<div dir="ltr">Hi Phil,<div>HDF5 is being called by the netcdf library; our application does not call it directly. I did remove hdf5-stubs and hdf5 from the makefile. However, I get the same error. I did this rather quick so I may have done it incorrectly. I will go over in detail and let you know. Thanks for the help.</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 Wed, Jul 8, 2015 at 8:05 AM, <span dir="ltr"><<a href="mailto:darshan-users-request@lists.mcs.anl.gov" target="_blank">darshan-users-request@lists.mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Darshan-users mailing list submissions to<br>
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<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 8 Jul 2015 11:05:27 -0400<br>
From: Phil Carns <<a href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a>><br>
To: <<a href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a>><br>
Subject: Re: [Darshan-users] Darshan-users Digest, Vol 47, Issue 1<br>
Message-ID: <<a href="mailto:559D3C37.1090208@mcs.anl.gov">559D3C37.1090208@mcs.anl.gov</a>><br>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
<br>
Is HDF5 being called directly, or is it an indirect dependency of the<br>
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<br>
modify the darhan-runtime makefile to omit the hdf5 and hdf5-stubs<br>
objects from libdarshan.so. They aren't strictly required (and won't<br>
tell you much except that HDF was used for a given file). That may get<br>
you to a point where you can observe the normal POSIX and MPIIO counters<br>
for now.<br>
<br>
thanks,<br>
-Phil<br>
<br>
On 07/06/2015 06:23 PM, Adnan Haider wrote:<br>
> Hey Phil,<br>
> After exclusively using LD_PRELOAD, i get 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>
> Also you are correct; our application during runtime loads mpi4py<br>
> which contains the MPI_Init and MPI_Finalize calls.<br>
><br>
> Thanks, Adnan Haider<br>
> B.S Candidate, Computer Science<br>
> Illinois Institute of Technology<br>
><br>
> On Thu, Jul 2, 2015 at 10:00 AM,<br>
> <<a href="mailto:darshan-users-request@lists.mcs.anl.gov">darshan-users-request@lists.mcs.anl.gov</a><br>
> <mailto:<a href="mailto:darshan-users-request@lists.mcs.anl.gov">darshan-users-request@lists.mcs.anl.gov</a>>> wrote:<br>
><br>
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><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Thu, 2 Jul 2015 09:40:10 -0400<br>
> From: Phil Carns <<a href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a> <mailto:<a href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a>>><br>
> To: <<a href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a><br>
> <mailto:<a 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 href="mailto:55953F3A.9020005@mcs.anl.gov">55953F3A.9020005@mcs.anl.gov</a><br>
> <mailto:<a href="mailto:55953F3A.9020005@mcs.anl.gov">55953F3A.9020005@mcs.anl.gov</a>>><br>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
><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<br>
> 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<br>
> 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<br>
> 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<br>
> 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 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<br>
> 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<br>
> 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 href="mailto:darshan-users-request@lists.mcs.anl.gov">darshan-users-request@lists.mcs.anl.gov</a><br>
> <mailto:<a href="mailto:darshan-users-request@lists.mcs.anl.gov">darshan-users-request@lists.mcs.anl.gov</a>><br>
> > <mailto:<a href="mailto:darshan-users-request@lists.mcs.anl.gov">darshan-users-request@lists.mcs.anl.gov</a><br>
> <mailto:<a href="mailto:darshan-users-request@lists.mcs.anl.gov">darshan-users-request@lists.mcs.anl.gov</a>>>> wrote:<br>
> ><br>
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> <mailto:<a 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<br>
> 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>
> ><br>
> > Message: 1<br>
> > Date: Thu, 28 May 2015 14:20:07 -0600<br>
> > From: Adnan Haider <<a href="mailto:ahaider3@hawk.iit.edu">ahaider3@hawk.iit.edu</a><br>
> <mailto:<a href="mailto:ahaider3@hawk.iit.edu">ahaider3@hawk.iit.edu</a>><br>
> > <mailto:<a href="mailto:ahaider3@hawk.iit.edu">ahaider3@hawk.iit.edu</a> <mailto:<a href="mailto:ahaider3@hawk.iit.edu">ahaider3@hawk.iit.edu</a>>>><br>
> > To: <a href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a><br>
> <mailto:<a href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a>><br>
> > <mailto:<a href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a><br>
> <mailto:<a 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>
> ><br>
> <<a href="mailto:CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com">CAM2fH+yEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com</a><br>
> <mailto:<a href="mailto:CAM2fH%252ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com">CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com</a>><br>
> <mailto:<a href="mailto:CAM2fH%252ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com">CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com</a><br>
> <mailto:<a href="mailto:CAM2fH%25252ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@mail.gmail.com">CAM2fH%252ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA@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<br>
> 2.3.1 and<br>
> > mvapich2<br>
> > for our mpi implementation. Darshan works fine for a<br>
> 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<br>
> 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>
> > An HTML attachment was scrubbed...<br>
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> ><br>
> > ------------------------------<br>
> ><br>
> > Message: 2<br>
> > Date: Thu, 28 May 2015 16:32:04 -0400<br>
> > From: Phil Carns <<a href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a><br>
> <mailto:<a href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a>> <mailto:<a href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a><br>
> <mailto:<a href="mailto:carns@mcs.anl.gov">carns@mcs.anl.gov</a>>>><br>
> > To: <<a href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a><br>
> <mailto:<a href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a>><br>
> > <mailto:<a href="mailto:darshan-users@lists.mcs.anl.gov">darshan-users@lists.mcs.anl.gov</a><br>
> <mailto:<a 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 href="mailto:55677B44.7060107@mcs.anl.gov">55677B44.7060107@mcs.anl.gov</a><br>
> <mailto:<a href="mailto:55677B44.7060107@mcs.anl.gov">55677B44.7060107@mcs.anl.gov</a>><br>
> > <mailto:<a href="mailto:55677B44.7060107@mcs.anl.gov">55677B44.7060107@mcs.anl.gov</a><br>
> <mailto:<a href="mailto:55677B44.7060107@mcs.anl.gov">55677B44.7060107@mcs.anl.gov</a>>>><br>
> > Content-Type: text/plain; charset="windows-1252";<br>
> 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<br>
> generated by<br>
> > the dynamic (ld-preloaded) darshan library, because it has<br>
> to locate<br>
> > underlying symbols at run time. The symbol name mapping<br>
> 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<br>
> Darshan<br>
> > > version 2.3.1 and mvapich2 for our mpi implementation.<br>
> 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<br>
> 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<br>
> am not<br>
> > > aware of. I used the static instrumentation approach for<br>
> 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>
> > -------------- next part --------------<br>
> > An HTML attachment was scrubbed...<br>
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> ><br>
> > ------------------------------<br>
> ><br>
> > _______________________________________________<br>
> > Darshan-users mailing list<br>
> > <a href="mailto:Darshan-users@lists.mcs.anl.gov">Darshan-users@lists.mcs.anl.gov</a><br>
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> ><br>
> > End of Darshan-users Digest, Vol 45, Issue 6<br>
> > ********************************************<br>
> ><br>
> ><br>
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