How to delete the files that aren't transferred properly

[Sanju Timsina]

Hello,

How do I delete the file config.json that isn't registered completely.

 stimsina          0 workResc;arcres01Work            0 2022-05-04.16:43 ? config.json

Thank you,

Sanju

[Alan King]

Hi,

The ? indicates an intermediate status - the data transfer is still in progress, or so supposes the system.

Please confirm that the iRODS agent performing this transfer is dead. If not, you can kill the process and it should mark the replica status as stale.

If the process is already dead/gone, this is a bug! Please describe how you got into this situation so that we can capture it in an issue and fix it.

In the meantime, you can try this Troubleshooting tip: https://docs.irods.org/4.2.11/system_overview/troubleshooting/#data-object-stuck-in-locked-or-intermediate-status

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Alan King

Senior Software Developer | iRODS Consortium

[Sanju Timsina]

Hi Alan,

When I am trying to modify the replica, I am getting the following error

rcModDataObjMeta failed when modifying replica: [CAT_SQL_ERR (-806000)]

This is the command I ran

 iadmin modrepl logical_path "/arctic/work/stimsina/config.json"  replica_number 0  DATA_REPL_STATUS good

Thank you,

Sanju

On Friday, May 6, 2022 at 1:00:13 PM UTC-4 Sanju Timsina wrote:

Hi Alan,

These are for the files while we are transferring from Globus. We are getting these logs on the icat server.

May  6 12:47:55 pid:172473 remote addresses: 10.245.11.176, 10.245.14.25 ERROR: [rsDataObjOpen_impl:907] - [HIERARCHY_ERROR: no valid resource found for data object

] [error_code=[-1803000], path=[/arctic/work/gchowell/Fitting Multi-Model Ensemble MLE flexible Mar 2021 light_v2/rolling_window_subepidemicFrameworkCoronavirusStatesUS.m], hierarchy=[]

May  6 12:47:55 pid:172473 remote addresses: 10.245.11.176, 10.245.14.25 ERROR: [rsDataObjOpen_impl:907] - [HIERARCHY_ERROR: no valid resource found for data object

] [error_code=[-1803000], path=[/arctic/work/gchowell/Fitting Multi-Model Ensemble MLE flexible Mar 2021 light_v2/rolling_window_subepidemicFrameworkCoronavirusStatesUS.m], hierarchy=[]

May  6 12:47:55 pid:172473 remote addresses: 10.245.11.176, 10.245.14.25 ERROR: [rsDataObjOpen_impl:907] - [HIERARCHY_ERROR: no valid resource found for data object

10.245.11.176 is the database server 

 10.245.14.25 is the globus server.

Also, we are getting SSL error on the icat and resource server. The below is the log of icat server

May  6 12:54:15 pid:163088 remote addresses: 10.245.11.176, 10.245.11.82 ERROR: [-]     /repos/irods/server/core/src/rsApiHandler.cpp:542:int readAndProcClientMsg(rsComm_t *, int) :  status [SYS_HEADER_READ_LEN_ERR]  errno [] -- message [failed to call 'read header']

        [-]     /repos/irods/lib/core/src/sockComm.cpp:198:irods::error readMsgHeader(irods::network_object_ptr, msgHeader_t *, struct timeval *) :  status [SYS_HEADER_READ_LEN_ERR]  errno [] -- message [failed to call 'read header']

                [-]     /repos/irods/plugins/network/ssl/libssl.cpp:572:irods::error ssl_read_msg_header(irods::plugin_context &, void *, struct timeval *) :  status [SYS_HEADER_READ_LEN_ERR]  errno [] -- message [read 0 expected 4]

May  6 12:54:15 pid:163484 remote addresses: 10.245.11.176, 10.245.11.82 ERROR: [-]     /repos/irods/server/core/src/rsApiHandler.cpp:542:int readAndProcClientMsg(rsComm_t *, int) :  status [SYS_HEADER_READ_LEN_ERR]  errno [] -- message [failed to call 'read header']

        [-]     /repos/irods/lib/core/src/sockComm.cpp:198:irods::error readMsgHeader(irods::network_object_ptr, msgHeader_t *, struct timeval *) :  status [SYS_HEADER_READ_LEN_ERR]  errno [] -- message [failed to call 'read header']

                [-]     /repos/irods/plugins/network/ssl/libssl.cpp:572:irods::error ssl_read_msg_header(irods::plugin_context &, void *, struct timeval *) :  status [SYS_HEADER_READ_LEN_ERR]  errno [] -- message [read 0 expected 4]

May  6 12:54:15 pid:163480 remote addresses: 10.245.11.176, 10.245.11.82 ERROR: readAndProcClientMsg:readMsgHeader error. status = -4000 status = 0 Unknown iRODS error

May  6 12:54:15 pid:163489 remote addresses: 10.245.11.176, 10.245.11.82 ERROR: readAndProcClientMsg:readMsgHeader error. status = -111 status = 0 Unknown iRODS error

May  6 12:54:15 pid:163079 remote addresses: 10.245.11.176, 10.245.11.82 ERROR: readAndProcClientMsg:readMsgHeader error. status = -4000 status = 0 Unknown iRODS error

May  6 12:54:15 pid:163088 remote addresses: 10.245.11.176, 10.245.11.82 ERROR: [-]     /repos/irods/server/core/src/rodsAgent.cpp:566:int runIrodsAgentFactory(sockaddr_un) :  status [SSL_SHUTDOWN_ERROR]  errno [] -- message [failed to call 'agent stop']

        [-]     /repos/irods/lib/core/src/sockComm.cpp:160:irods::error sockAgentStop(irods::network_object_ptr) :  status [SSL_SHUTDOWN_ERROR]  errno [] -- message [failed to call 'agent stop']

                [-]     /repos/irods/plugins/network/ssl/libssl.cpp:952:irods::error ssl_agent_stop(irods::plugin_context &) :  status [SSL_SHUTDOWN_ERROR]  errno [] -- message [error completing shutdown of SSL connection]

May  6 12:54:15 pid:163480 remote addresses: 10.245.11.176, 10.245.11.82 ERROR: readAndProcClientMsg:readMsgHeader error. status = -4000 status = 0 Unknown iRODS error

Thank you,

Sanju

[Alan King]

Ah, that did reveal the problem. Thanks for sharing the extra information!

I've created an issue for this bug with an explanation for what I think happened: https://github.com/irods/irods/issues/6378

This should be fixed in 4.2.12/4.3.0.

As for the modrepl error, you actually need to use an integer to set the replica status. So if you want the status to be "good", you should use the value 1. Here are the statuses as they relate to the values in the catalog:

0 - stale

1 - good

2 - intermediate

3 - read-locked (not yet implemented)

4 - write-locked

To view this discussion on the web visit https://groups.google.com/d/msgid/irod-chat/d704b2eb-7e81-45be-97f0-2e3faa7ec814n%40googlegroups.com.

[Sanju Timsina]

Hi Alan,

What is the best way to resolve this issue? 

I am trying to transfer these files from Globus. And the logs are showing this error.

NOTICE: remoteFileCreate: rcFileCreate failed for /work/work/stimsina/config.json

ERROR: [chkAndHandleOrphanFile:643] - [/work/work/stimsina/config.json] is not an orphan file...replStatus:[2]

 ERROR: [chkAndHandleOrphanFile:661] - [/work/work/stimsina/config.json] got a new file path:[/work/replica/work/stimsina/config.json.2354633320]

Thank you,

Sanju