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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Simon,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">(My first ever post – queue being shot down in flames)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Whilst this doesn’t answer any of your questions (directly)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">One thing we do tend to look at when we see (what appears) to be a static “Queue Length” value, is the data which is actually inflight
from an AFM perspective, so that we can ascertain whether the reason is something like, a user writing huge files to the cache, which take time to sync with home, and thus remain in the queue, providing a static “Queue Length”<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">[root@server ~]# mmafmctl gpfs getstate | awk ' $6 >=50 '<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Fileset Name Fileset Target Fileset State Gateway Node Queue State Queue Length Queue
numExec<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">afmcancergenetics <IP here>:/leo/res_hpc/afm-leo Dirty csgpfs01 Active 60 126157822<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">[root@server ~]#<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">So for instance, by using the tsfindinode command, to have a look at the size of the file which is currently “inflight” from an AFM
perspective:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">[root@server ~]# mmfsadm dump afm | more<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> Fileset: afm-leo 12 (gpfs)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> mode: independent-writer queue: Normal myFileset MDS: <c0n334><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> home: <IP> proto: nfs port: 2049 lastCmd: 6<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> handler: Mounted Dirty refCount: 5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> queue: delay 300 QLen 0+9 flushThds 4 maxFlushThds 4 numExec 436 qfs 0 err 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> i/o: readBuf: 33554432 writeBuf: 2097152 sparseReadThresh: 134217728 pReadThreads 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> i/o: pReadGWs 0 (All) pReadChunkSize 134217728 pReadThresh: -2 >> Disabled <<<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> i/o: prefetchThresh 0 (Prefetch)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> iw: afmIwTakeoverTime 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Priority Queue: (listed by execution order) (state: Active)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> Write [601414711.601379492] inflight (377743888481 @ 0) chunks 0 bytes 0 0 thread_id 7630<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> Write [601717612.601465868] inflight (462997479227 @ 0) chunks 0 bytes 0 1 thread_id 10200<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> Write [601717612.601465870] inflight (391663667550 @ 0) chunks 0 bytes 0 2 thread_id 10287<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> Write [601717612.601465871] inflight (377743888481 @ 0) chunks 0 bytes 0 3 thread_id 10333<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> Write [601717612.601573418] queued (387002794104 @ 0) chunks 0 bytes 0 4<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> Write [601414711.601650195] queued (342305480538 @ 0) chunks 0 bytes 0 5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> ResetDirty [538455296.-1] queued etype normal normal 19061213<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> ResetDirty [601623334.-1] queued etype normal normal 19061213<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> RecoveryMarker [-1.-1] queued etype normal normal 19061213<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> Normal Queue: Empty (state: Active)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Fileset: afmdata 20 (gpfs)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">#Use the file inode ID to determine the actual file which is inflight between cache and home<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">[root@server cancergenetics]# tsfindinode -i 601379492 /gpfs/afm/cancergenetics > inode.out<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">[root@server ~]# cat /root/inode.out<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">601379492 0 0xCCB6 /gpfs/afm/cancergenetics/Claudia/fastq/PD7446i.fastq<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">[root@server ~]# ls -l /gpfs/afm/cancergenetics/Claudia/fastq/PD7446i.fastq<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">-rw-r--r-- 1 bbn16cku MED_pg 377743888481 Mar 25 05:48 /gpfs/afm/cancergenetics/Claudia/fastq/PD7446i.fastq<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">[root@server<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I am not sure if that helps and you probably already know about it inflight checking…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#1F497D">Kind Regards,<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#1F497D">Leo<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#1F497D">Leo Earl </span></b><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#A6A6A6">|</span></b><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#1F497D"> </span></b><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#7F7F7F">Head
of </span></b><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#7F7F7F">Research & Specialist Computing
<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Room ITCS 01.16, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D">+44 (0) 1603 593856<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> gpfsug-discuss-bounces@spectrumscale.org [mailto:gpfsug-discuss-bounces@spectrumscale.org]
<b>On Behalf Of </b>Venkateswara R Puvvada<br>
<b>Sent:</b> 10 October 2017 05:56<br>
<b>To:</b> gpfsug main discussion list <gpfsug-discuss@spectrumscale.org><br>
<b>Subject:</b> Re: [gpfsug-discuss] AFM fun (more!)<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif">Simon,</span><br>
<br>
<tt><span style="font-size:10.0pt">>Question 1.</span></tt><span style="font-size:10.0pt;font-family:"Courier New""><br>
<tt>>Can we force the gateway node for the other file-sets to our "02" node.</tt><br>
<tt>>I.e. So that we can get the queue services for the other filesets.</tt><br>
</span><br>
<tt><span style="font-size:10.0pt">AFM automatically maps the fileset to gateway node, and today there is no option available for users to assign fileset to a particular gateway node. This feature will be supported in future releases.</span></tt><br>
<span style="font-size:10.0pt;font-family:"Courier New""><br>
<tt>>Question 2.</tt><br>
<tt>>How can we make AFM actually work for the "facility" file-set. If we shut</tt><br>
<tt>>down GPFS on the node, on the secondary node, we'll see log entires like:</tt><br>
<tt>>2017-10-09_13:35:30.330+0100: [I] AFM: Found 1069575 local remove</tt><br>
<tt>>operations...</tt><br>
<tt>>So I'm assuming the massive queue is all file remove operations?</tt><br>
</span><br>
<tt><span style="font-size:10.0pt">These are the files which were created in cache, and were deleted before they get replicated to home. AFM recovery will delete them locally. Yes, it is possible that most of these operations are local remove operations.Try
finding those operations using dump command.</span></tt><br>
<br>
<tt><span style="font-size:10.0pt"> mmfsadm saferdump afm all | grep 'Remove\|Rmdir' | grep local | wc -l</span></tt><br>
<br>
<span style="font-size:10.0pt;font-family:"Courier New""><br>
<tt>>Alarmingly, we are also seeing entires like:</tt><br>
<tt>>2017-10-09_13:54:26.591+0100: [E] AFM: WriteSplit file system rds-cache</tt><br>
<tt>>fileset rds-projects-2017 file IDs [5389550.5389550.-1.-1,R] name remote</tt><br>
<tt>>error 5</tt><br>
</span><br>
<tt><span style="font-size:10.0pt">Traces are needed to verify IO errors. Also try disabling the parallel IO and see if replication speed improves.</span></tt><br>
<br>
<span style="font-size:10.0pt;font-family:"Arial",sans-serif">mmchfileset device fileset -p afmParallelWriteThreshold=disable</span><br>
<br>
<span style="font-size:10.0pt;font-family:"Arial",sans-serif">~Venkat (<a href="mailto:vpuvvada@in.ibm.com">vpuvvada@in.ibm.com</a>)</span><br>
<br>
<br>
<br>
<span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5F5F5F">From: </span><span style="font-size:7.5pt;font-family:"Arial",sans-serif">"Simon Thompson (IT Research Support)" <<a href="mailto:S.J.Thompson@bham.ac.uk">S.J.Thompson@bham.ac.uk</a>></span><br>
<span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5F5F5F">To: </span><span style="font-size:7.5pt;font-family:"Arial",sans-serif">"<a href="mailto:gpfsug-discuss@spectrumscale.org">gpfsug-discuss@spectrumscale.org</a>" <<a href="mailto:gpfsug-discuss@spectrumscale.org">gpfsug-discuss@spectrumscale.org</a>></span><br>
<span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5F5F5F">Date: </span><span style="font-size:7.5pt;font-family:"Arial",sans-serif">10/09/2017 06:27 PM</span><br>
<span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5F5F5F">Subject: </span><span style="font-size:7.5pt;font-family:"Arial",sans-serif">[gpfsug-discuss] AFM fun (more!)</span><br>
<span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5F5F5F">Sent by: </span><span style="font-size:7.5pt;font-family:"Arial",sans-serif"><a href="mailto:gpfsug-discuss-bounces@spectrumscale.org">gpfsug-discuss-bounces@spectrumscale.org</a></span><o:p></o:p></p>
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<br>
<br>
<span style="font-size:10.0pt;font-family:"Courier New""><br>
<tt>Hi All,</tt><br>
<br>
<tt>We're having fun (ok not fun ...) with AFM.</tt><br>
<br>
<tt>We have a file-set where the queue length isn't shortening, watching it</tt><br>
<tt>over 5 sec periods, the queue length increases by ~600-1000 items, and the</tt><br>
<tt>numExec goes up by about 15k.</tt><br>
<br>
<tt>The queues are steadily rising and we've seen them over 1000000 ...</tt><br>
<br>
<tt>This is on one particular fileset e.g.:</tt><br>
<br>
<tt>mmafmctl rds-cache getstate</tt><br>
<tt> Mon Oct 9 08:43:58 2017</tt><br>
<br>
<tt>Fileset Name Fileset Target Cache State</tt><br>
<tt> Gateway Node Queue Length Queue numExec</tt><br>
<tt>------------ --------------</tt><br>
<tt>------------- ------------ ------------ -------------</tt><br>
<tt>rds-projects-facility gpfs:///rds/projects/facility Dirty</tt><br>
<tt> bber-afmgw01 3068953 520504</tt><br>
<tt>rds-projects-2015 gpfs:///rds/projects/2015 Active</tt><br>
<tt> bber-afmgw01 0 3</tt><br>
<tt>rds-projects-2016 gpfs:///rds/projects/2016 Dirty</tt><br>
<tt> bber-afmgw01 1482 70</tt><br>
<tt>rds-projects-2017 gpfs:///rds/projects/2017 Dirty</tt><br>
<tt> bber-afmgw01 713 9104</tt><br>
<tt>bear-apps gpfs:///rds/bear-apps Dirty</tt><br>
<tt> bber-afmgw02 3 2472770871</tt><br>
<tt>user-homes gpfs:///rds/homes Active</tt><br>
<tt> bber-afmgw02 0 19</tt><br>
<tt>bear-sysapps gpfs:///rds/bear-sysapps Active</tt><br>
<tt> bber-afmgw02 0 4</tt><br>
<br>
<br>
<br>
<tt>This is having the effect that other filesets on the same "Gateway" are</tt><br>
<tt>not getting their queues processed.</tt><br>
<br>
<tt>Question 1.</tt><br>
<tt>Can we force the gateway node for the other file-sets to our "02" node.</tt><br>
<tt>I.e. So that we can get the queue services for the other filesets.</tt><br>
<br>
<tt>Question 2.</tt><br>
<tt>How can we make AFM actually work for the "facility" file-set. If we shut</tt><br>
<tt>down GPFS on the node, on the secondary node, we'll see log entires like:</tt><br>
<tt>2017-10-09_13:35:30.330+0100: [I] AFM: Found 1069575 local remove</tt><br>
<tt>operations...</tt><br>
<br>
<tt>So I'm assuming the massive queue is all file remove operations?</tt><br>
<br>
<tt>Alarmingly, we are also seeing entires like:</tt><br>
<tt>2017-10-09_13:54:26.591+0100: [E] AFM: WriteSplit file system rds-cache</tt><br>
<tt>fileset rds-projects-2017 file IDs [5389550.5389550.-1.-1,R] name remote</tt><br>
<tt>error 5</tt><br>
<br>
<tt>Anyone any suggestions?</tt><br>
<br>
<tt>Thanks</tt><br>
<br>
<tt>Simon</tt><br>
<br>
<br>
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