<html><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body>
<p>Hunh, that's interesting. On most systems, the install process
would set either RUNPATH or RPATH in the executable to point to
the install directory's lib path so that LD_LIBRARY_PATH does not
need to be set. For example, the darshan-parser binary installed
in /home/carns/working/install/bin on my laptop shows this:</p>
<p>carns-x1-7g ~/w/i/bin> readelf -d darshan-parser |grep RUNPATH<br>
0x000000000000001d (RUNPATH) Library runpath:
[/home/carns/working/install/lib]</p>
<p>carns-x1-7g ~/w/i/bin> readelf -d darshan-parser |grep RPATH<br>
</p>
<p>You have to check both because some platforms might use RUNPATH
or RPATH. They have slightly different semantics but accomplish
the same thing for our purposes. At any rate, since the
executable has the path embedded within it, it will work without
having to set LD_LIBRARY_PATH.</p>
<p>I'm not sure why you are having a different experience, but it
sounds like things are up and running for you anyhow.</p>
<p>thanks,</p>
<p>-Phil<br>
</p>
<div class="moz-cite-prefix">On 5/9/22 1:59 AM, Jiří Nádvorník
wrote:<br>
</div>
<blockquote type="cite" cite="mid:CAAsB-qJXaHO5hAn1==1tQmG5HF+M0a3Oo+UkqxHoxbkFA=Vr-A@mail.gmail.com">
<div dir="ltr">Hi Phil and others,
<div><br>
</div>
<div>in the end the problem was somewhere else and much more
prosaic :/. The path where darshan was installed by default
(lib folder specifically) was missing from the <span style="font-family:Calibri;font-size:11pt">LD_LIBRARY_PATH
environment variable and therefore the library could not be
found at runtime.</span></div>
<div><span style="font-family:Calibri;font-size:11pt"><br>
</span></div>
<div><span style="font-family:Calibri;font-size:11pt">BR,</span></div>
<div><span style="font-family:Calibri;font-size:11pt"><br>
</span></div>
<div><span style="font-family:Calibri;font-size:11pt">Jiri</span></div>
<div><span style="font-family:Calibri;font-size:11pt"></span>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">pá 6. 5. 2022 v 15:56
odesílatel Jiří Nádvorník <<a href="mailto:nadvornik.ji@gmail.com" moz-do-not-send="true" class="moz-txt-link-freetext">nadvornik.ji@gmail.com</a>>
napsal:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Aha,
<div><br>
</div>
<div>maybe I formulated it wrongly. The problem is that the
version that is installed by make install is taken from
the .lib folder and not from the darshan-util one. So when
trying to run for example darshan-parser, it complains
about ".libs/libdarshan-util.so.0" missing.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Jiri</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">st 4. 5. 2022 v 22:41
odesílatel Phil Carns <<a href="mailto:carns@mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">carns@mcs.anl.gov</a>>
napsal:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi Jiri,</p>
<p>For #2, are you talking about .libs/darshan-parser in
the build path? If so, I wouldn't expect to be able
to run that directly (in general, not particular to
Darshan's build system).</p>
<p>Autotools and libtool create executables in .libs
subdirs as part of the build process, but those are
intermediate executables that don't have final library
paths set. The copy installed in <prefix>/bin
should be fine (and should use corresponding installed
libraries), and you should also be able to run
darshan-parser one level up in the build tree (that's
actually a shell script wrapper created by libtool
that will run the .libs/darshan-parser with library
paths set to the build tree).</p>
<p>Sometimes .libs/ executables might work, but it's a
little dicey what libraries they will pick up so it's
usually not a good idea.<br>
</p>
<p>thanks,</p>
<p>-Phil<br>
</p>
<div>On 4/27/22 1:34 PM, Jiří Nádvorník wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>to reproduce the installation issue:</div>
<div>mkdir darshan_root</div>
<div>cd darshan_root</div>
<div>git clone <a href="https://github.com/darshan-hpc/darshan.git" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/darshan-hpc/darshan.git</a>
.<br>
<div><br>
</div>
<div>Then cd darshan-utils/ and then run:</div>
<div>autoconf</div>
<div>configure</div>
<div>make install</div>
<div><br>
</div>
<div>Then:</div>
<div>
<ol>
<li>If running darshan-parser within the same
folder it runs fine.</li>
<li>If running .lib/darshan-parser (which is
installed by make install) it crashes with
the library not available, see the previous
email.</li>
</ol>
</div>
<div>Cheers,</div>
<div><br>
Jiri</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">st 27. 4. 2022
v 18:23 odesílatel Snyder, Shane <<a href="mailto:ssnyder@mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">ssnyder@mcs.anl.gov</a>>
napsal:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px
0px 0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Great,
I'm glad that you were able to get the
instrumentation mostly working!</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I
think it's sensible to ignore Python
source/compiled code for most cases -- I doubt
there's any insight to gain and you'll just
end up trying to filter them out when
analyzing logs anyways.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I'm
not sure what's going on with the installation
issues you mention. If you think something
might be wrong with Darshan's build, then
would you mind sharing how you ran configure,
etc.? I could see if I'm able to reproduce
anything. <br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">If
you wouldn't mind starting a new thread
related to the HDF5 issue, I think that would
be helpful -- it might help if other users
ever want to search the list archive for
h5py/HDF5 related issues if you include those
in the title.<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">--Shane<br>
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-9014243290627863420gmail-m_6519552878307446660gmail-m_-2273691217974330162divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b>
Jiří Nádvorník <<a href="mailto:nadvornik.ji@gmail.com" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">nadvornik.ji@gmail.com</a>><br>
<b>Sent:</b> Wednesday, April 27, 2022 11:06
AM<br>
<b>To:</b> Snyder, Shane <<a href="mailto:ssnyder@mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">ssnyder@mcs.anl.gov</a>><br>
<b>Cc:</b> <a href="mailto:darshan-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">darshan-users@lists.mcs.anl.gov</a>
<<a href="mailto:darshan-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">darshan-users@lists.mcs.anl.gov</a>><br>
<b>Subject:</b> Re: [Darshan-users] Module
contains incomplete data</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>Hi,</div>
<div dir="ltr"><br>
</div>
<div dir="ltr">yes, that NAMEMEM got it
done. I also excluded .py and .pyc files -
those reads are only loading of them,
right? No data access itself (and no, I'm
not reading and manually interpreting my
own python files :), so I'm not interested
into that ). Actually, I'm reading
thousands of small files which I'm
ingesting into HDF5 and I'm interested
into how many reads, etc. are happening. </div>
<div dir="ltr"><br>
</div>
<div dir="ltr">I'm trying to make some sense
of what I see but for now I'm just going
to say it's very valuable data for me.
Pity I can't get the Hdf5 module, if it
would give me more granularity it would be
very helpful.
<div><br>
</div>
<div>Regarding the darshan-utils you were
right, I didn't reinstall them. I
actually ran into an install problem -
for some reason, the git installation
takes the .lib/darshan-parser when
installing it to /usr/local/... and that
one throws:</div>
<div>darshan-parser: error while loading
shared libraries: libdarshan-util.so.0:
cannot open shared object file: No such
file or directory</div>
<div><br>
</div>
<div>But if I run the darshan-parser
within darshan_root_folder/darshan-util/
then the error is gone and
--show-incomplete |grep incomplete
prints nothing.</div>
<div><br>
</div>
<div>Could we now focus on the HDF5 issue
or should I create a new thread for
clarity?</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Jiri</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div>
<div dir="ltr">st 27. 4. 2022 v 17:21
odesílatel Snyder, Shane <<a href="mailto:ssnyder@mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">ssnyder@mcs.anl.gov</a>>
napsal:<br>
</div>
<blockquote style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Thanks
for working through the build issues
and giving this a shot.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">A
couple of things stand out to me
(ignoring your HDF5 issue for now):</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<ul>
<li>It looks like at least the
MPI-IO module is no longer
reporting partial data? Small
progress...</li>
<li>There is a new warning about
there being no log utility
handlers for a "null" module.
Are you perhaps parsing a log
generated by your prior Darshan
install? Maybe you have not
completely re-installed a new
darshan-util? We should figure
out what's going on there, too,
to be safe.<br>
</li>
</ul>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I'd
also suggest two things for your
config file:</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<ul>
<li>Dial back MODMEM and
MAX_RECORDS values. Your MODMEM
value is asking Darshan to
allocate a GiB of memory (it is
expressed in MiB units and you
set to 1024), which Darshan will
happily try to do, I'm not sure
it's a good idea though. I'd
probably start with a MODMEM
value of 8 and MAX_RECORDS of
2000, and just double those
again if needed -- anything
beyond that would be surprising
unless you know your workload is
really opening hundreds of
thousands of files. You might
also have a look at the files
Darshan is currently
instrumenting and see if you
really want it to -- I've
noticed when instrumenting
Python frameworks that you can
get tons of records for things
like shared libraries, source
files, etc. that can just be
ignored using NAME_EXCLUDE
mechanisms. <br>
</li>
<li>Add "NAMEMEM 2" to your
config file to force Darshan to
allocate more memory (2 MiB) for
storing the filenames associated
with each record. This might
actually be the main reason your
log is reporting partial data
rather than actually running out
of module data, which is another
reason not to get too aggressive
with the MODMEM/MAX_RECORDS
parameters. I should have
mentioned this setting
originally as there have been
other users who have reported
exceeding it recently.<br>
</li>
</ul>
<div>Hopefully that gets you further
along and we can move onto the
HDF5 issue you mention.<br>
</div>
<div><br>
</div>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Thanks,<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">--Shane<br>
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-9014243290627863420gmail-m_6519552878307446660gmail-m_-2273691217974330162x_gmail-m_6650929377004058598divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Jiří
Nádvorník <<a href="mailto:nadvornik.ji@gmail.com" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">nadvornik.ji@gmail.com</a>><br>
<b>Sent:</b> Wednesday, April 27,
2022 6:37 AM<br>
<b>To:</b> Snyder, Shane <<a href="mailto:ssnyder@mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">ssnyder@mcs.anl.gov</a>><br>
<b>Cc:</b> <a href="mailto:darshan-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">darshan-users@lists.mcs.anl.gov</a>
<<a href="mailto:darshan-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">darshan-users@lists.mcs.anl.gov</a>><br>
<b>Subject:</b> Re:
[Darshan-users] Module contains
incomplete data</font>
<div> </div>
</div>
<div>
<div dir="ltr">Aha! I just realized
there is an obvious "prepare.sh"
script that I didn't run, I found
out by trial and error though,
could be more documented :).
<div><br>
</div>
<div>Now I'm further.. With a
config file:</div>
<div>MAX_RECORDS 102400
POSIX,MPI-IO,STDIO<br>
</div>
<div>MODMEM 1024<br>
</div>
<div>APP_EXCLUDE git,ls<br>
</div>
<div><br>
</div>
<div>I'm getting for:</div>
<div>darshan-parser
--show-incomplete
caucau_python_id127447-127447_4-27-48556-1842455298968263838_1.darshan
|grep incomplete<br>
</div>
<div><br>
</div>
<div>output:</div>
<div># *WARNING*: The POSIX module
contains incomplete data!<br>
# *WARNING*: The STDIO module
contains incomplete data!<br>
Warning: no log utility handlers
defined for module (null),
SKIPPING.<br>
</div>
<div><br>
</div>
<div>I don't think I have more
than 100000 files to be touched
by my poor tiny python script,
right?</div>
<div><br>
</div>
<div>By the way I've encountered
another problem, not sure
whether to put it to another
thread. If I compile with HDF5
(the results above are without
it):</div>
<div>./configure
--with-log-path=/gpfs/raid/darshan-logs
--with-jobid-env=PBS_JOBID
CC=mpicc --enable-hdf5-mod
--with-hdf5=/gpfs/raid/SDSSCube/ext_lib//hdf5-1.12.0/hdf5/<br>
</div>
<div><br>
</div>
<div>It messes up my runtime and
causes python to crash:</div>
<div>mpirun -x
DARSHAN_CONFIG_PATH=/gpfs/raid/SDSSCube/darshan.conf
-x
LD_PRELOAD=/gpfs/raid/shared_libs/darshan/darshan-runtime/lib/.libs/libdarshan.so:/gpfs/raid/SDSSCube/ext_lib/hdf5-1.12.0/hdf5/lib/libhdf5.so
-np 65 --hostfile hosts --map-by
node
/gpfs/raid/SDSSCube/venv_par/bin/python
hisscube.py --truncate
../sdss_data/
results/SDSS_cube_c_par.h5<br>
</div>
<div><br>
</div>
<div>Resulting in:</div>
<div><a moz-do-not-send="true">INFO:rank</a>[0]:Rank
0 pid: 137058<br>
Darshan HDF5 module error:
runtime library version (1.12)
incompatible with Darshan module
(1.10-).<br>
Traceback (most recent call
last):<br>
File "hisscube.py", line 74,
in <module><br>
writer.ingest(fits_image_path,
fits_spectra_path,
truncate_file=args.truncate)<br>
File
"/gpfs/raid/SDSSCube/hisscube/ParallelWriterMWMR.py",
line 45, in ingest<br>
self.process_metadata(image_path,
image_pattern, spectra_path,
spectra_pattern, truncate_file)<br>
File
"/gpfs/raid/SDSSCube/hisscube/CWriter.py",
line 150, in process_metadata<br>
h5_file =
self.open_h5_file_serial(truncate_file)<br>
File
"/gpfs/raid/SDSSCube/hisscube/CWriter.py",
line 170, in open_h5_file_serial<br>
return
h5py.File(self.h5_path, 'w',
fs_strategy="page",
fs_page_size=4096,
libver="latest")<br>
File
"/gpfs/raid/SDSSCube/venv_par/lib/python3.8/site-packages/h5py-3.6.0-py3.8-linux-x86_64.egg/h5py/_hl/files.py",
line 533, in __init__<br>
fid = make_fid(name, mode,
userblock_size, fapl, fcpl,
swmr=swmr)<br>
File
"/gpfs/raid/SDSSCube/venv_par/lib/python3.8/site-packages/h5py-3.6.0-py3.8-linux-x86_64.egg/h5py/_hl/files.py",
line 232, in make_fid<br>
fid = h5f.create(name,
h5f.ACC_TRUNC, fapl=fapl,
fcpl=fcpl)<br>
File "h5py/_objects.pyx", line
54, in
h5py._objects.with_phil.wrapper<br>
File "h5py/_objects.pyx", line
55, in
h5py._objects.with_phil.wrapper<br>
File "h5py/h5f.pyx", line 126,
in h5py.h5f.create<br>
File "h5py/defs.pyx", line
693, in h5py.defs.H5Fcreate<br>
RuntimeError: Unspecified error
in H5Fcreate (return value
<0)<br>
</div>
<div><br>
</div>
<div>You are saying that darshan
should be compatible with HDF5
> 1.8, which 1.12 should be,
right?</div>
<div><br>
</div>
<div>Thanks for help!</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Jiri</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
<div>
<div dir="ltr">st 27. 4. 2022
v 8:43 odesílatel Jiří Nádvorník
<<a href="mailto:nadvornik.ji@gmail.com" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">nadvornik.ji@gmail.com</a>>
napsal:<br>
</div>
<blockquote style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hi,
<div><br>
</div>
<div>I think I will chew
through the documentation
just fine but two things are
not clear:</div>
<div>
<ol>
<li>Does the darshan
library provide its own
config file that I need
to change or do I need
to always create my own?</li>
<li>How can I build the
git version? I didn't
find any instructions
and the usual autoconf
just throws:</li>
<ol>
<li>root@kub-b1:/gpfs/raid/shared_libs/darshan/darshan-runtime#
autoconf<br>
<a href="http://configure.ac:19" target="_blank" moz-do-not-send="true">configure.ac:19</a>:
error: possibly
undefined macro:
AC_CONFIG_MACRO_DIRS<br>
If this token
and others are
legitimate, please use
m4_pattern_allow.<br>
See the Autoconf
documentation.<br>
<a href="http://configure.ac:21" target="_blank" moz-do-not-send="true">configure.ac:21</a>:
error: possibly
undefined macro:
AM_INIT_AUTOMAKE<br>
<a href="http://configure.ac:22" target="_blank" moz-do-not-send="true">configure.ac:22</a>:
error: possibly
undefined macro:
AM_SILENT_RULES<br>
<a href="http://configure.ac:23" target="_blank" moz-do-not-send="true">configure.ac:23</a>:
error: possibly
undefined macro:
AM_MAINTAINER_MODE<br>
<a href="http://configure.ac:713" target="_blank" moz-do-not-send="true">configure.ac:713</a>:
error: possibly
undefined macro:
AM_CONDITIONAL<br>
root@kub-b1:/gpfs/raid/shared_libs/darshan/darshan-runtime# ./configure<br>
configure: error:
cannot find
install-sh,
install.sh, or shtool
in ../maint/scripts
"."/../maint/scripts<br>
</li>
</ol>
</ol>
<div>Thanks for help.</div>
</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Jiri</div>
</div>
<br>
<div>
<div dir="ltr">út 26. 4. 2022
v 17:43 odesílatel Snyder,
Shane <<a href="mailto:ssnyder@mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">ssnyder@mcs.anl.gov</a>>
napsal:<br>
</div>
<blockquote style="margin:0px
0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Hi
Jiri,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">For
some background, Darshan
enforces some internal
memory limits to avoid
ballooning memory usage
at runtime.
Specifically, all of our
instrumentation modules
should pre-allocate file
records for up to 1,024
files opened by the app
-- if your app opens
more than 1,024 files
per-process, Darshan
stops instrumenting and
issues those warning
messages when parsing
the log file.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">We
have users hit this
issue pretty frequently
now, and we actually
just wrapped up
development of some new
mechanisms to help out
with this. They were
just merged into our
main branch, and we will
be formally releasing a
pre-release version of
this code in the next
week or so. For the time
being, you should be
able to use the 'main'
branch of our repo (<a href="https://github.com/darshan-hpc/darshan" id="gmail-m_-9014243290627863420gmail-m_6519552878307446660gmail-m_-2273691217974330162x_gmail-m_6650929377004058598x_gmail-m_8980332545816639580gmail-m_8205458234077072596LPNoLPOWALinkPreview" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/darshan-hpc/darshan</a>)
to leverage this new
functionality.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">There
are 2 new mechanisms
that can help out, both
of which require you to
provide a configuration
file to Darshan at
runtime:</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<ul style="list-style-position:inside">
<li>MAX_RECORDS
setting can be used
to bump up the
number of
pre-allocated
records for
different modules.
In your case, you
might try to bump up
the default number
of records for the
POSIX, MPI-IO, and
STDIO modules by
setting something
like this in your
config file (this
would allow you to
instrument up to
4000 files
per-process for each
of these modules):</li>
<ul>
<li>MAX_RECORDS
4000
POSIX,MPI-IO,STDIO</li>
</ul>
<li>An alternative (or
complementary)
approach to bumping
up the record limit
is to limit
instrumentation to
particular files.
You can use the
NAME_EXCLUDE setting
to avoid
instrumenting
specific directory
paths, file
extensions, etc by
specifying regular
expressions. E.g,
the following
settings would avoid
instrumenting files
with .so prefixes or
files located in a
directory we don't
care about for all
modules (* denotes
all modules):</li>
<ul>
<li>NAME_EXCLUDE
.so$ *</li>
<li>NAME_EXCLUDE
^/path/to/avoid
*</li>
</ul>
</ul>
<div>I'm attaching the
updated runtime
documentation for
Darshan for your
reference. Section 8
provides a ton of
details on how to
provide a config file
to Darshan that should
help clear up any
missing gaps in my
description above.</div>
<div><br>
</div>
<div>Please let us know
if you have any
further questions or
issues, though!</div>
<div><br>
</div>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Thanks,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">--Shane<br>
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-9014243290627863420gmail-m_6519552878307446660gmail-m_-2273691217974330162x_gmail-m_6650929377004058598x_gmail-m_8980332545816639580gmail-m_8205458234077072596divRplyFwdMsg" dir="ltr"> <font style="font-size:11pt" face="Calibri,
sans-serif" color="#000000"><b>From:</b>
Darshan-users <<a href="mailto:darshan-users-bounces@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">darshan-users-bounces@lists.mcs.anl.gov</a>>
on behalf of Jiří
Nádvorník <<a href="mailto:nadvornik.ji@gmail.com" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">nadvornik.ji@gmail.com</a>><br>
<b>Sent:</b> Sunday,
April 24, 2022 3:00 PM<br>
<b>To:</b> <a href="mailto:darshan-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">darshan-users@lists.mcs.anl.gov</a> <<a href="mailto:darshan-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">darshan-users@lists.mcs.anl.gov</a>><br>
<b>Subject:</b>
[Darshan-users] Module
contains incomplete
data</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi All,
<div><br>
</div>
<div>I just tried out
Darshan and the
potential output
seems perfect for my
HDF5 MPI
application!
Although I'm not
able to get there
:(.</div>
<div><br>
</div>
<div>I have a log that
has a big stamp
"This darshan log
contains incomplete
data".</div>
<div><br>
</div>
<div>When I run:</div>
<div>darshan-parser
--show-incomplete
mylog.darshan |grep
incomplete<br>
</div>
<div>Output is:</div>
<div># *WARNING*: The
POSIX module
contains incomplete
data!<br>
# *WARNING*: The
MPI-IO module
contains incomplete
data!<br>
# *WARNING*: The
STDIO module
contains incomplete
data!<br>
</div>
<div><br>
</div>
<div>Would you be able
to point me to some
setting that would
improve the
measurements? Can I
actually rely on the
profiling results if
it says the data is
incomplete in some
of the categories?</div>
<div><br>
</div>
<div>Thank you very
much for your help!</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Jiri</div>
<div><br>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<fieldset></fieldset>
<pre>_______________________________________________
Darshan-users mailing list
<a href="mailto:Darshan-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Darshan-users@lists.mcs.anl.gov</a>
<a href="https://lists.mcs.anl.gov/mailman/listinfo/darshan-users" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.mcs.anl.gov/mailman/listinfo/darshan-users</a>
</pre>
</blockquote>
</div>
_______________________________________________<br>
Darshan-users mailing list<br>
<a href="mailto:Darshan-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">Darshan-users@lists.mcs.anl.gov</a><br>
<a href="https://lists.mcs.anl.gov/mailman/listinfo/darshan-users" rel="noreferrer" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.mcs.anl.gov/mailman/listinfo/darshan-users</a><br>
</blockquote>
</div>
</blockquote>
</div>
</blockquote>
</body>
</html>