New: NFS client has inconsistent write flushing to non-linux serversa
Subsystems (2)
(switched to email. Please respond via emailed reply-to-all, not via the bugzilla web interface).
Quoted 53 lines · On Thu, 28 Aug 2008 11:41:08 -0700 (PDT)…
http://bugzilla.kernel.org/show_bug.cgi?id=11448
Summary: NFS client has inconsistent write flushing to non-linux
serversa
Product: File System
Version: 2.5
KernelVersion: 2.6.22.15
Platform: All
OS/Version: Linux
Tree: Mainline
Status: NEW
Severity: normal
Priority: P1
Component: NFS
AssignedTo: [email protected]
ReportedBy: [email protected]Latest working kernel version: N/A (works on 2.6.18 with Linux NFS server, but we cannot continue to use that kernel for various reasons) Earliest failing kernel version: N/A (2.6.18, 2.6.24, and 2.6.25 are also known to fail by another party experiencing same bug against non-Linux NFS servers). Not currently known to be reproducible against NetApp, but this is not authoritative (lack of seeing a bug does not guarantee lack of existence)
Distribution: CentOS 4.6
Hardware Environment: supermicro twin, 2 quad core Harpertown CPU, 16G ram. Software Environment: CentOS 4.6
Problem Description:NFS client writes to Sun Solaris 10 U4 server.
at some point in time, there is an empty portion of the output file from the writer containing missing data (shows as NULL bytes from another NFS client issuing a tail -f on the file being written).
confirmed that the file as exists on the NFS server is sparse, missing bytes (not necessarily multiple of 512 or 1024, one sample is a gap of 3818 bytes, another is 1895 bytes, another is 423 bytes)if you do a read of the entire file from the NFS client doing the writing, it causes the non-flushed writes to be instantly flushed to the server followed by a NFS3 commit operation. The data then can be seen on all other NFS clients.
If you do an open of the file alone, no flush
if you do an open and a close, no flush
if you do an open and a read at the beginning of the file (far before the data that is outstanding), *usually* no flush (one case where it did). If you do a read at another position in the file, no flush (other than as indicated above).
If you do a read at the indicated offset where the bytes are null, it causes the NFS client to write and NFS commit to the server (truss output available)The missing blocks may flush themselves after undefined periods of time which can be hours. Our runs last days.
Quoted 8 lines
Steps to reproduce:
Chemist running NAMD sees frequent cases of this in his output trajectory index files. We don't have an exact sequence of steps to reproduce. After I file this ticket I will be giving ticket number to another person I know at a different company experiencing the same problem as described above (to the best of my knowledge)
That seems rather ugly.
2.6.22 is getting a bit old though. It's quite possible that this was subsequently fixed, in which case upgrading your kernel or hassling the vendor to backport the fix would be needed.
Quoted 68 lines · Andrew Morton
(switched to email. Please respond via emailed reply-to-all, not via the bugzilla web interface).
Quoted 51 lines · On Thu, 28 Aug 2008 11:41:08 -0700 (PDT)…
http://bugzilla.kernel.org/show_bug.cgi?id=11448
Summary: NFS client has inconsistent write flushing to non-linux
serversa
Product: File System
Version: 2.5
KernelVersion: 2.6.22.15
Platform: All
OS/Version: Linux
Tree: Mainline
Status: NEW
Severity: normal
Priority: P1
Component: NFS
AssignedTo: [email protected]
ReportedBy: [email protected]Latest working kernel version: N/A (works on 2.6.18 with Linux NFS server, but we cannot continue to use that kernel for various reasons) Earliest failing kernel version: N/A (2.6.18, 2.6.24, and 2.6.25 are also known to fail by another party experiencing same bug against non-Linux NFS servers). Not currently known to be reproducible against NetApp, but this is not authoritative (lack of seeing a bug does not guarantee lack of existence)
Distribution: CentOS 4.6
Hardware Environment: supermicro twin, 2 quad core Harpertown CPU, 16G ram. Software Environment: CentOS 4.6
Problem Description:NFS client writes to Sun Solaris 10 U4 server. at some point in time, there is an empty portion of the output file from the writer containing missing data (shows as NULL bytes from another NFS client
issuing a tail -f on the file being written). confirmed that the file as exists on the NFS server is sparse, missing bytes (not necessarily multiple of 512 or 1024, one sample is a gap of 3818 bytes,
another is 1895 bytes, another is 423 bytes)if you do a read of the entire file from the NFS client doing the writing, it causes the non-flushed writes to be instantly flushed to the server followed by a NFS3 commit operation. The data then can be seen on all other NFS clients.
If you do an open of the file alone, no flush
if you do an open and a close, no flush
if you do an open and a read at the beginning of the file (far before the data that is outstanding), *usually* no flush (one case where it did). If you do a read at another position in the file, no flush (other than as indicated above).
If you do a read at the indicated offset where the bytes are null, it causes the NFS client to write and NFS commit to the server (truss output available)The missing blocks may flush themselves after undefined periods of time which can be hours. Our runs last days.
Quoted 9 lines
Steps to reproduce:
Chemist running NAMD sees frequent cases of this in his output trajectory index files. We don't have an exact sequence of steps to reproduce. After I file this ticket I will be giving ticket number to another person I know at a different company experiencing the same problem as described above (to the best of my knowledge)
Quoted 6 lines
That seems rather ugly.
2.6.22 is getting a bit old though. It's quite possible that this was subsequently fixed, in which case upgrading your kernel or hassling the vendor to backport the fix would be needed.
I am in the process of trying to duplicate this on 2.6.26.. I need the chemist to change his machine. (it's a kernel.org kernel for reasons of IB support, so no vendor to hassle). There is another party to this bug who seems to have the same symptoms in 2.6.25 who is trying to capture packet data and reproduce.
confirmed that this bug is present in same way in 2.6.26 using default ASYNC NFS, but so far does not exhibit when sync mount option is used.
Quoted 13 lines · Andrew Morton
(switched to email. Please respond via emailed reply-to-all, not via the bugzilla web interface).
Quoted 7 lines · On Thu, 28 Aug 2008 11:41:08 -0700 (PDT)…
NFS client writes to Sun Solaris 10 U4 server.
at some point in time, there is an empty portion of the output file from the writer containing missing data (shows as NULL bytes from another NFS client issuing a tail -f on the file being written).
confirmed that the file as exists on the NFS server is sparse, missing bytes (not necessarily multiple of 512 or 1024, one sample is a gap of 3818 bytes, another is 1895 bytes, another is 423 bytes)
Seems like something that could happen if for example two write rpc's got reordered on the network. That's not necessarily a bug--the nfs client isn't required to wait for confirmation of every previous write before sending the next one.
However if the client isn't flushing dirty data to the server before returning from close, then that's a violation of NFS's close-to-open semantics:...
Quoted 7 lines
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if you do a read of the entire file from the NFS client doing the writing, it causes the non-flushed writes to be instantly flushed to the server followed by a NFS3 commit operation. The data then can be seen on all other NFS clients.
If you do an open of the file alone, no flush
if you do an open and a close, no flush
... so this "close, no flush" could be a bug (depending on who is doing that close when--I don't completely understand the described situation).
--b.
Quoted 29 lines · J. Bruce Fields
Quoted 12 lines · Andrew Morton
(switched to email. Please respond via emailed reply-to-all, not via the bugzilla web interface).
Quoted 6 lines · On Thu, 28 Aug 2008 11:41:08 -0700 (PDT)…
NFS client writes to Sun Solaris 10 U4 server. at some point in time, there is an empty portion of the output file from the writer containing missing data (shows as NULL bytes from another NFS client
issuing a tail -f on the file being written). confirmed that the file as exists on the NFS server is sparse, missing bytes (not necessarily multiple of 512 or 1024, one sample is a gap of 3818 bytes,
another is 1895 bytes, another is 423 bytes)Seems like something that could happen if for example two write rpc's got reordered on the network. That's not necessarily a bug--the nfs client isn't required to wait for confirmation of every previous write before sending the next one.
However if the client isn't flushing dirty data to the server before returning from close, then that's a violation of NFS's close-to-open semantics:...
Quoted 4 lines
Quoted 4 lines
if you do a read of the entire file from the NFS client doing the writing, it causes the non-flushed writes to be instantly flushed to the server followed by a NFS3 commit operation. The data then can be seen on all other NFS clients.
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If you do an open of the file alone, no flush
if you do an open and a close, no flush... so this "close, no flush" could be a bug (depending on who is doing that close when--I don't completely understand the described situation).
I suspect that this last might depend upon 1) what options were used when the file system was mounted and 2) how the file was opened. The flush-on-close wouldn't be needed if the file was opened read-only.
It seems a little odd that the holes aren't page aligned or page sized multiples.
What application is being used to generate the file which is showing these holes?
Thanx...
ps
Quoted 16 lines · Peter Staubach
Quoted 15 lines · J. Bruce Fields
Quoted 12 lines · Andrew Morton
(switched to email. Please respond via emailed reply-to-all, not via the bugzilla web interface).
Quoted 6 lines · On Thu, 28 Aug 2008 11:41:08 -0700 (PDT)…
NFS client writes to Sun Solaris 10 U4 server. at some point in time, there is an empty portion of the output file from the writer containing missing data (shows as NULL bytes from another NFS client
issuing a tail -f on the file being written). confirmed that the file as exists on the NFS server is sparse, missing bytes (not necessarily multiple of 512 or 1024, one sample is a gap of 3818 bytes,
another is 1895 bytes, another is 423 bytes)
Quoted 5 lines
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Seems like something that could happen if for example two write rpc's got reordered on the network. That's not necessarily a bug--the nfs client isn't required to wait for confirmation of every previous write before sending the next one.
if two RPCs got reordered on the network, and they encompass all the data, then there shouldn't be any missing data. It seems to me like pieces of data are just being skipped, for whatever reason, but I haven't exhaustively examined the NFS network data.
Quoted 4 lines
Quoted 4 lines
However if the client isn't flushing dirty data to the server before returning from close, then that's a violation of NFS's close-to-open semantics:...
this is not confirmed yet. No solid cases of data not being present after close.
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if you do a read of the entire file from the NFS client doing the writing, it causes the non-flushed writes to be instantly flushed to the server followed by a NFS3 commit operation. The data then can be seen on all other NFS clients.
If you do an open of the file alone, no flush
if you do an open and a close, no flush
Quoted 7 lines
Quoted 2 lines
... so this "close, no flush" could be a bug (depending on who is doing that close when--I don't completely understand the described situation).
I suspect that this last might depend upon 1) what options were used when the file system was mounted and 2) how the file was opened. The flush-on-close wouldn't be needed if the file was opened read-only.
no special options on open. Here are the mount options:
retry=1000,tcp,noatime,nosuid,nodev,dirsync,timeo=100,rsize=32768,wsize=32768 ,hard,intr
Quoted 3 lines
It seems a little odd that the holes aren't page aligned or page sized multiples.
indeed. and the time for them to actually get to the server is indeterminate (days is not uncommon. We have not as yet confirmed that some of the data never gets sent to the server until close)
Quoted 3 lines
What application is being used to generate the file which is showing these holes?
namd and some custom code developed in-house for chemistry research (at the very least)
Quoted 54 lines · Doug Hughes
Quoted 16 lines · Peter Staubach
Quoted 15 lines · J. Bruce Fields
Quoted 12 lines · Andrew Morton
(switched to email. Please respond via emailed reply-to-all, not via the bugzilla web interface).
Quoted 6 lines · On Thu, 28 Aug 2008 11:41:08 -0700 (PDT)…
NFS client writes to Sun Solaris 10 U4 server. at some point in time, there is an empty portion of the output file from the writer containing missing data (shows as NULL bytes from another NFS client
issuing a tail -f on the file being written). confirmed that the file as exists on the NFS server is sparse, missing bytes (not necessarily multiple of 512 or 1024, one sample is a gap of 3818 bytes,
another is 1895 bytes, another is 423 bytes)Quoted 5 lines
Quoted 5 lines
Seems like something that could happen if for example two write rpc's got reordered on the network. That's not necessarily a bug--the nfs client isn't required to wait for confirmation of every previous write before sending the next one.
if two RPCs got reordered on the network, and they encompass all the data, then there shouldn't be any missing data. It seems to me like pieces of data are just being skipped, for whatever reason, but I haven't exhaustively examined the NFS network data.
Quoted 4 lines
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However if the client isn't flushing dirty data to the server before returning from close, then that's a violation of NFS's close-to-open semantics:...
this is not confirmed yet. No solid cases of data not being present after close.
Quoted 9 lines
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if you do a read of the entire file from the NFS client doing the writing, it causes the non-flushed writes to be instantly flushed to the server followed by a NFS3 commit operation. The data then can be seen on all other NFS clients.
If you do an open of the file alone, no flush
if you do an open and a close, no flushQuoted 7 lines
Quoted 2 lines
... so this "close, no flush" could be a bug (depending on who is doing that close when--I don't completely understand the described situation).
I suspect that this last might depend upon 1) what options were used when the file system was mounted and 2) how the file was opened. The flush-on-close wouldn't be needed if the file was opened read-only.
no special options on open. Here are the mount options:
retry=1000,tcp,noatime,nosuid,nodev,dirsync,timeo=100,rsize=32768,wsize=32768,hard,intr
Quoted 3 lines
It seems a little odd that the holes aren't page aligned or page sized multiples.
Quoted 6 lines
indeed. and the time for them to actually get to the server is indeterminate (days is not uncommon. We have not as yet confirmed that some of the data never gets sent to the server until close)
Quoted 3 lines
What application is being used to generate the file which is showing these holes?
namd and some custom code developed in-house for chemistry research (at the very least)
Do these applications use mmap() or generate the file contents serially or randomly?
Thanx...
ps
Quoted 60 lines · Peter Staubach
Quoted 59 lines · Doug Hughes
Quoted 16 lines · Peter Staubach
Quoted 15 lines · J. Bruce Fields
Quoted 12 lines · Andrew Morton
(switched to email. Please respond via emailed reply-to-all, not via the bugzilla web interface).
Quoted 6 lines · On Thu, 28 Aug 2008 11:41:08 -0700 (PDT)…
NFS client writes to Sun Solaris 10 U4 server. at some point in time, there is an empty portion of the output file from the writer containing missing data (shows as NULL bytes from another NFS client
issuing a tail -f on the file being written). confirmed that the file as exists on the NFS server is sparse, missing bytes (not necessarily multiple of 512 or 1024, one sample is a gap of 3818 bytes,
another is 1895 bytes, another is 423 bytes)Quoted 5 lines
Quoted 5 lines
Seems like something that could happen if for example two write rpc's got reordered on the network. That's not necessarily a bug--the nfs client isn't required to wait for confirmation of every previous write before sending the next one.
if two RPCs got reordered on the network, and they encompass all the data, then there shouldn't be any missing data. It seems to me like pieces of data are just being skipped, for whatever reason, but I haven't exhaustively examined the NFS network data.
Quoted 4 lines
Quoted 4 lines
However if the client isn't flushing dirty data to the server before returning from close, then that's a violation of NFS's close-to-open semantics:...
this is not confirmed yet. No solid cases of data not being present after close.
Quoted 9 lines
Quoted 9 lines
Quoted 8 lines
Quoted 8 lines
if you do a read of the entire file from the NFS client doing the writing, it causes the non-flushed writes to be instantly flushed to the server followed by a NFS3 commit operation. The data then can be seen on all other NFS clients.
If you do an open of the file alone, no flush
if you do an open and a close, no flushQuoted 7 lines
Quoted 2 lines
... so this "close, no flush" could be a bug (depending on who is doing that close when--I don't completely understand the described situation).
I suspect that this last might depend upon 1) what options were used when the file system was mounted and 2) how the file was opened. The flush-on-close wouldn't be needed if the file was opened read-only.
no special options on open. Here are the mount options:
retry=1000,tcp,noatime,nosuid,nodev,dirsync,timeo=100,rsize=32768,wsize=32768,hard,intr
Quoted 3 lines
It seems a little odd that the holes aren't page aligned or page sized multiples.
indeed. and the time for them to actually get to the server is indeterminate (days is not uncommon. We have not as yet confirmed that some of the data never gets sent to the server until close)
Quoted 3 lines
What application is being used to generate the file which is showing these holes?
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namd and some custom code developed in-house for chemistry research (at the very least)
Do these applications use
mmap()or generate the file contents serially or randomly?Thanx...
open file at beginning. write, write, write, write, write, (no seek, no offset, entirely serial), run a very long time, end.
strace excerpt:
16:42:56.143512 write(8, "1948900 47.1225 0 0 0 47.7759 0 "..., 118) = 118 16:43:01.845742 write(8, "1949000 47.0474 0 0 0 47.8865 0 "..., 116) = 116 16:43:07.481889 write(8, "1949100 47.045 0 0 0 48.0742 0 0"..., 116) = 116 16:43:13.150555 write(8, "1949200 47.1848 0 0 0 47.8868 0 "..., 116) = 116 16:43:18.788863 write(8, "1949300 47.251 0 0 0 47.7743 0 0"..., 113) = 113 16:43:24.429424 write(8, "1949400 47.2722 0 0 0 47.6937 0 "..., 118) = 118 16:43:30.057179 write(8, "1949500 47.4865 0 0 0 47.6251 0 "..., 117) = 117