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<div class="moz-cite-prefix">Hi Adnan,<br>
<br>
Python indeed might be a little trickier, but I think its
possible. 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
static instrumentation and use the dynamic LD_PRELOAD approach
instead in this case. I imagine that the Python MPI bindings are
dynamically loading the MPI library at runtime even though the
Python program itself doesn't show up as a dynamic executable.<br>
<br>
The critical point in getting a Darshan log to be generated is
that it must intercept MPI_Init() and MPI_Finalize(). If it can
achieve that much then it should at least produce a log file.<br>
<br>
Can you try that method again (disabling the static
instrumentation and 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>
</div>
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cite="mid:b541cf1934a64faca5ebed26528c831d@NAGURSKI.anl.gov"
type="cite">
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<div dir="ltr">Hi Phil,
<div><br>
<div>Sorry for the late reply, we were focusing on some other
aspects but now we are back to using Darshan for analyzing
our application. Our executable is statically linked; the
previous error was caused by LD_PRELOAD being set in our
environment. After resetting LD_PRELOAD (so that we are not
dynamically instrumenting), the application runs and there
are no symbol mapping errors. However after job completion,
no trace file appears in the log directory. We used
environment variables with the latest MPICH release in an
attempt to statically instrument our application. Compiling
a simple mpi application with the environment variables set
does produce a Darshan trace file, but our application does
not. Also for our executable, using ldd <python
script> we get: "not a dynamic executable"</div>
<div><br>
</div>
<div><br>
</div>
<div>Here is some more detail about our application and its
dependencies. Our application is written in python. The
application uses mpi4py for all MPI calls. Also we are
reading and writing netcdf files but are using PyNIO which
breaks down python calls into standard netcdf I/O. This <a
moz-do-not-send="true"
href="http://www.alcf.anl.gov/user-guides/darshan"
target="_blank">
site</a> says that dealing with languages other than
c,c++,and Fortran could cause issues. I was thinking the
python code could be causing the issue. Possibly, the PyNIO
package on top of netcdf or mpi4py are not being detected by
Darshan. Or more likely, I am not correctly compiling the
correct software with the environment variables. The only
software that directly uses the mpi compiler is mpi4py, and
I did recompile this after setting the environment
variables. I also recompiled PyNIO and our application for
good measure. <br>
</div>
<div><br>
</div>
</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 Fri, May 29, 2015 at 10:00 AM, <span
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Today's Topics:<br>
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1. Darshan error with HDF5 (Adnan Haider)<br>
2. Re: Darshan error with HDF5 (Phil Carns)<br>
<br>
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----------------------------------------------------------------------<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>
To: <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>
<<a moz-do-not-send="true"
href="mailto:CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com">CAM2fH+yEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com</a>><br>
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<br>
Hi,<br>
I am hoping to use Darshan for analyzing our application's
performance. We<br>
are using HDF5 and netcdf 4. I installed Darshan version
2.3.1 and mvapich2<br>
for our mpi implementation. Darshan works fine for a
standard mpi pingpong<br>
application. When we run our application, however, it gives
the 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 ranks<br>
specified at runtime. Nothing is written into the log
directory. This is<br>
the only output, unless there is some error file I am not
aware of. I used<br>
the static instrumentation approach for enabling Darshan.
Thanks for the<br>
help!<br>
<br>
Thanks, Adnan Haider<br>
B.S Candidate, Computer Science<br>
Illinois Institute of Technology<br>
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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>><br>
To: <<a moz-do-not-send="true"
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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>
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<br>
Hi Adnan!<br>
<br>
Is everything in the application statically linked (maybe
check 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 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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