[Darshan-users] Darshan-users Digest, Vol 45, Issue 6
Phil Carns
carns at mcs.anl.gov
Thu Jul 2 08:40:10 CDT 2015
Hi Adnan,
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.
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.
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.
Can you try that method again (disabling the static instrumentation and
instead using LD_PRELOAD exclusively) and confirm the error?
thanks,
-Phil
On 06/29/2015 02:47 PM, Adnan Haider wrote:
> Hi Phil,
>
> 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"
>
>
> 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 site <http://www.alcf.anl.gov/user-guides/darshan> 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.
>
>
> Thanks, Adnan Haider
> B.S Candidate, Computer Science
> Illinois Institute of Technology
>
> On Fri, May 29, 2015 at 10:00 AM,
> <darshan-users-request at lists.mcs.anl.gov
> <mailto:darshan-users-request at lists.mcs.anl.gov>> wrote:
>
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> Today's Topics:
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> 1. Darshan error with HDF5 (Adnan Haider)
> 2. Re: Darshan error with HDF5 (Phil Carns)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 28 May 2015 14:20:07 -0600
> From: Adnan Haider <ahaider3 at hawk.iit.edu
> <mailto:ahaider3 at hawk.iit.edu>>
> To: darshan-users at lists.mcs.anl.gov
> <mailto:darshan-users at lists.mcs.anl.gov>
> Subject: [Darshan-users] Darshan error with HDF5
> Message-ID:
>
> <CAM2fH+yEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA at mail.gmail.com <mailto:CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
> I am hoping to use Darshan for analyzing our application's
> performance. We
> are using HDF5 and netcdf 4. I installed Darshan version 2.3.1 and
> mvapich2
> for our mpi implementation. Darshan works fine for a standard mpi
> pingpong
> application. When we run our application, however, it gives the
> following
> error:
> Darshan failed to map symbol: H5Fopen
> Darshan failed to map symbol: H5Fopen
> Darshan failed to map symbol: H5Fopen
> Darshan failed to map symbol: H5Fopen
>
> The four instances of the error probably have to do with the 4 mpi
> ranks
> specified at runtime. Nothing is written into the log directory.
> This is
> the only output, unless there is some error file I am not aware
> of. I used
> the static instrumentation approach for enabling Darshan. Thanks
> for the
> help!
>
> Thanks, Adnan Haider
> B.S Candidate, Computer Science
> Illinois Institute of Technology
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>
> Message: 2
> Date: Thu, 28 May 2015 16:32:04 -0400
> From: Phil Carns <carns at mcs.anl.gov <mailto:carns at mcs.anl.gov>>
> To: <darshan-users at lists.mcs.anl.gov
> <mailto:darshan-users at lists.mcs.anl.gov>>
> Subject: Re: [Darshan-users] Darshan error with HDF5
> Message-ID: <55677B44.7060107 at mcs.anl.gov
> <mailto:55677B44.7060107 at mcs.anl.gov>>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi Adnan!
>
> Is everything in the application statically linked (maybe check
> with ldd
> <executable>)? That error message is supposed to only be generated by
> the dynamic (ld-preloaded) darshan library, because it has to locate
> underlying symbols at run time. The symbol name mapping should be set
> at link time for a static executable.
>
> thanks,
> -Phil
>
> On 05/28/2015 04:20 PM, Adnan Haider wrote:
> > Hi,
> > I am hoping to use Darshan for analyzing our application's
> > performance. We are using HDF5 and netcdf 4. I installed Darshan
> > version 2.3.1 and mvapich2 for our mpi implementation. Darshan works
> > fine for a standard mpi pingpong application. When we run our
> > application, however, it gives the following error:
> > Darshan failed to map symbol: H5Fopen
> > Darshan failed to map symbol: H5Fopen
> > Darshan failed to map symbol: H5Fopen
> > Darshan failed to map symbol: H5Fopen
> >
> > The four instances of the error probably have to do with the 4 mpi
> > ranks specified at runtime. Nothing is written into the log
> directory.
> > This is the only output, unless there is some error file I am not
> > aware of. I used the static instrumentation approach for enabling
> > Darshan. Thanks for the help!
> >
> > Thanks, Adnan Haider
> > B.S Candidate, Computer Science
> > Illinois Institute of Technology
>
>
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