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<div class="moz-cite-prefix">Is HDF5 being called directly, or is it
an indirect dependency of the netcdf library in this case?<br>
<br>
Thanks, and sorry for the slow response times this week. <br>
<br>
If you want to get off the ground with something, you could
probably modify the darhan-runtime makefile to omit the hdf5 and
hdf5-stubs objects from libdarshan.so. They aren't strictly
required (and won't tell you much except that HDF was used for a
given file). That may get you to a point where you can observe
the normal POSIX and MPIIO counters for now.<br>
<br>
thanks,<br>
-Phil<br>
<br>
On 07/06/2015 06:23 PM, Adnan Haider wrote:<br>
</div>
<blockquote
cite="mid:f38c6ea394a14a4fad00d31de45ed249@LUCKMAN.anl.gov"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
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<div dir="ltr">Hey Phil,
<div>After exclusively using LD_PRELOAD, i get the following
error:</div>
<div>Darshan failed to map symbol: H5FOpen</div>
<div>Darshan failed to map symbol: H5FOpen<br>
</div>
<div>Darshan failed to map symbol: H5FOpen<br>
</div>
<div>Darshan failed to map symbol: H5FOpen<br>
</div>
<div><br>
</div>
<div>Also you are correct; our application during runtime loads
mpi4py which contains the MPI_Init and MPI_Finalize calls.</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="gmail_signature">
<div dir="ltr">Thanks, Adnan Haider
<div>B.S Candidate, Computer Science</div>
<div>Illinois Institute of Technology </div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On Thu, Jul 2, 2015 at 10:00 AM, <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:darshan-users-request@lists.mcs.anl.gov"
target="_blank">darshan-users-request@lists.mcs.anl.gov</a>></span>
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Today's Topics:<br>
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1. Re: Darshan-users Digest, Vol 45, Issue 6 (Phil Carns)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 2 Jul 2015 09:40:10 -0400<br>
From: Phil Carns <<a moz-do-not-send="true"
href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a>><br>
To: <<a moz-do-not-send="true"
href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a>><br>
Subject: Re: [Darshan-users] Darshan-users Digest, Vol 45,
Issue 6<br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:55953F3A.9020005@mcs.anl.gov">55953F3A.9020005@mcs.anl.gov</a>><br>
Content-Type: text/plain; charset="windows-1252";
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<br>
Hi Adnan,<br>
<br>
Python indeed might be a little trickier, but I think its
possible.<br>
I'll see if I can find more information about this and
report back.<br>
<br>
I *think* that you need to actually do the reverse and
disable the<br>
static instrumentation and use the dynamic LD_PRELOAD
approach instead<br>
in this case. I imagine that the Python MPI bindings are
dynamically<br>
loading the MPI library at runtime even though the Python
program itself<br>
doesn't show up as a dynamic executable.<br>
<br>
The critical point in getting a Darshan log to be generated
is that it<br>
must intercept MPI_Init() and MPI_Finalize(). If it can
achieve that<br>
much then it should at least produce a log file.<br>
<br>
Can you try that method again (disabling the static
instrumentation and<br>
instead using LD_PRELOAD exclusively) and confirm the error?<br>
<br>
thanks,<br>
-Phil<br>
<br>
On 06/29/2015 02:47 PM, Adnan Haider wrote:<br>
> Hi Phil,<br>
><br>
> Sorry for the late reply, we were focusing on some
other aspects but<br>
> now we are back to using Darshan for analyzing our
application. Our<br>
> executable is statically linked; the previous error was
caused by<br>
> LD_PRELOAD being set in our environment. After
resetting LD_PRELOAD<br>
> (so that we are not dynamically instrumenting), the
application runs<br>
> and there are no symbol mapping errors. However after
job completion,<br>
> no trace file appears in the log directory. We used
environment<br>
> variables with the latest MPICH release in an attempt
to statically<br>
> instrument our application. Compiling a simple mpi
application with<br>
> the environment variables set does produce a Darshan
trace file, but<br>
> our application does not. Also for our executable,
using ldd <python<br>
> script> we get: "not a dynamic executable"<br>
><br>
><br>
> Here is some more detail about our application and its
dependencies.<br>
> Our application is written in python. The application
uses mpi4py for<br>
> all MPI calls. Also we are reading and writing netcdf
files but are<br>
> using PyNIO which breaks down python calls into
standard netcdf I/O.<br>
> This site <<a moz-do-not-send="true"
href="http://www.alcf.anl.gov/user-guides/darshan"
rel="noreferrer" target="_blank">http://www.alcf.anl.gov/user-guides/darshan</a>>
says that<br>
> dealing with languages other than c,c++,and Fortran
could cause<br>
> issues. I was thinking the python code could be causing
the issue.<br>
> Possibly, the PyNIO package on top of netcdf or mpi4py
are not being<br>
> detected by Darshan. Or more likely, I am not correctly
compiling the<br>
> correct software with the environment variables. The
only software<br>
> that directly uses the mpi compiler is mpi4py, and I
did recompile<br>
> this after setting the environment variables. I also
recompiled PyNIO<br>
> and our application for good measure.<br>
><br>
><br>
> Thanks, Adnan Haider<br>
> B.S Candidate, Computer Science<br>
> Illinois Institute of Technology<br>
><br>
> On Fri, May 29, 2015 at 10:00 AM,<br>
> <<a moz-do-not-send="true"
href="mailto:darshan-users-request@lists.mcs.anl.gov">darshan-users-request@lists.mcs.anl.gov</a><br>
> <mailto:<a moz-do-not-send="true"
href="mailto:darshan-users-request@lists.mcs.anl.gov">darshan-users-request@lists.mcs.anl.gov</a>>>
wrote:<br>
><br>
> Send Darshan-users mailing list submissions to<br>
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><br>
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><br>
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> <a moz-do-not-send="true"
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> <mailto:<a moz-do-not-send="true"
href="mailto:darshan-users-owner@lists.mcs.anl.gov">darshan-users-owner@lists.mcs.anl.gov</a>><br>
><br>
> When replying, please edit your Subject line so it
is more specific<br>
> than "Re: Contents of Darshan-users digest..."<br>
><br>
><br>
> Today's Topics:<br>
><br>
> 1. Darshan error with HDF5 (Adnan Haider)<br>
> 2. Re: Darshan error with HDF5 (Phil Carns)<br>
><br>
><br>
>
----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Thu, 28 May 2015 14:20:07 -0600<br>
> From: Adnan Haider <<a moz-do-not-send="true"
href="mailto:ahaider3@hawk.iit.edu">ahaider3@hawk.iit.edu</a><br>
> <mailto:<a moz-do-not-send="true"
href="mailto:ahaider3@hawk.iit.edu">ahaider3@hawk.iit.edu</a>>><br>
> To: <a moz-do-not-send="true"
href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a><br>
> <mailto:<a moz-do-not-send="true"
href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a>><br>
> Subject: [Darshan-users] Darshan error with HDF5<br>
> Message-ID:<br>
><br>
> <<a moz-do-not-send="true"
href="mailto:CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com">CAM2fH+yEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com</a>
<mailto:<a moz-do-not-send="true"
href="mailto:CAM2fH%252ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com">CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com</a>>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hi,<br>
> I am hoping to use Darshan for analyzing our
application's<br>
> performance. We<br>
> are using HDF5 and netcdf 4. I installed Darshan
version 2.3.1 and<br>
> mvapich2<br>
> for our mpi implementation. Darshan works fine for
a standard mpi<br>
> pingpong<br>
> application. When we run our application, however,
it gives the<br>
> following<br>
> error:<br>
> Darshan failed to map symbol: H5Fopen<br>
> Darshan failed to map symbol: H5Fopen<br>
> Darshan failed to map symbol: H5Fopen<br>
> Darshan failed to map symbol: H5Fopen<br>
><br>
> The four instances of the error probably have to do
with the 4 mpi<br>
> ranks<br>
> specified at runtime. Nothing is written into the
log directory.<br>
> This is<br>
> the only output, unless there is some error file I
am not aware<br>
> of. I used<br>
> the static instrumentation approach for enabling
Darshan. Thanks<br>
> for the<br>
> help!<br>
><br>
> Thanks, Adnan Haider<br>
> B.S Candidate, Computer Science<br>
> Illinois Institute of Technology<br>
> -------------- next part --------------<br>
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> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Thu, 28 May 2015 16:32:04 -0400<br>
> From: Phil Carns <<a moz-do-not-send="true"
href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a>
<mailto:<a moz-do-not-send="true"
href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a>>><br>
> To: <<a moz-do-not-send="true"
href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a><br>
> <mailto:<a moz-do-not-send="true"
href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a>>><br>
> Subject: Re: [Darshan-users] Darshan error with
HDF5<br>
> Message-ID: <<a moz-do-not-send="true"
href="mailto:55677B44.7060107@mcs.anl.gov">55677B44.7060107@mcs.anl.gov</a><br>
> <mailto:<a moz-do-not-send="true"
href="mailto:55677B44.7060107@mcs.anl.gov">55677B44.7060107@mcs.anl.gov</a>>><br>
> Content-Type: text/plain; charset="windows-1252";
Format="flowed"<br>
><br>
> Hi Adnan!<br>
><br>
> Is everything in the application statically linked
(maybe check<br>
> with ldd<br>
> <executable>)? That error message is
supposed to only be generated by<br>
> the dynamic (ld-preloaded) darshan library, because
it has to locate<br>
> underlying symbols at run time. The symbol name
mapping should be set<br>
> at link time for a static executable.<br>
><br>
> thanks,<br>
> -Phil<br>
><br>
> On 05/28/2015 04:20 PM, Adnan Haider wrote:<br>
> > Hi,<br>
> > I am hoping to use Darshan for analyzing our
application's<br>
> > performance. We are using HDF5 and netcdf 4. I
installed Darshan<br>
> > version 2.3.1 and mvapich2 for our mpi
implementation. Darshan works<br>
> > fine for a standard mpi pingpong application.
When we run our<br>
> > application, however, it gives the following
error:<br>
> > Darshan failed to map symbol: H5Fopen<br>
> > Darshan failed to map symbol: H5Fopen<br>
> > Darshan failed to map symbol: H5Fopen<br>
> > Darshan failed to map symbol: H5Fopen<br>
> ><br>
> > The four instances of the error probably have
to do with the 4 mpi<br>
> > ranks specified at runtime. Nothing is written
into the log<br>
> directory.<br>
> > This is the only output, unless there is some
error file I am not<br>
> > aware of. I used the static instrumentation
approach for enabling<br>
> > Darshan. Thanks for the help!<br>
> ><br>
> > Thanks, Adnan Haider<br>
> > B.S Candidate, Computer Science<br>
> > Illinois Institute of Technology<br>
><br>
><br>
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