RE: accumulo.metadata table online but scans hang

[Nick Wise]

Thank you Mike!  It’s alive!!

I’ve got 5TB showing free now (which previously was spuriously showing as 
non-DFS used).  I’ll get trash enabled tomorrow now.

The touchz approach seems to have worked, and all tables and tablets are 
showing online.  I am able to access some data, so next steps are to find out 
where we need to reingest from.  Reingestion should be the easier approach for 
us, and I can live with duplicate data.

I realise this is an RTFM kind of question, but as a novice I’d like to be sure 
I’m taking the right next steps.  What’s the best way to check the integrity of 
the system, and look for further problems?  Are there integrity checking admin 
tools I should know about?

Thank you again, and also Dave and Ivan for helping us through this!

Nick


From: Michael Wall [mailto:mjw...@gmail.com]
Sent: 31 August 2017 14:08
To: user@accumulo.apache.org; d...@accumulo.apache.org
Subject: Re: accumulo.metadata table online but scans hang

Nick

First step to make sure you have plenty of HDFS space.  Seems like restarting 
fixed your du bug, so hopefully you are good there.  Consider turning on HDFS 
trash as well, it can be very useful for recovery.

Second step is to get your metadata table happy.  Try the touchz for the WAL 
logs and get to a point where you can at least scan the metadata from the shell.

Next step will be to recover data.  I see 2 options.  Dave already mentioned 
one, replay all your ingest from a point in time that was known good.  That is 
probably the best way to reduce data loss.  You could also try creating a new 
table and then bulk importing all the rfiles for a given table into that new 
table.  You would want to import all rfiles referenced by the metadata and all 
rfiles you find in HDFS for that table that aren't referenced.

Mike

On Thu, Aug 31, 2017 at 8:17 AM Nick Wise 
> 
wrote:
Thank you Dave.  I will try the touchz approach and see what happens.



From: Dave Marion [mailto:dlmar...@comcast.net]
Sent: 31 August 2017 13:12
To: user@accumulo.apache.org; Nick Wise 
>; 
d...@accumulo.apache.org

Subject: RE: accumulo.metadata table online but scans hang

I don't have any other options for you at this point. Seems like you have the 
necessary information to fixup the missing files and recover the system. You 
might be able to determine the timestamp of the first missing WAL file and 
replay data from that point.

> On August 31, 2017 at 5:51 AM Nick Wise 
> > 
> wrote:
>
>
>
> It does run as the accumulo user, but sadly still no trash. I'm told that 
> this is probably because we move a lot of files in and out of HDFS for 
> ingestion, and it's a space saving thing. In hindsight I'd rather have bought 
> more disks than have lost important files!
>
> I can't find any reference to deleting the WAL files in the gc logs, I do see 
> lots of lines like this around the time that things went wrong though:
>
> 2017-08-28 19:51:02,210 [gc.GarbageCollectWriteAheadLogs] INFO : Checking 
> replication table for 
> hdfs://master01:9000/user/accumulo/accumulo/wal/node08+9997/0007bea2-bf57-44ab-b2ca-a8a924c6b3c8
>
> And after logs like the above for all of the referenced WAL files, lines like 
> this:
>
> 2017-08-28 19:51:05,775 [gc.GarbageCollectWriteAheadLogs] INFO : 1822 
> replication entries scanned in 6.83 seconds
> 2017-08-28 19:51:05,780 [gc.GarbageCollectWriteAheadLogs] INFO : 0 total logs 
> removed from 1 servers in 6.83 seconds
> 2017-08-28 19:53:05,971 [impl.ThriftTransportPool] WARN : Thread "gc" stuck 
> on IO to master02: (0) for at least 120022 ms
>
> The only gc logging that happens after this point is startup properties print 
> outs. No further operational log messages come out.
>
> In terms of creating an empty table, when trying to do this it just hangs. I 
> assume this is because the metadata table is not working.
>
> root@instance> createtable emptytable
> 2017-08-31 10:43:57,315 [impl.ThriftTransportPool] WARN : Thread "shell" 
> stuck on IO to master01: (0) for at least 120029 ms
>
> Are tables instance specific, or is it possible to get an empty rfile from 
> any instance? I don't suppose someone has such a file I could have..?!
>
> I believe it was Ivan who recommended using touchz to create an empty file in 
> place of the missing WALs, I'm assuming from the procedure to create an empty 
> table that this isn't the right thing to do, so I will hold off doing that 
> unless someone can confirm it is good enough.
>
> Thank you again for your help!
>
>
>
>
>
> -Original Message-
> From: dlmar...@comcast.net 
> [mailto:dlmar...@comcast.net]
> Sent: 31 August 2017 00:07
> To: 

Re: accumulo.metadata table online but scans hang

[Michael Wall]

Nick

First step to make sure you have plenty of HDFS space.  Seems like
restarting fixed your du bug, so hopefully you are good there.  Consider
turning on HDFS trash as well, it can be very useful for recovery.

Second step is to get your metadata table happy.  Try the touchz for the
WAL logs and get to a point where you can at least scan the metadata from
the shell.

Next step will be to recover data.  I see 2 options.  Dave already
mentioned one, replay all your ingest from a point in time that was known
good.  That is probably the best way to reduce data loss.  You could also
try creating a new table and then bulk importing all the rfiles for a given
table into that new table.  You would want to import all rfiles referenced
by the metadata and all rfiles you find in HDFS for that table that aren't
referenced.

Mike

On Thu, Aug 31, 2017 at 8:17 AM Nick Wise 
wrote:

> Thank you Dave.  I will try the touchz approach and see what happens.
>
>
>
>
>
>
>
> *From:* Dave Marion [mailto:dlmar...@comcast.net]
> *Sent:* 31 August 2017 13:12
> *To:* user@accumulo.apache.org; Nick Wise <
> nicholas.w...@sa.catapult.org.uk>; d...@accumulo.apache.org
>
>
> *Subject:* RE: accumulo.metadata table online but scans hang
>
>
>
> I don't have any other options for you at this point. Seems like you have
> the necessary information to fixup the missing files and recover the
> system. You might be able to determine the timestamp of the first missing
> WAL file and replay data from that point.
>
> > On August 31, 2017 at 5:51 AM Nick Wise <
> nicholas.w...@sa.catapult.org.uk> wrote:
> >
> >
> >
> > It does run as the accumulo user, but sadly still no trash. I'm told
> that this is probably because we move a lot of files in and out of HDFS for
> ingestion, and it's a space saving thing. In hindsight I'd rather have
> bought more disks than have lost important files!
> >
> > I can't find any reference to deleting the WAL files in the gc logs, I
> do see lots of lines like this around the time that things went wrong
> though:
> >
> > 2017-08-28 19:51:02,210 [gc.GarbageCollectWriteAheadLogs] INFO :
> Checking replication table for
> hdfs://master01:9000/user/accumulo/accumulo/wal/node08+9997/0007bea2-bf57-44ab-b2ca-a8a924c6b3c8
> >
> > And after logs like the above for all of the referenced WAL files, lines
> like this:
> >
> > 2017-08-28 19:51:05,775 [gc.GarbageCollectWriteAheadLogs] INFO : 1822
> replication entries scanned in 6.83 seconds
> > 2017-08-28 19:51:05,780 [gc.GarbageCollectWriteAheadLogs] INFO : 0 total
> logs removed from 1 servers in 6.83 seconds
> > 2017-08-28 19:53:05,971 [impl.ThriftTransportPool] WARN : Thread "gc"
> stuck on IO to master02: (0) for at least 120022 ms
> >
> > The only gc logging that happens after this point is startup properties
> print outs. No further operational log messages come out.
> >
> > In terms of creating an empty table, when trying to do this it just
> hangs. I assume this is because the metadata table is not working.
> >
> > root@instance> createtable emptytable
> > 2017-08-31 10:43:57,315 [impl.ThriftTransportPool] WARN : Thread "shell"
> stuck on IO to master01: (0) for at least 120029 ms
> >
> > Are tables instance specific, or is it possible to get an empty rfile
> from any instance? I don't suppose someone has such a file I could have..?!
> >
> > I believe it was Ivan who recommended using touchz to create an empty
> file in place of the missing WALs, I'm assuming from the procedure to
> create an empty table that this isn't the right thing to do, so I will hold
> off doing that unless someone can confirm it is good enough.
> >
> > Thank you again for your help!
> >
> >
> >
> >
> >
> > -Original Message-
> > From: dlmar...@comcast.net [mailto:dlmar...@comcast.net
> ]
> > Sent: 31 August 2017 00:07
> > To: user@accumulo.apache.org; d...@accumulo.apache.org
> > Subject: RE: accumulo.metadata table online but scans hang
> >
> > Re #2: Does your Accumulo processes run as the hdfs user on the O/S, or
> as the accumulo user? Make sure you are checking the correct users trash
> folder. Also, check the Accumulo garbage collector log to see if the GC
> process deleted the WAL files. Take a look at [1] to see if you are hitting
> this case.
> >
> > You can create empty rfiles and copy them into place. I believe the
> procedure to do this is to create an empty table and run a compaction on
> the table. Then you should be able to copy the resulting file into the
> desired locations (devs - please correct me here if this is not correct).
> >
> > Finally, I would not do anything destructive yet. Let's see if we can
> get some other devs to chime in with some ideas.
> >
> > [1] https://issues.apache.org/jira/browse/ACCUMULO-4157
> >
> >
> > -Original Message-
> > From: Nick Wise [mailto:nicholas.w...@sa.catapult.org.uk
> ]
> > Sent: Wednesday, August 30, 2017 5:36 PM
> > To: 

RE: accumulo.metadata table online but scans hang

[Nick Wise]

Thank you Dave.  I will try the touchz approach and see what happens.



From: Dave Marion [mailto:dlmar...@comcast.net]
Sent: 31 August 2017 13:12
To: user@accumulo.apache.org; Nick Wise ; 
d...@accumulo.apache.org
Subject: RE: accumulo.metadata table online but scans hang

I don't have any other options for you at this point. Seems like you have the 
necessary information to fixup the missing files and recover the system. You 
might be able to determine the timestamp of the first missing WAL file and 
replay data from that point.

> On August 31, 2017 at 5:51 AM Nick Wise 
> > 
> wrote:
>
>
>
> It does run as the accumulo user, but sadly still no trash. I'm told that 
> this is probably because we move a lot of files in and out of HDFS for 
> ingestion, and it's a space saving thing. In hindsight I'd rather have bought 
> more disks than have lost important files!
>
> I can't find any reference to deleting the WAL files in the gc logs, I do see 
> lots of lines like this around the time that things went wrong though:
>
> 2017-08-28 19:51:02,210 [gc.GarbageCollectWriteAheadLogs] INFO : Checking 
> replication table for 
> hdfs://master01:9000/user/accumulo/accumulo/wal/node08+9997/0007bea2-bf57-44ab-b2ca-a8a924c6b3c8
>
> And after logs like the above for all of the referenced WAL files, lines like 
> this:
>
> 2017-08-28 19:51:05,775 [gc.GarbageCollectWriteAheadLogs] INFO : 1822 
> replication entries scanned in 6.83 seconds
> 2017-08-28 19:51:05,780 [gc.GarbageCollectWriteAheadLogs] INFO : 0 total logs 
> removed from 1 servers in 6.83 seconds
> 2017-08-28 19:53:05,971 [impl.ThriftTransportPool] WARN : Thread "gc" stuck 
> on IO to master02: (0) for at least 120022 ms
>
> The only gc logging that happens after this point is startup properties print 
> outs. No further operational log messages come out.
>
> In terms of creating an empty table, when trying to do this it just hangs. I 
> assume this is because the metadata table is not working.
>
> root@instance> createtable emptytable
> 2017-08-31 10:43:57,315 [impl.ThriftTransportPool] WARN : Thread "shell" 
> stuck on IO to master01: (0) for at least 120029 ms
>
> Are tables instance specific, or is it possible to get an empty rfile from 
> any instance? I don't suppose someone has such a file I could have..?!
>
> I believe it was Ivan who recommended using touchz to create an empty file in 
> place of the missing WALs, I'm assuming from the procedure to create an empty 
> table that this isn't the right thing to do, so I will hold off doing that 
> unless someone can confirm it is good enough.
>
> Thank you again for your help!
>
>
>
>
>
> -Original Message-
> From: dlmar...@comcast.net 
> [mailto:dlmar...@comcast.net]
> Sent: 31 August 2017 00:07
> To: user@accumulo.apache.org; 
> d...@accumulo.apache.org
> Subject: RE: accumulo.metadata table online but scans hang
>
> Re #2: Does your Accumulo processes run as the hdfs user on the O/S, or as 
> the accumulo user? Make sure you are checking the correct users trash folder. 
> Also, check the Accumulo garbage collector log to see if the GC process 
> deleted the WAL files. Take a look at [1] to see if you are hitting this case.
>
> You can create empty rfiles and copy them into place. I believe the procedure 
> to do this is to create an empty table and run a compaction on the table. 
> Then you should be able to copy the resulting file into the desired locations 
> (devs - please correct me here if this is not correct).
>
> Finally, I would not do anything destructive yet. Let's see if we can get 
> some other devs to chime in with some ideas.
>
> [1] https://issues.apache.org/jira/browse/ACCUMULO-4157
>
>
> -Original Message-
> From: Nick Wise [mailto:nicholas.w...@sa.catapult.org.uk]
> Sent: Wednesday, August 30, 2017 5:36 PM
> To: user@accumulo.apache.org
> Subject: RE: accumulo.metadata table online but scans hang
>
>
> Thank you very much for the pointers Dave. Looking at those:
>
> 1. That seems reasonable, I’m not sure how to check after the fact but makes 
> sense.
> 2. Ah. Looks like we don’t have trash enabled, there’s no /user/hdfs/.Trash 
> folder that I can see. I’m getting a sinking feeling… 3. I had to allocate 4G 
> but that worked and now I have a folder listing of 758k files. I’ve cross 
> referenced with the 1101 WAL files referred to in our logs and not a single 
> one exists. Sinking some more.
>
> So, it sounds like (speaking from a position of ignorance) that we have a 
> system where accumulo.metadata has outstanding WAL files to recover, but the 
> files don't exist, but the only way to restore the system is to convince the 
> metadata table that it doesn't need the WAL files, but to edit the metadata 
> table we have to 

RE: accumulo.metadata table online but scans hang

[Dave Marion]

I don't have any other options for you at this point. Seems like you have the 
necessary information to fixup the missing files and recover the system. You 
might be able to determine the timestamp of the first missing WAL file and 
replay data from that point.

> On August 31, 2017 at 5:51 AM Nick Wise  
> wrote:
>
>
>
> It does run as the accumulo user, but sadly still no trash. I'm told that 
> this is probably because we move a lot of files in and out of HDFS for 
> ingestion, and it's a space saving thing. In hindsight I'd rather have bought 
> more disks than have lost important files!
>
> I can't find any reference to deleting the WAL files in the gc logs, I do see 
> lots of lines like this around the time that things went wrong though:
>
> 2017-08-28 19:51:02,210 [gc.GarbageCollectWriteAheadLogs] INFO : Checking 
> replication table for 
> hdfs://master01:9000/user/accumulo/accumulo/wal/node08+9997/0007bea2-bf57-44ab-b2ca-a8a924c6b3c8
>
> And after logs like the above for all of the referenced WAL files, lines like 
> this:
>
> 2017-08-28 19:51:05,775 [gc.GarbageCollectWriteAheadLogs] INFO : 1822 
> replication entries scanned in 6.83 seconds
> 2017-08-28 19:51:05,780 [gc.GarbageCollectWriteAheadLogs] INFO : 0 total logs 
> removed from 1 servers in 6.83 seconds
> 2017-08-28 19:53:05,971 [impl.ThriftTransportPool] WARN : Thread "gc" stuck 
> on IO to master02: (0) for at least 120022 ms
>
> The only gc logging that happens after this point is startup properties print 
> outs. No further operational log messages come out.
>
> In terms of creating an empty table, when trying to do this it just hangs. I 
> assume this is because the metadata table is not working.
>
> root@instance> createtable emptytable
> 2017-08-31 10:43:57,315 [impl.ThriftTransportPool] WARN : Thread "shell" 
> stuck on IO to master01: (0) for at least 120029 ms
>
> Are tables instance specific, or is it possible to get an empty rfile from 
> any instance? I don't suppose someone has such a file I could have..?!
>
> I believe it was Ivan who recommended using touchz to create an empty file in 
> place of the missing WALs, I'm assuming from the procedure to create an empty 
> table that this isn't the right thing to do, so I will hold off doing that 
> unless someone can confirm it is good enough.
>
> Thank you again for your help!
>
>
>
>
>
> -Original Message-
> From: dlmar...@comcast.net [mailto:dlmar...@comcast.net]
> Sent: 31 August 2017 00:07
> To: user@accumulo.apache.org; d...@accumulo.apache.org
> Subject: RE: accumulo.metadata table online but scans hang
>
> Re #2: Does your Accumulo processes run as the hdfs user on the O/S, or as 
> the accumulo user? Make sure you are checking the correct users trash folder. 
> Also, check the Accumulo garbage collector log to see if the GC process 
> deleted the WAL files. Take a look at [1] to see if you are hitting this case.
>
> You can create empty rfiles and copy them into place. I believe the procedure 
> to do this is to create an empty table and run a compaction on the table. 
> Then you should be able to copy the resulting file into the desired locations 
> (devs - please correct me here if this is not correct).
>
> Finally, I would not do anything destructive yet. Let's see if we can get 
> some other devs to chime in with some ideas.
>
> [1] https://issues.apache.org/jira/browse/ACCUMULO-4157
>
>
> -Original Message-
> From: Nick Wise [mailto:nicholas.w...@sa.catapult.org.uk]
> Sent: Wednesday, August 30, 2017 5:36 PM
> To: user@accumulo.apache.org
> Subject: RE: accumulo.metadata table online but scans hang
>
>
> Thank you very much for the pointers Dave. Looking at those:
>
> 1. That seems reasonable, I’m not sure how to check after the fact but makes 
> sense.
> 2. Ah. Looks like we don’t have trash enabled, there’s no /user/hdfs/.Trash 
> folder that I can see. I’m getting a sinking feeling… 3. I had to allocate 4G 
> but that worked and now I have a folder listing of 758k files. I’ve cross 
> referenced with the 1101 WAL files referred to in our logs and not a single 
> one exists. Sinking some more.
>
> So, it sounds like (speaking from a position of ignorance) that we have a 
> system where accumulo.metadata has outstanding WAL files to recover, but the 
> files don't exist, but the only way to restore the system is to convince the 
> metadata table that it doesn't need the WAL files, but to edit the metadata 
> table we have to resolve the outstanding WAL files, etc.
>
> What would happen if we created an empty file in place of the missing WAL 
> files? Would they be considered to be an invalid format and break things more 
> (I'm not sure that's possible), or might they be accepted as needing no 
> further resolution?
>
> Any other thoughts (anyone) on how we might save ourselves, besides starting 
> from scratch? (When we first loaded our 16TB of data it took 6 weeks using 
> the map/reduce method!)
>
> 

RE: accumulo.metadata table online but scans hang

[Nick Wise]

It does run as the accumulo user, but sadly still no trash.  I'm told that this 
is probably because we move a lot of files in and out of HDFS for ingestion, 
and it's a space saving thing.  In hindsight I'd rather have bought more disks 
than have lost important files!

I can't find any reference to deleting the WAL files in the gc logs, I do see 
lots of lines like this around the time that things went wrong though:

2017-08-28 19:51:02,210 [gc.GarbageCollectWriteAheadLogs] INFO : Checking 
replication table for 
hdfs://master01:9000/user/accumulo/accumulo/wal/node08+9997/0007bea2-bf57-44ab-b2ca-a8a924c6b3c8

And after logs like the above for all of the referenced WAL files, lines like 
this:

2017-08-28 19:51:05,775 [gc.GarbageCollectWriteAheadLogs] INFO : 1822 
replication entries scanned in 6.83 seconds
2017-08-28 19:51:05,780 [gc.GarbageCollectWriteAheadLogs] INFO : 0 total logs 
removed from 1 servers in 6.83 seconds
2017-08-28 19:53:05,971 [impl.ThriftTransportPool] WARN : Thread "gc" stuck on 
IO to master02: (0) for at least 120022 ms

The only gc logging that happens after this point is startup properties print 
outs.  No further operational log messages come out.

In terms of creating an empty table, when trying to do this it just hangs.  I 
assume this is because the metadata table is not working.

root@instance> createtable emptytable
2017-08-31 10:43:57,315 [impl.ThriftTransportPool] WARN : Thread "shell" stuck 
on IO to master01: (0) for at least 120029 ms

Are tables instance specific, or is it possible to get an empty rfile from any 
instance?  I don't suppose someone has such a file I could have..?!

I believe it was Ivan who recommended using touchz to create an empty file in 
place of the missing WALs, I'm assuming from the procedure to create an empty 
table that this isn't the right thing to do, so I will hold off doing that 
unless someone can confirm it is good enough.

Thank you again for your help!





-Original Message-
From: dlmar...@comcast.net [mailto:dlmar...@comcast.net]
Sent: 31 August 2017 00:07
To: user@accumulo.apache.org; d...@accumulo.apache.org
Subject: RE: accumulo.metadata table online but scans hang

Re #2: Does your Accumulo processes run as the hdfs user on the O/S, or as the 
accumulo user? Make sure you are checking the correct users trash folder. Also, 
check the Accumulo garbage collector log to see if the GC process deleted the 
WAL files. Take a look at [1] to see if you are hitting this case.

You can create empty rfiles and copy them into place. I believe the procedure 
to do this is to create an empty table and run a compaction on the table. Then 
you should be able to copy the resulting file into the desired locations (devs 
- please correct me here if this is not correct).

Finally, I would not do anything destructive yet. Let's see if we can get some 
other devs to chime in with some ideas.

[1] https://issues.apache.org/jira/browse/ACCUMULO-4157


-Original Message-
From: Nick Wise [mailto:nicholas.w...@sa.catapult.org.uk]
Sent: Wednesday, August 30, 2017 5:36 PM
To: user@accumulo.apache.org
Subject: RE: accumulo.metadata table online but scans hang


Thank you very much for the pointers Dave.  Looking at those:

1. That seems reasonable, I’m not sure how to check after the fact but makes 
sense.
2. Ah.  Looks like we don’t have trash enabled, there’s no /user/hdfs/.Trash 
folder that I can see.  I’m getting a sinking feeling… 3. I had to allocate 4G 
but that worked and now I have a folder listing of 758k files.  I’ve cross 
referenced with the 1101 WAL files referred to in our logs and not a single one 
exists. Sinking some more.

So, it sounds like (speaking from a position of ignorance) that we have a 
system where accumulo.metadata has outstanding WAL files to recover, but the 
files don't exist, but the only way to restore the system is to convince the 
metadata table that it doesn't need the WAL files, but to edit the metadata 
table we have to resolve the outstanding WAL files, etc.

What would happen if we created an empty file in place of the missing WAL 
files?  Would they be considered to be an invalid format and break things more 
(I'm not sure that's possible), or might they be accepted as needing no further 
resolution?

Any other thoughts (anyone) on how we might save ourselves, besides starting 
from scratch?  (When we first loaded our 16TB of data it took 6 weeks using the 
map/reduce method!)

Thank you again!

Nick



From: Dave Marion [mailto:dlmar...@comcast.net]
Sent: 30 August 2017 20:13
To: user@accumulo.apache.org; Nick Wise 
Subject: Re: accumulo.metadata table online but scans hang

Some immediate thoughts:

1. Regarding node08 having so many files, maybe it was the last DN that had 
free space?
2. Look in the trash folder for the missing referenced WAL files 3. For you 
OOME using the HDFS CLI, I think you can increase the amount of memory that the 
client will