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<p>Hi Phil</p>
<p><br>
</p>
<p>in attach</p>
<p>dn stands for different names....</p>
<p><br>
</p>
<p>cheers</p>
<p>Piero<br>
</p>
<div class="moz-cite-prefix">Il 12/02/2020 16:13, Carns, Philip H.
ha scritto:<br>
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255, 255);">
Ah, great, thank you for the confirmation.</div>
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<br>
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font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
In that case it looks like Darshan is instrumenting properly at
run time, but I think Kevin is on the right track that Darshan's
heuristics for calculating performance in post processing are
getting confused for some reason.<br>
</div>
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font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
Probably GPFS is client-side caching aggressively in the single
client case, but that wouldn't explain why the benchmark output
reports a much different number than Darshan, though. They
should both perceive roughly the same performance; neither the
benchmark itself nor Darshan know if caching is happening or
not.</div>
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font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
It's hard to see where the performance heuristic went wrong from
looking at the log, in large part because the app repeatedly
opens a file with the same name (there is a clue to this in the
OPEN counters; the same file name is opened 20 times):</div>
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font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<span># WARNING: POSIX_OPENS counter includes both POSIX_FILENOS
and POSIX_DUPS counts<br>
</span><span>POSIX 0 6563482044800691889 POSIX_OPENS 20
/gpfs/scratch/userinternal/planucar/benchio-master/shared-file/source/benchio_files/serial.dat
/gpfs/scratch gpfs</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
Every time the file is opened (regardless of whether it was
unlinked in between or not), Darshan keeps adding counters to
the same record, which are associated with that serial.dat file
name. So things like close() timestamps become nonsensical
because Darshan records when the first close() starts and when
the last one finishes:</div>
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font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<span>[carns@carns-x1-7g Downloads]$ darshan-parser
benchio_1202.darshan |grep CLOSE<br>
</span>
<div>POSIX 0 6563482044800691889 POSIX_F_CLOSE_START_TIMESTAMP
4.536853/gpfs/scratch/userinternal/planucar/benchio-master/shared-file/source/benchio_files/serial.dat
/gpfs/scratch gpfs<br>
</div>
<div>POSIX 0 6563482044800691889 POSIX_F_CLOSE_END_TIMESTAMP
43.041987
/gpfs/scratch/userinternal/planucar/benchio-master/shared-file/source/benchio_files/serial.dat
/gpfs/scratch gpfs<br>
</div>
<span></span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
(This doesn't mean there was one close() that took ~40 seconds;
in this case there were many close() calls and ~40 seconds
elapsed between the start of the first one and completion of the
last one).</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
If it is possible for you to modify the benchmark (as an
experiment) so that it chooses a new file name on each
iteration, then I think it would probably disentangle the
counters enough for us to tell what went wrong.<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
thanks,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255,
255, 255);">
-Phil<br>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b> Piero
LANUCARA <a class="moz-txt-link-rfc2396E" href="mailto:p.lanucara@cineca.it"><p.lanucara@cineca.it></a><br>
<b>Sent:</b> Wednesday, February 12, 2020 9:47 AM<br>
<b>To:</b> Carns, Philip H. <a class="moz-txt-link-rfc2396E" href="mailto:carns@mcs.anl.gov"><carns@mcs.anl.gov></a>; Snyder,
Shane <a class="moz-txt-link-rfc2396E" href="mailto:ssnyder@mcs.anl.gov"><ssnyder@mcs.anl.gov></a>; Harms, Kevin
<a class="moz-txt-link-rfc2396E" href="mailto:harms@alcf.anl.gov"><harms@alcf.anl.gov></a><br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a>
<a class="moz-txt-link-rfc2396E" href="mailto:darshan-users@lists.mcs.anl.gov"><darshan-users@lists.mcs.anl.gov></a><br>
<b>Subject:</b> Re: [Darshan-users] Darshan & EPCC benchio
different behaviour</font>
<div> </div>
</div>
<div>
<p>Hi Phil.....POSIX</p>
<p>this is a well known benchmark ....you can easily verify it!</p>
<p><br>
</p>
<p>by the way it's something like that</p>
<p><br>
</p>
<p>! Serial write is unconditionally compiled<br>
subroutine serialwrite(filename, iodata, n1, n2, n3, cartcomm)<br>
<br>
character*(*) :: filename<br>
<br>
integer :: n1, n2, n3<br>
double precision, dimension(0:n1+1,0:n2+1,0:n3+1) :: iodata<br>
<br>
integer :: cartcomm, ierr, rank, size<br>
integer, parameter :: iounit = 10<br>
<br>
integer :: i<br>
<br>
call MPI_Comm_size(cartcomm, size, ierr)<br>
call MPI_Comm_rank(cartcomm, rank, ierr)<br>
<br>
! Write same amount of data as the parallel write but do it
all from rank 0<br>
! This is just to get a baseline figure for serial IO
performance - note<br>
! that the contents of the file will be differnent from the
parallel calls<br>
<br>
if (rank == 0) then<br>
<br>
open(file=filename, unit=iounit, access='stream')<br>
<br>
do i = 1, size<br>
write(unit=iounit) iodata(1:n1, 1:n2, 1:n3)<br>
end do<br>
<br>
close(iounit)<br>
<br>
end if<br>
<br>
end subroutine serialwrite<br>
<br>
</p>
<p><br>
</p>
<p>Piero<br>
</p>
<div class="x_moz-cite-prefix">Il 12/02/2020 14:13, Carns,
Philip H. ha scritto:<br>
</div>
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Hi Piero,</div>
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font-size:12pt; color:rgb(0,0,0);
background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0);
background-color:rgb(255,255,255)">
In the serial case, is the rank that's doing I/O still using
MPI-IO, or is it making calls directly to POSIX in that
case?</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0);
background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0);
background-color:rgb(255,255,255)">
The Darshan log for the serial case doesn't show any MPI-IO
activity, but I'm not sure if that's accurate, or if it's an
indication that we missed some instrumentation.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0);
background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0);
background-color:rgb(255,255,255)">
thanks,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0);
background-color:rgb(255,255,255)">
-Phil<br>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri, sans-serif"
color="#000000"><b>From:</b> Darshan-users
<a class="x_moz-txt-link-rfc2396E"
href="mailto:darshan-users-bounces@lists.mcs.anl.gov"
moz-do-not-send="true">
<darshan-users-bounces@lists.mcs.anl.gov></a> on
behalf of Piero LANUCARA <a
class="x_moz-txt-link-rfc2396E"
href="mailto:p.lanucara@cineca.it"
moz-do-not-send="true">
<p.lanucara@cineca.it></a><br>
<b>Sent:</b> Wednesday, February 12, 2020 5:29 AM<br>
<b>To:</b> Snyder, Shane <a
class="x_moz-txt-link-rfc2396E"
href="mailto:ssnyder@mcs.anl.gov" moz-do-not-send="true">
<ssnyder@mcs.anl.gov></a>; Harms, Kevin <a
class="x_moz-txt-link-rfc2396E"
href="mailto:harms@alcf.anl.gov" moz-do-not-send="true">
<harms@alcf.anl.gov></a><br>
<b>Cc:</b> <a class="x_moz-txt-link-abbreviated"
href="mailto:darshan-users@lists.mcs.anl.gov"
moz-do-not-send="true">
darshan-users@lists.mcs.anl.gov</a> <a
class="x_moz-txt-link-rfc2396E"
href="mailto:darshan-users@lists.mcs.anl.gov"
moz-do-not-send="true">
<darshan-users@lists.mcs.anl.gov></a><br>
<b>Subject:</b> Re: [Darshan-users] Darshan & EPCC
benchio different behaviour</font>
<div> </div>
</div>
<div class="x_BodyFragment"><font size="2"><span
style="font-size:11pt">
<div class="x_PlainText">Hi Shane, Kevin<br>
<br>
thanks for the update.<br>
<br>
I attached a new upated files (log and pdf) to this
email.<br>
<br>
Also, the log from BENCHIO is attached.<br>
<br>
thanks again<br>
<br>
regards<br>
<br>
Piero<br>
<br>
<br>
Il 11/02/2020 20:15, Shane Snyder ha scritto:<br>
> Definitely looks like something strange is
happening when Darshan is <br>
> estimating the time spent in I/O operations (as
seen in the very first <br>
> figure, observed write time barely even
registers) in the serial case, <br>
> which it is ultimately used to provide the
performance estimate.<br>
><br>
> If you could provide them, the raw Darshan logs
would be really <br>
> helpful. That should make it clear whether it's
an instrumentation <br>
> issue (i.e., under accounting for time spent in
I/O operations at <br>
> runtime) or if its an issue with the heuristics
in the PDF summary <br>
> tool you are using, as Kevin points out. If it's
the latter, having an <br>
> example log to test modifications to our
heuristics would be very <br>
> helpful to us.<br>
><br>
> Thanks,<br>
> --Shane<br>
><br>
> On 2/11/20 8:36 AM, Harms, Kevin wrote:<br>
>> Piero,<br>
>><br>
>> the performance estimate is based on
heuristics, it's possible the <br>
>> 'serial' model is breaking some assumptions
about how the I/O is <br>
>> done. Is every rank opening the file, but
only rank 0 is doing actual <br>
>> I/O?<br>
>><br>
>> If possible, you could provide the log and
we could check to see <br>
>> what the counters look like.<br>
>><br>
>> kevin<br>
>><br>
>> ________________________________________<br>
>> From: Piero LANUCARA <a
class="x_moz-txt-link-rfc2396E"
href="mailto:p.lanucara@cineca.it"
moz-do-not-send="true">
<p.lanucara@cineca.it></a><br>
>> Sent: Tuesday, February 11, 2020 2:28 AM<br>
>> To: Harms, Kevin<br>
>> Cc: <a class="x_moz-txt-link-abbreviated"
href="mailto:darshan-users@lists.mcs.anl.gov"
moz-do-not-send="true">
darshan-users@lists.mcs.anl.gov</a><br>
>> Subject: Re: [Darshan-users] Darshan &
EPCC benchio different behaviour<br>
>><br>
>> Hi Kevin<br>
>><br>
>> first of all thanks for the investigation..I
did some futher test and it<br>
>> seems like the issue may appear using Fortran
(MPI, mainly IntelMPI) <br>
>> codes.<br>
>><br>
>> Is this information useful?<br>
>><br>
>> regards<br>
>> Piero<br>
>> Il 07/02/2020 16:07, Harms, Kevin ha scritto:<br>
>>> Piero,<br>
>>><br>
>>> just to confirm, the serial case is
still running in parallel, <br>
>>> 36 processes, but the I/O is only from
rank 0?<br>
>>><br>
>>> kevin<br>
>>><br>
>>> ________________________________________<br>
>>> From: Darshan-users <a
class="x_moz-txt-link-rfc2396E"
href="mailto:darshan-users-bounces@lists.mcs.anl.gov"
moz-do-not-send="true">
<darshan-users-bounces@lists.mcs.anl.gov></a>
on <br>
>>> behalf of Piero LANUCARA <a
class="x_moz-txt-link-rfc2396E"
href="mailto:p.lanucara@cineca.it"
moz-do-not-send="true">
<p.lanucara@cineca.it></a><br>
>>> Sent: Wednesday, February 5, 2020 4:56 AM<br>
>>> To: <a
class="x_moz-txt-link-abbreviated"
href="mailto:darshan-users@lists.mcs.anl.gov"
moz-do-not-send="true">
darshan-users@lists.mcs.anl.gov</a><br>
>>> Subject: Re: [Darshan-users] Darshan
& EPCC benchio different behaviour<br>
>>><br>
>>> p.s<br>
>>><br>
>>> to be more "verbose" I add to the
discussion:<br>
>>><br>
>>> Darshan output for the "serial" run
(serial.pdf)<br>
>>><br>
>>> Darshan output for the MPI-IO run
(mpiio.pdf)<br>
>>><br>
>>> benchio output for "serial" run
(serial.out)<br>
>>><br>
>>> benchio output for "MPI-IO" run
(mpi-io.out)<br>
>>><br>
>>> thanks<br>
>>><br>
>>> Piero<br>
>>><br>
>>> Il 04/02/2020 19:44, Piero LANUCARA ha
scritto:<br>
>>>> Dear all<br>
>>>><br>
>>>> I'm using Darshan to measure EPCC
benchio benchmark<br>
>>>> (<a
href="https://github.com/EPCCed/benchio"
moz-do-not-send="true">https://github.com/EPCCed/benchio</a>)
behaviour on a given x86 Tier1<br>
>>>> machine.<br>
>>>><br>
>>>> running two benchio tests (MPI-IO and
serial) a different behaviour<br>
>>>> appear<br>
>>>><br>
>>>> while Darhsan pdf log file is able to
recover the estimated time and<br>
>>>> bandwidth in the MPI-IO case, the
"serial" run is completely<br>
>>>> underestimated by Darshan (the time
and bandwidth are less/greater<br>
>>>> than benchio output).<br>
>>>><br>
>>>> Suggestions are welcomed<br>
>>>><br>
>>>> thanks<br>
>>>><br>
>>>> Piero<br>
>>>><br>
>>>>
_______________________________________________<br>
>>>> Darshan-users mailing list<br>
>>>> <a
class="x_moz-txt-link-abbreviated"
href="mailto:Darshan-users@lists.mcs.anl.gov"
moz-do-not-send="true">
Darshan-users@lists.mcs.anl.gov</a><br>
>>>> <a
href="https://lists.mcs.anl.gov/mailman/listinfo/darshan-users"
moz-do-not-send="true">https://lists.mcs.anl.gov/mailman/listinfo/darshan-users</a><br>
>>
_______________________________________________<br>
>> Darshan-users mailing list<br>
>> <a class="x_moz-txt-link-abbreviated"
href="mailto:Darshan-users@lists.mcs.anl.gov"
moz-do-not-send="true">
Darshan-users@lists.mcs.anl.gov</a><br>
>> <a
href="https://lists.mcs.anl.gov/mailman/listinfo/darshan-users"
moz-do-not-send="true">https://lists.mcs.anl.gov/mailman/listinfo/darshan-users</a><br>
><br>
> _______________________________________________<br>
> Darshan-users mailing list<br>
> <a class="x_moz-txt-link-abbreviated"
href="mailto:Darshan-users@lists.mcs.anl.gov"
moz-do-not-send="true">
Darshan-users@lists.mcs.anl.gov</a><br>
> <a
href="https://lists.mcs.anl.gov/mailman/listinfo/darshan-users"
moz-do-not-send="true">https://lists.mcs.anl.gov/mailman/listinfo/darshan-users</a><br>
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