Hi Phil,
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.
Thanks, Adnan Haider
B.S Candidate, Computer Science
Illinois Institute of Technology
On Wed, Jul 8, 2015 at 8:05 AM, <darshan-users-request(a)lists.mcs.anl.gov>
wrote:
> Send Darshan-users mailing list submissions to
> darshan-users(a)lists.mcs.anl.gov
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>
> Today's Topics:
>
> 1. Re: Darshan-users Digest, Vol 47, Issue 1 (Phil Carns)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 8 Jul 2015 11:05:27 -0400
> From: Phil Carns <carns(a)mcs.anl.gov>
> To: <darshan-users(a)lists.mcs.anl.gov>
> Subject: Re: [Darshan-users] Darshan-users Digest, Vol 47, Issue 1
> Message-ID: <559D3C37.1090208(a)mcs.anl.gov>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> 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(a)lists.mcs.anl.gov
> > <mailto:[email protected]>> wrote:
> >
> > Send Darshan-users mailing list submissions to
> > darshan-users(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://lists.mcs.anl.gov/mailman/listinfo/darshan-users
> > <https://lists.mcs.anl.gov/mailman/listinfo/darshan-users>
> > or, via email, send a message with subject or body 'help' to
> > darshan-users-request(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> >
> > You can reach the person managing the list at
> > darshan-users-owner(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Darshan-users digest..."
> >
> >
> > Today's Topics:
> >
> > 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(a)mcs.anl.gov <mailto:[email protected]>>
> > To: <darshan-users(a)lists.mcs.anl.gov
> > <mailto:[email protected]>>
> > Subject: Re: [Darshan-users] Darshan-users Digest, Vol 45, Issue 6
> > Message-ID: <55953F3A.9020005(a)mcs.anl.gov
> > <mailto:[email protected]>>
> > 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(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> > > <mailto:[email protected]
> > <mailto:[email protected]>>> wrote:
> > >
> > > Send Darshan-users mailing list submissions to
> > > darshan-users(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> > > <mailto:[email protected]
> > <mailto:[email protected]>>
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > https://lists.mcs.anl.gov/mailman/listinfo/darshan-users
> > > <https://lists.mcs.anl.gov/mailman/listinfo/darshan-users>
> > > or, via email, send a message with subject or body 'help' to
> > > darshan-users-request(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> > > <mailto:[email protected]
> > <mailto:[email protected]>>
> > >
> > > You can reach the person managing the list at
> > > darshan-users-owner(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> > > <mailto:[email protected]
> > <mailto:[email protected]>>
> > >
> > > When replying, please edit your Subject line so it is more
> > specific
> > > than "Re: Contents of Darshan-users digest..."
> > >
> > >
> > > 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(a)hawk.iit.edu
> > <mailto:[email protected]>
> > > <mailto:[email protected] <mailto:[email protected]>>>
> > > To: darshan-users(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> > > <mailto:[email protected]
> > <mailto:[email protected]>>
> > > Subject: [Darshan-users] Darshan error with HDF5
> > > Message-ID:
> > >
> > >
> > <CAM2fH+yEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA(a)mail.gmail.com
> > <mailto:
> CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA(a)mail.gmail.com>
> > <mailto:
> CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA(a)mail.gmail.com
> > <mailto:
> CAM2fH%252ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA(a)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
> > >
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(a)lists.mcs.anl.gov
> <mailto:[email protected]>> wrote:
>
> Send Darshan-users mailing list submissions to
> darshan-users(a)lists.mcs.anl.gov
> <mailto:[email protected]>
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.mcs.anl.gov/mailman/listinfo/darshan-users
> <https://lists.mcs.anl.gov/mailman/listinfo/darshan-users>
> or, via email, send a message with subject or body 'help' to
> darshan-users-request(a)lists.mcs.anl.gov
> <mailto:[email protected]>
>
> You can reach the person managing the list at
> darshan-users-owner(a)lists.mcs.anl.gov
> <mailto:[email protected]>
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Darshan-users digest..."
>
>
> Today's Topics:
>
> 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(a)mcs.anl.gov <mailto:[email protected]>>
> To: <darshan-users(a)lists.mcs.anl.gov
> <mailto:[email protected]>>
> Subject: Re: [Darshan-users] Darshan-users Digest, Vol 45, Issue 6
> Message-ID: <55953F3A.9020005(a)mcs.anl.gov
> <mailto:[email protected]>>
> 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(a)lists.mcs.anl.gov
> <mailto:[email protected]>
> > <mailto:[email protected]
> <mailto:[email protected]>>> wrote:
> >
> > Send Darshan-users mailing list submissions to
> > darshan-users(a)lists.mcs.anl.gov
> <mailto:[email protected]>
> > <mailto:[email protected]
> <mailto:[email protected]>>
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://lists.mcs.anl.gov/mailman/listinfo/darshan-users
> > <https://lists.mcs.anl.gov/mailman/listinfo/darshan-users>
> > or, via email, send a message with subject or body 'help' to
> > darshan-users-request(a)lists.mcs.anl.gov
> <mailto:[email protected]>
> > <mailto:[email protected]
> <mailto:[email protected]>>
> >
> > You can reach the person managing the list at
> > darshan-users-owner(a)lists.mcs.anl.gov
> <mailto:[email protected]>
> > <mailto:[email protected]
> <mailto:[email protected]>>
> >
> > When replying, please edit your Subject line so it is more
> specific
> > than "Re: Contents of Darshan-users digest..."
> >
> >
> > 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(a)hawk.iit.edu
> <mailto:[email protected]>
> > <mailto:[email protected] <mailto:[email protected]>>>
> > To: darshan-users(a)lists.mcs.anl.gov
> <mailto:[email protected]>
> > <mailto:[email protected]
> <mailto:[email protected]>>
> > Subject: [Darshan-users] Darshan error with HDF5
> > Message-ID:
> >
> >
> <CAM2fH+yEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA(a)mail.gmail.com
> <mailto:CAM2fH%[email protected]>
> <mailto:CAM2fH%[email protected]
> <mailto:CAM2fH%[email protected]>>>
> > 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
> >
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(a)lists.mcs.anl.gov>
wrote:
> Send Darshan-users mailing list submissions to
> darshan-users(a)lists.mcs.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.mcs.anl.gov/mailman/listinfo/darshan-users
> or, via email, send a message with subject or body 'help' to
> darshan-users-request(a)lists.mcs.anl.gov
>
> You can reach the person managing the list at
> darshan-users-owner(a)lists.mcs.anl.gov
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Darshan-users digest..."
>
>
> Today's Topics:
>
> 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(a)mcs.anl.gov>
> To: <darshan-users(a)lists.mcs.anl.gov>
> Subject: Re: [Darshan-users] Darshan-users Digest, Vol 45, Issue 6
> Message-ID: <55953F3A.9020005(a)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(a)lists.mcs.anl.gov
> > <mailto:[email protected]>> wrote:
> >
> > Send Darshan-users mailing list submissions to
> > darshan-users(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://lists.mcs.anl.gov/mailman/listinfo/darshan-users
> > <https://lists.mcs.anl.gov/mailman/listinfo/darshan-users>
> > or, via email, send a message with subject or body 'help' to
> > darshan-users-request(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> >
> > You can reach the person managing the list at
> > darshan-users-owner(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Darshan-users digest..."
> >
> >
> > 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(a)hawk.iit.edu
> > <mailto:[email protected]>>
> > To: darshan-users(a)lists.mcs.anl.gov
> > <mailto:[email protected]>
> > Subject: [Darshan-users] Darshan error with HDF5
> > Message-ID:
> >
> > <CAM2fH+yEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA(a)mail.gmail.com
> <mailto:
> CAM2fH%2ByEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA(a)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
> >
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(a)lists.mcs.anl.gov
> <mailto:[email protected]>> wrote:
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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(a)hawk.iit.edu
> <mailto:[email protected]>>
> To: darshan-users(a)lists.mcs.anl.gov
> <mailto:[email protected]>
> Subject: [Darshan-users] Darshan error with HDF5
> Message-ID:
>
> <CAM2fH+yEoqtPOnxVPvZNm853kCXEmhWQMrDpWWxZ8UEWC8jUcA(a)mail.gmail.com <mailto:CAM2fH%[email protected]>>
> 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
>
