<span style=" font-size:10pt;font-family:sans-serif">This could be related
to the following flash:</span><br><br><a href="http://www-01.ibm.com/support/docview.wss?uid=ssg1S1012054"><span style=" font-size:10pt;color:blue;font-family:sans-serif">http://www-01.ibm.com/support/docview.wss?uid=ssg1S1012054</span></a><br><br><span style=" font-size:10pt;font-family:sans-serif">You should contact
IBM service to obtain the fix for your release.<br><br>Steve Y. Xiao<br></span><br><tt><span style=" font-size:10pt">gpfsug-discuss-bounces@spectrumscale.org
wrote on 02/14/2018 02:18:02 PM:<br><br>> From: gpfsug-discuss-request@spectrumscale.org</span></tt><br><tt><span style=" font-size:10pt">> To: gpfsug-discuss@spectrumscale.org</span></tt><br><tt><span style=" font-size:10pt">> Date: 02/14/2018 02:18 PM</span></tt><br><tt><span style=" font-size:10pt">> Subject: gpfsug-discuss Digest,
Vol 73, Issue 36</span></tt><br><tt><span style=" font-size:10pt">> Sent by: gpfsug-discuss-bounces@spectrumscale.org</span></tt><br><tt><span style=" font-size:10pt">> <br>> Send gpfsug-discuss mailing list submissions to<br>> gpfsug-discuss@spectrumscale.org<br>> <br>> To subscribe or unsubscribe via the World Wide Web, visit<br>> </span></tt><a href=https://urldefense.proofpoint.com/v2/url?><tt><span style=" font-size:10pt">https://urldefense.proofpoint.com/v2/url?</span></tt></a><tt><span style=" font-size:10pt"><br>> u=http-3A__gpfsug.org_mailman_listinfo_gpfsug-2Ddiscuss&d=DwICAg&c=jf_iaSHvJObTbx-<br>> siA1ZOg&r=ck4PYlaRFvCcNKlfHMPhoA&m=Jv87Pffe4kSlhiO2NmMbL4HQo_zJ-8s8CkIRy7p92r4&s=aVWMptxcCR3po3ijmRweTyjbs1Pp5D7WEiJTYvSYLUk&e=<br>> or, via email, send a message with subject or body 'help' to<br>> gpfsug-discuss-request@spectrumscale.org<br>> <br>> You can reach the person managing the list at<br>> gpfsug-discuss-owner@spectrumscale.org<br>> <br>> When replying, please edit your Subject line so it is more specific<br>> than "Re: Contents of gpfsug-discuss digest..."<br>> <br>> <br>> Today's Topics:<br>> <br>> 1. Re: Odd behavior with cat followed by grep. (John
Hanks)<br>> <br>> <br>> ----------------------------------------------------------------------<br>> <br>> Message: 1<br>> Date: Wed, 14 Feb 2018 11:17:19 -0800<br>> From: John Hanks <griznog@gmail.com><br>> To: gpfsug main discussion list <gpfsug-discuss@spectrumscale.org><br>> Subject: Re: [gpfsug-discuss] Odd behavior with cat followed by grep.<br>> Message-ID:<br>> <CAGrHuK7okijzHLysDNCxR8tn1fKeMDwW_iT5898tBvaCR_QJUg@mail.gmail.com><br>> Content-Type: text/plain; charset="utf-8"<br>> <br>> Thanks Bryan, mystery solved :)<br>> <br>> We also stumbled across these related items, in case anyone else wanders<br>> into this thread.<br>> <br>> </span></tt><a href=https://urldefense.proofpoint.com/v2/url?><tt><span style=" font-size:10pt">https://urldefense.proofpoint.com/v2/url?</span></tt></a><tt><span style=" font-size:10pt"><br>> u=http-3A__bug-2Dgrep.gnu.narkive.com_Y8cfvWDt_bug-2D27666-2Dgrep-2Don-2Dgpfs-2Dfilesystem-2Dseek-2Dhole-2Dproblem&d=DwICAg&c=jf_iaSHvJObTbx-<br>> siA1ZOg&r=ck4PYlaRFvCcNKlfHMPhoA&m=Jv87Pffe4kSlhiO2NmMbL4HQo_zJ-8s8CkIRy7p92r4&s=FgxYBxqHZ0bHdWirEs1U_B3oDpeHJe8iRd-<br>> TYrXh6FI&e=<br>> <br>> </span></tt><a href=https://www.ibm.com/developerworks/community/forums/html/topic?><tt><span style=" font-size:10pt">https://www.ibm.com/developerworks/community/forums/html/topic?</span></tt></a><tt><span style=" font-size:10pt"><br>> id=c2a94433-9ec0-4a4b-abfe-d0a1e721d630<br>> <br>> GPFS, the gift that keeps on giving ... me more things to do instead
of<br>> doing the things I want to be doing.<br>> <br>> Thanks all,<br>> <br>> jbh<br>> <br>> On Wed, Feb 14, 2018 at 10:48 AM, Bryan Banister <bbanister@jumptrading.com><br>> wrote:<br>> <br>> > Hi all,<br>> ><br>> ><br>> ><br>> > We found this a while back and IBM fixed it. Here?s your
answer:<br>> > </span></tt><a href="http://www-01.ibm.com/support/docview.wss?uid=isg1IV87385"><tt><span style=" font-size:10pt">http://www-01.ibm.com/support/docview.wss?uid=isg1IV87385</span></tt></a><tt><span style=" font-size:10pt"><br>> ><br>> ><br>> ><br>> > Cheers,<br>> ><br>> > -Bryan<br>> ><br>> ><br>> ><br>> > *From:* gpfsug-discuss-bounces@spectrumscale.org [</span></tt><a href="mailto:gpfsug-discuss-"><tt><span style=" font-size:10pt">mailto:gpfsug-discuss-</span></tt></a><tt><span style=" font-size:10pt"><br>> > bounces@spectrumscale.org] *On Behalf Of *John Hanks<br>> > *Sent:* Wednesday, February 14, 2018 12:31 PM<br>> > *To:* gpfsug main discussion list <gpfsug-discuss@spectrumscale.org><br>> > *Subject:* Re: [gpfsug-discuss] Odd behavior with cat followed
by grep.<br>> ><br>> ><br>> ><br>> > *Note: External Email*<br>> > ------------------------------<br>> ><br>> > Straces are interesting, but don't immediately open my eyes:<br>> ><br>> ><br>> ><br>> > strace of grep on NFS (works as expected)<br>> ><br>> ><br>> ><br>> > openat(AT_FDCWD, "/home/griznog/pipetest.tmp.txt",
O_RDONLY) = 3<br>> ><br>> > fstat(3, {st_mode=S_IFREG|0644, st_size=530721, ...}) = 0<br>> ><br>> > ioctl(3, TCGETS, 0x7ffe2c26b0b0) =
-1 ENOTTY (Inappropriate ioctl<br>> > for device)<br>> ><br>> > read(3, "chr1\t43452652\t43452652\tL1HS\tlib1"...,
32768) = 32768<br>> ><br>> > lseek(3, 32768, SEEK_HOLE)
= 530721<br>> ><br>> > lseek(3, 32768, SEEK_SET)
= 32768<br>> ><br>> > fstat(1, {st_mode=S_IFREG|0644, st_size=5977, ...}) = 0<br>> ><br>> > mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS,
-1, 0) =<br>> > 0x7f3bf6c43000<br>> ><br>> > write(1, "chr1\t43452652\t43452652\tL1HS\tlib1"...,
8192chr1<br>> ><br>> ><br>> ><br>> > strace on GPFS (thinks file is binary)<br>> ><br>> ><br>> ><br>> > openat(AT_FDCWD, "/srv/gsfs0/projects/pipetest.tmp.txt",
O_RDONLY) = 3<br>> ><br>> > fstat(3, {st_mode=S_IFREG|0644, st_size=530721, ...}) = 0<br>> ><br>> > ioctl(3, TCGETS, 0x7ffc9b52caa0) =
-1 ENOTTY (Inappropriate ioctl<br>> > for device)<br>> ><br>> > read(3, "chr1\t43452652\t43452652\tL1HS\tlib1"...,
32768) = 32768<br>> ><br>> > lseek(3, 32768, SEEK_HOLE)
= 262144<br>> ><br>> > lseek(3, 32768, SEEK_SET)
= 32768<br>> ><br>> > fstat(1, {st_mode=S_IFREG|0644, st_size=6011, ...}) = 0<br>> ><br>> > mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS,
-1, 0) =<br>> > 0x7fd45ee88000<br>> ><br>> > close(3)
= 0<br>> ><br>> > write(1, "Binary file /srv/gsfs0/projects/"..., 72Binary
file<br>> > /srv/gsfs0/projects/levinson/xwzhu/pipetest.tmp.txt matches<br>> ><br>> > ) = 72<br>> ><br>> ><br>> ><br>> > Do the lseek() results indicate that the grep on the GPFS mounted
version<br>> > thinks the file is a sparse file? For comparison I strace'd md5sum
in place<br>> > of the grep and it does not lseek() with SEEK_HOLE, it's access
in both<br>> > cases look identical, like:<br>> ><br>> ><br>> ><br>> > open("/home/griznog/pipetest.tmp.txt", O_RDONLY) =
3<br>> ><br>> > fadvise64(3, 0, 0, POSIX_FADV_SEQUENTIAL) = 0<br>> ><br>> > fstat(3, {st_mode=S_IFREG|0644, st_size=530721, ...}) = 0<br>> ><br>> > mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS,
-1, 0) =<br>> > 0x7fb7d2c2b000<br>> ><br>> > read(3, "chr1\t43452652\t43452652\tL1HS\tlib1"...,
32768) = 32768<br>> ><br>> > ...[reads clipped]...<br>> ><br>> > read(3, "", 24576)
= 0<br>> ><br>> > lseek(3, 0, SEEK_CUR)
= 530721<br>> ><br>> > close(3)
= 0<br>> ><br>> ><br>> ><br>> ><br>> ><br>> > jbh<br>> ><br>> ><br>> ><br>> ><br>> ><br>> > On Wed, Feb 14, 2018 at 9:51 AM, Aaron Knister <aaron.s.knister@nasa.gov><br>> > wrote:<br>> ><br>> > Just speculating here (also known as making things up) but I
wonder if<br>> > grep is somehow using the file's size in its determination of
binary<br>> > status. I also see mmap in the strace so maybe there's some issue
with<br>> > mmap where some internal GPFS buffer is getting truncated<br>> > inappropriately but leaving a bunch of null values which gets
returned<br>> > to grep.<br>> ><br>> > -Aaron<br>> ><br>> > On 2/14/18 10:21 AM, John Hanks wrote:<br>> > > Hi Valdis,<br>> > ><br>> > > I tired with the grep replaced with 'ls -ls' and 'md5sum',
I don't think<br>> > > this is a data integrity issue, thankfully:<br>> > ><br>> > > $ ./pipetestls.sh<br>> > > 256 -rw-r--r-- 1 39073 3001 530721 Feb 14 07:16<br>> > > /srv/gsfs0/projects/pipetest.tmp.txt<br>> > > 0 -rw-r--r-- 1 39073 3953 530721 Feb 14 07:16<br>> > /home/griznog/pipetest.tmp.txt<br>> > ><br>> > > $ ./pipetestmd5.sh<br>> > > 15cb81a85c9e450bdac8230309453a0a /srv/gsfs0/projects/pipetest.tmp.txt<br>> > > 15cb81a85c9e450bdac8230309453a0a /home/griznog/pipetest.tmp.txt<br>> > ><br>> > > And replacing grep with 'file' even properly sees the files
as ASCII:<br>> > > $ ./pipetestfile.sh<br>> > > /srv/gsfs0/projects/pipetest.tmp.txt: ASCII text, with very
long lines<br>> > > /home/griznog/pipetest.tmp.txt: ASCII text, with very long
lines<br>> > ><br>> > > I'll poke a little harder at grep next and see what the
difference in<br>> > > strace of each reveals.<br>> > ><br>> > > Thanks,<br>> > ><br>> > > jbh<br>> > ><br>> > ><br>> > ><br>> > ><br>> > > On Wed, Feb 14, 2018 at 7:08 AM, <valdis.kletnieks@vt.edu<br>> ><br>> > > <</span></tt><a href=mailto:valdis.kletnieks@vt.edu><tt><span style=" font-size:10pt">mailto:valdis.kletnieks@vt.edu</span></tt></a><tt><span style=" font-size:10pt">>>
wrote:<br>> > ><br>> > > On Wed, 14 Feb 2018 06:20:32 -0800, John Hanks
said:<br>> > ><br>> > > > # ls -aln /srv/gsfs0/projects/pipetest.tmp.txt<br>> > $HOME/pipetest.tmp.txt<br>> > > > -rw-r--r-- 1 39073 3953 530721 Feb 14
06:10<br>> > /home/griznog/pipetest.tmp.txt<br>> > > > -rw-r--r-- 1 39073 3001 530721 Feb 14
06:10<br>> > > > /srv/gsfs0/projects/pipetest.tmp.txt<br>> > > ><br>> > > > We can "fix" the user case
that exposed this by not using a temp<br>> > file or<br>> > > > inserting a sleep, but I'd still like
to know why GPFS is behaving<br>> > this way<br>> > > > and make it stop.<br>> > ><br>> > > May be related to replication, or other behind-the-scenes
behavior.<br>> > ><br>> > > Consider this example - 4.2.3.6, data and
metadata replication both<br>> > > set to 2, 2 sites 95 cable miles apart, each
is 3 Dell servers with<br>> > > a full<br>> > > fiberchannel mesh to 3 Dell MD34something
arrays.<br>> > ><br>> > > % dd if=/dev/zero bs=1k count=4096 of=sync.test;
ls -ls sync.test;<br>> > > sleep 5; ls -ls sync.test; sleep 5; ls -ls
sync.test<br>> > > 4096+0 records in<br>> > > 4096+0 records out<br>> > > 4194304 bytes (4.2 MB) copied, 0.0342852 s,
122 MB/s<br>> > > 2048 -rw-r--r-- 1 root root 4194304 Feb 14
09:35 sync.test<br>> > > 8192 -rw-r--r-- 1 root root 4194304 Feb 14
09:35 sync.test<br>> > > 8192 -rw-r--r-- 1 root root 4194304 Feb 14
09:35 sync.test<br>> > ><br>> > > Notice that the first /bin/ls shouldn't be
starting until after the<br>> > > dd has<br>> > > completed - at which point it's only allocated
half the blocks<br>> > > needed to hold<br>> > > the 4M of data at one site. 5 seconds
later, it's allocated the<br>> > > blocks at both<br>> > > sites and thus shows the full 8M needed for
2 copies.<br>> > ><br>> > > I've also seen (but haven't replicated it
as I write this) a small<br>> > > file (4-8K<br>> > > or so) showing first one full-sized block,
then a second full-sized<br>> > > block, and<br>> > > then dropping back to what's needed for 2
1/32nd fragments. That<br>> > had me<br>> > > scratching my head<br>> > ><br>> > > Having said that, that's all metadata fun
and games, while your case<br>> > > appears to have some problems with data integrity
(which is a whole<br>> > lot<br>> > > scarier). It would be *really* nice
if we understood the problem<br>> > here.<br>> > ><br>> > > The scariest part is:<br>> > ><br>> > > > The first grep | wc -l returns 1, because
grep outputs "Binary<br>> > file /path/to/<br>> > > > gpfs/mount/test matches"<br>> > ><br>> > > which seems to be implying that we're failing
on semantic<br>> > consistency.<br>> > > Basically, your 'cat' command is completing
and closing the file,<br>> > > but then a<br>> > > temporally later open of the same find is
reading something other<br>> > > that only the<br>> > > just-written data. My first guess is
that it's a race condition<br>> > > similar to the<br>> > > following: The cat command is causing a write
on one NSD server, and<br>> > > the first<br>> > > grep results in a read from a *different*
NSD server, returning the<br>> > > data that<br>> > > *used* to be in the block because the read
actually happens before<br>> > > the first<br>> > > NSD server actually completes the write.<br>> > ><br>> > > It may be interesting to replace the grep's
with pairs of 'ls -ls /<br>> > > dd' commands to grab the<br>> > > raw data and its size, and check the following:<br>> > ><br>> > > 1) does the size (both blocks allocated and
logical length) reported<br>> > by<br>> > > ls match the amount of data actually read
by the dd?<br>> > ><br>> > > 2) Is the file length as actually read equal
to the written length,<br>> > > or does it<br>> > > overshoot and read all the way to the next
block boundary?<br>> > ><br>> > > 3) If the length is correct, what's wrong
with the data that's<br>> > > telling grep that<br>> > > it's a binary file? ( od -cx is your
friend here).<br>> > ><br>> > > 4) If it overshoots, is the remainder all-zeros
(good) or does it<br>> > > return semi-random<br>> > > "what used to be there" data (bad,
due to data exposure issues)?<br>> > ><br>> > > (It's certainly not the most perplexing data
consistency issue I've<br>> > > hit in 4 decades - the<br>> > > winner *has* to be a intermittent data read
corruption on a GPFS 3.5<br>> > > cluster that<br>> > > had us, IBM, SGI, DDN, and at least one vendor
of networking gear<br>> > > all chasing our<br>> > > tails for 18 months before we finally tracked
it down. :)<br>> > ><br>> > > _______________________________________________<br>> > > gpfsug-discuss mailing list<br>> ><br>> > > gpfsug-discuss at spectrumscale.org <https://<br>> urldefense.proofpoint.com/v2/url?<br>> u=http-3A__spectrumscale.org&d=DwICAg&c=jf_iaSHvJObTbx-<br>> siA1ZOg&r=ck4PYlaRFvCcNKlfHMPhoA&m=Jv87Pffe4kSlhiO2NmMbL4HQo_zJ-8s8CkIRy7p92r4&s=jUBFb8C9yai1TUTu1BVnNTNcOnJXGxupWiEKkEjT4pM&e=<br>> ><br>> > > </span></tt><a href=https://urldefense.proofpoint.com/v2/url?><tt><span style=" font-size:10pt">https://urldefense.proofpoint.com/v2/url?</span></tt></a><tt><span style=" font-size:10pt"><br>> u=http-3A__gpfsug.org_mailman_listinfo_gpfsug-2Ddiscuss&d=DwICAg&c=jf_iaSHvJObTbx-<br>> siA1ZOg&r=ck4PYlaRFvCcNKlfHMPhoA&m=Jv87Pffe4kSlhiO2NmMbL4HQo_zJ-8s8CkIRy7p92r4&s=aVWMptxcCR3po3ijmRweTyjbs1Pp5D7WEiJTYvSYLUk&e=<br>> > > <</span></tt><a href=https://urldefense.proofpoint.com/v2/url?><tt><span style=" font-size:10pt">https://urldefense.proofpoint.com/v2/url?</span></tt></a><tt><span style=" font-size:10pt"><br>> u=http-3A__gpfsug.org_mailman_listinfo_gpfsug-2Ddiscuss&d=DwICAg&c=jf_iaSHvJObTbx-<br>> siA1ZOg&r=ck4PYlaRFvCcNKlfHMPhoA&m=Jv87Pffe4kSlhiO2NmMbL4HQo_zJ-8s8CkIRy7p92r4&s=aVWMptxcCR3po3ijmRweTyjbs1Pp5D7WEiJTYvSYLUk&e=<br>> ><br>> > ><br>> > ><br>> > ><br>> > ><br>> > > _______________________________________________<br>> > > gpfsug-discuss mailing list<br>> > > gpfsug-discuss at spectrumscale.org<br>> > > </span></tt><a href=https://urldefense.proofpoint.com/v2/url?><tt><span style=" font-size:10pt">https://urldefense.proofpoint.com/v2/url?</span></tt></a><tt><span style=" font-size:10pt"><br>> u=http-3A__gpfsug.org_mailman_listinfo_gpfsug-2Ddiscuss&d=DwICAg&c=jf_iaSHvJObTbx-<br>> siA1ZOg&r=ck4PYlaRFvCcNKlfHMPhoA&m=Jv87Pffe4kSlhiO2NmMbL4HQo_zJ-8s8CkIRy7p92r4&s=aVWMptxcCR3po3ijmRweTyjbs1Pp5D7WEiJTYvSYLUk&e=<br>> > ><br>> ><br>> > --<br>> > Aaron Knister<br>> > NASA Center for Climate Simulation (Code 606.2)<br>> > Goddard Space Flight Center<br>> > (301) 286-2776<br>> ><br>> > _______________________________________________<br>> > gpfsug-discuss mailing list<br>> > gpfsug-discuss at spectrumscale.org<br>> > </span></tt><a href=https://urldefense.proofpoint.com/v2/url?><tt><span style=" font-size:10pt">https://urldefense.proofpoint.com/v2/url?</span></tt></a><tt><span style=" font-size:10pt"><br>> u=http-3A__gpfsug.org_mailman_listinfo_gpfsug-2Ddiscuss&d=DwICAg&c=jf_iaSHvJObTbx-<br>> siA1ZOg&r=ck4PYlaRFvCcNKlfHMPhoA&m=Jv87Pffe4kSlhiO2NmMbL4HQo_zJ-8s8CkIRy7p92r4&s=aVWMptxcCR3po3ijmRweTyjbs1Pp5D7WEiJTYvSYLUk&e=<br>> ><br>> ><br>> ><br>> > ------------------------------<br>> ><br>> > Note: This email is for the confidential use of the named addressee(s)<br>> > only and may contain proprietary, confidential or privileged
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