[Darshan-users] Darshan-users Digest, Vol 47, Issue 1
Phil Carns
carns at mcs.anl.gov
Wed Jul 8 10:05:27 CDT 2015
Is HDF5 being called directly, or is it an indirect dependency of the
netcdf library in this case?
Thanks, and sorry for the slow response times this week.
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.
thanks,
-Phil
On 07/06/2015 06:23 PM, Adnan Haider wrote:
> Hey Phil,
> After exclusively using LD_PRELOAD, i get 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
>
> Also you are correct; our application during runtime loads mpi4py
> which contains the MPI_Init and MPI_Finalize calls.
>
> Thanks, Adnan Haider
> B.S Candidate, Computer Science
> Illinois Institute of Technology
>
> On Thu, Jul 2, 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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> 1. Re: Darshan-users Digest, Vol 45, Issue 6 (Phil Carns)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 2 Jul 2015 09:40:10 -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-users Digest, Vol 45, Issue 6
> Message-ID: <55953F3A.9020005 at mcs.anl.gov
> <mailto:55953F3A.9020005 at mcs.anl.gov>>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> 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>
> > <mailto:darshan-users-request at lists.mcs.anl.gov
> <mailto:darshan-users-request at lists.mcs.anl.gov>>> wrote:
> >
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> <mailto:darshan-users at lists.mcs.anl.gov>>
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> > Today's Topics:
> >
> > 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>
> > <mailto: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>
> > <mailto: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>
> <mailto:CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA at mail.gmail.com
> <mailto:CAM2fH%252ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA 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
> > -------------- next part --------------
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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> <mailto: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>
> > <mailto: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>
> > <mailto: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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