workspace_chc/irods/usr/sbin/hostname_resolves_to_local_address: error while loading shared libraries: libirods_common.so.4.3.0: cannot open shared object file: No such file or directory
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trel
commented on July 19, 2024
I've just tried to build 4-2-stable non-package-install.... and it almost worked.
4-2-stable irods/externals needed more spdlog1.50-1, but then when building the server, I saw this...
[ 89%] Generating lib/core/include/server_control_plane_command.hpp
/home/alice/externals/avro1.9.0-0/bin/avrogencpp: error while loading shared libraries: libc++abi.so.1: cannot open shared object file: No such file or directory
CMakeFiles/irodsServer.dir/build.make:61: recipe for target 'lib/core/include/server_control_plane_command.hpp' failed
make[3]: *** [lib/core/include/server_control_plane_command.hpp] Error 127
CMakeFiles/Makefile2:943: recipe for target 'CMakeFiles/irodsServer.dir/all' failed
make[2]: *** [CMakeFiles/irodsServer.dir/all] Error 2
CMakeFiles/Makefile2:264: recipe for target 'CMakeFiles/non-package-install-postgres.dir/rule' failed
make[1]: *** [CMakeFiles/non-package-install-postgres.dir/rule] Error 2
Makefile:212: recipe for target 'non-package-install-postgres' failed
make: *** [non-package-install-postgres] Error 2
So, it's not quite working as promised. We'll fix it up.
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xkdzml
commented on July 19, 2024
I think I've almost succeeded in iRODS, but I haven't solved this error now.
syslab@chu: ~/workspace_chu/install_irods/var/lib/irods$ python3 ./scripts/setup_irods.py < ./packaging/localhost_setup_postgres.input
Warning: Hostname `chu` should be a fully qualified domain name.
iRODS user [syslab]:
iRODS group [syslab]:
iRODS server's role:
1. provider
2. consumer
Please select a number or choose 0 to enter a new value [1]:
No default ODBC drivers configured for postgres; falling back to bare library paths:
Database server's hostname or IP address [localhost]:
Database server's port [5432]:
Database name [ICAT]:
Database username [irods]:
-------------------------------------------
Database Type: postgres
ODBC Driver:
Database Host: localhost
Database Port: 5432
Database Name: ICAT
Database User: irods
-------------------------------------------
Please confirm [yes]:
Warning: Cannot control echo output on the terminal (stdin is not a tty). Input may be echoed.
Error encountered running setup_irods:
Traceback (most recent call last):
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/database_connect.py", line 200, in get_database_connection
conn = pyodbc.connect(connection_string, ansi=True)
pyodbc.InterfaceError: ('IM002', '[IM002] [unixODBC][Driver Manager]Data source name not found, and no default driver specified (0) (SQLDriverConnect)')
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./scripts/setup_irods.py", line 445, in main
setup_server(irods_config,
File "./scripts/setup_irods.py", line 118, in setup_server
database_interface.setup_database_config(irods_config)
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/database_interface.py", line 176, in setup_database_config
if database_already_in_use_by_irods(irods_config):
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/database_interface.py", line 73, in database_already_in_use_by_irods
with contextlib.closing(database_connect.get_database_connection(irods_config)) as connection:
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/database_connect.py", line 232, in get_database_connection
six.reraise(IrodsError,
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/six.py", line 671, in reraise
raise value.with_traceback(tb)
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/database_connect.py", line 200, in get_database_connection
conn = pyodbc.connect(connection_string, ansi=True)
irods.exceptions.IrodsError: pyodbc encountered an error connecting to the database:
('IM002', '[IM002] [unixODBC][Driver Manager]Data source name not found, and no default driver specified (0) (SQLDriverConnect)')
What should I do to solve this problem?
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trel
commented on July 19, 2024
You used the default testing input file, which assumes a packaged installation.
If you've got a non-package-install, then you'll need to provide the correct location for your existing ODBC driver.
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xkdzml
commented on July 19, 2024
Thanks to you, I solved it.
But I saw another error.
syslab@chu:~/workspace_chu/install_irods/var/lib/irods$ python3 ./scripts/setup_irods.py < ./packaging/localhost_setup_postgres.input
Warning: Hostname `chu` should be a fully qualified domain name.
iRODS user [syslab]:
iRODS group [syslab]:
iRODS server's role:
1. provider
2. consumer
Please select a number or choose 0 to enter a new value [1]:
ODBC driver for postgres:
1. PostgreSQL ANSI
2. PostgreSQL Unicode
Please select a number or choose 0 to enter a new value [1]:
Database server's hostname or IP address [localhost]:
Database server's port [5432]:
Database name [ICAT]:
Database username [irods]:
-------------------------------------------
Database Type: postgres
ODBC Driver: PostgreSQL ANSI
Database Host: localhost
Database Port: 5432
Database Name: ICAT
Database User: irods
-------------------------------------------
Please confirm [yes]:
Warning: Cannot control echo output on the terminal (stdin is not a tty). Input may be echoed.
+-----------------------------------------------------+
| WARNING: |
| The database specified is an already-configured |
| iRODS database, so first-time database setup will |
| not be performed. Providing different inputs from |
| those provided the first time this script was run |
| will result in unspecified behavior, and may put |
| a previously working zone in a broken state. It's |
| recommended that you exit this script now if you |
| are running it manually. If you wish to wipe out |
| your current iRODS installation and associated data |
| catalog, drop the database and recreate it before |
| re-running this script. |
+-----------------------------------------------------+
Warning: Cannot control echo output on the terminal (stdin is not a tty). Input may be echoed.
iRODS server's zone name [tempZone]:
iRODS server's port [1247]:
iRODS port range (begin) [20000]:
iRODS port range (end) [20199]:
Control Plane port [1248]:
Schema Validation Base URI (or off) [file:///home/syslab/workspace_chu/install_irods/var/lib/irods/configuration_schemas]:
iRODS server's administrator username [rods]:
-------------------------------------------
Zone name: tempZone
iRODS server port: 1247
iRODS port range (begin): 20000
iRODS port range (end): 20199
Control plane port: 1248
Schema validation base URI: file:///home/syslab/workspace_chu/install_irods/var/lib/irods/configuration_schemas
iRODS server administrator: rods
-------------------------------------------
Please confirm [yes]:
Warning: Cannot control echo output on the terminal (stdin is not a tty). Input may be echoed.
Warning: Cannot control echo output on the terminal (stdin is not a tty). Input may be echoed.
Warning: Cannot control echo output on the terminal (stdin is not a tty). Input may be echoed.
Warning: Cannot control echo output on the terminal (stdin is not a tty). Input may be echoed.
iRODS Vault directory [/home/syslab/workspace_chu/install_irods/var/lib/irods/Vault]:
WARNING: Validation Failed for [/home/syslab/workspace_chu/install_irods/etc/irods/server_config.json]:
against [file:///home/syslab/workspace_chu/install_irods/var/lib/irods/configuration_schemas/v4/server_config.json]
RefResolutionError: unknown url type: 'host_access_control.json'
Warning encountered in json_validation for /home/syslab/workspace_chu/install_irods/etc/irods/server_config.json, skipping validation...
WARNING: Validation Failed for [/home/syslab/.irods/irods_environment.json]:
against [file:///home/syslab/workspace_chu/install_irods/var/lib/irods/configuration_schemas/v4/service_account_environment.json]
RefResolutionError: unknown url type: 'client_environment.json'
Warning encountered in json_validation for /home/syslab/.irods/irods_environment.json, skipping validation...
Warning encountered in validation:
Traceback (most recent call last):
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/controller.py", line 94, in start
self.config.validate_configuration()
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/configuration.py", line 280, in validate_configuration
raise IrodsWarning('%s\n%s' % (
irods.exceptions.IrodsWarning: Skipped validation for the following files:
/home/syslab/workspace_chu/install_irods/etc/irods/server_config.json
/home/syslab/.irods/irods_environment.json
Error encountered running setup_irods:
Traceback (most recent call last):
File "./scripts/setup_irods.py", line 445, in main
setup_server(irods_config,
File "./scripts/setup_irods.py", line 129, in setup_server
IrodsController(irods_config).start(test_mode=test_mode)
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/controller.py", line 197, in start
six.reraise(IrodsError, e, sys.exc_info()[2])
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/six.py", line 672, in reraise
raise value
File "/home/syslab/workspace_chu/install_irods/var/lib/irods/scripts/irods/controller.py", line 189, in start
raise IrodsError('iRODS server failed to start.')
irods.exceptions.IrodsError: iRODS server failed to start.
Can I know how to solve this problem?
And I wonder if I can set up a directory that stores data.
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trel
commented on July 19, 2024
The validation warnings, you can probably ignore for now.
However, the WARNING about an already configured database is very important. You need to make sure you don't have an existing installation that you're installing on top of. Make sure you clear out the database if you're trying to install for the first time. The installation script will not do that for you.
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alanking
commented on July 19, 2024
The warning shown at the end of the output regarding JSON schema validation
is already captured in an issue on Github:
irods/irods#6160
The server fails to start, probably, because of what Terrell mentioned. I
haven't seen the server fail to start due to the JSON schema validation
warnings.
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xkdzml
commented on July 19, 2024
I'm reinstalling the irods on ubuntu 20.04 now.
It is being installed referring to the irods document.
I have completed installation of externals, irods, irods_client_icommand, and cannot be installed due to errors in sudo python3 ./scripts/setup_irods.py < ./packaging/localhost_setup_postgres.input.
syslab@chu:/mnt/data/irods/var/lib/irods$ sudo python3 ./scripts/setup_irods.py < ./packaging/localhost_setup_postgres.input
Warning: Hostname `chu` should be a fully qualified domain name.
iRODS user [syslab]:
iRODS group [syslab]:
iRODS server's role:
1. provider
2. consumer
Please select a number or choose 0 to enter a new value [1]:
ODBC driver for postgres:
1. PostgreSQL ANSI
2. PostgreSQL Unicode
Please select a number or choose 0 to enter a new value [1]:
Database server's hostname or IP address [localhost]:
Database server's port [5432]:
Database name [ICAT]:
Database username [irods]:
-------------------------------------------
Database Type: postgres
ODBC Driver: PostgreSQL ANSI
Database Host: localhost
Database Port: 5432
Database Name: ICAT
Database User: irods
-------------------------------------------
Please confirm [yes]:
Warning: Cannot control echo output on the terminal (stdin is not a tty). Input may be echoed.
Error encountered running setup_irods:
Traceback (most recent call last):
File "/mnt/data/irods/var/lib/irods/scripts/irods/database_connect.py", line 200, in get_database_connection
conn = pyodbc.connect(connection_string, ansi=True)
pyodbc.OperationalError: ('08001', '[08001] could not connect to server: Connection refused\n\tIs the server running on host "localhost" (127.0.0.1) and accepting\n\tTCP/IP connections on port 5432?\n (101) (SQLDriverConnect)')
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./scripts/setup_irods.py", line 445, in main
setup_server(irods_config,
File "./scripts/setup_irods.py", line 118, in setup_server
database_interface.setup_database_config(irods_config) File "/mnt/data/irods/var/lib/irods/scripts/irods/database_interface.py", line 176, in setup_database_config
if database_already_in_use_by_irods(irods_config):
File "/mnt/data/irods/var/lib/irods/scripts/irods/database_interface.py", line 73, in database_already_in_use_by_irods
with contextlib.closing(database_connect.get_database_connection(irods_config)) as connection:
File "/mnt/data/irods/var/lib/irods/scripts/irods/database_connect.py", line 232, in get_database_connection
six.reraise(IrodsError,
File "/mnt/data/irods/var/lib/irods/scripts/irods/six.py", line 671, in reraise
raise value.with_traceback(tb)
File "/mnt/data/irods/var/lib/irods/scripts/irods/database_connect.py", line 200, in get_database_connection
conn = pyodbc.connect(connection_string, ansi=True)
irods.exceptions.IrodsError: pyodbc encountered an error connecting to the database:
('08001', '[08001] could not connect to server: Connection refused\n\tIs the server running on host "localhost" (127.0.0.1) and accepting\n\tTCP/IP connections on port 5432?\n (101) (SQLDriverConnect)')
How can I solve this problem?
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trel
commented on July 19, 2024
That error message says that the database is not listening/running on port 5432?
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trel
commented on July 19, 2024
Closing - no action needed here.
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