[Darshan-users] Darshan trace file creation

Wed Nov 30 18:06:21 CST 2016

Hi Shane,

I had to look in the latex.output file to see what happened because summary.log was empty. From the latex.output file, I saw that I needed the following RPMs which my laptop did not have:

texlive-lastpage
texlive-subfigmat.noarch
texlive-subfigure.noarch
texlive-threeparttable.noarch
texlive-threeparttablex.noarch

After installing the above, the problem was resolved and the PDF report was created. You should list the above as prerequisites to using Darshan. Thanks for your help.

Best regards,

Wadud.

________________________________
From: Shane Snyder <ssnyder at mcs.anl.gov>
Sent: 30 November 2016 21:07:19
To: Wadud Miah; darshan-users at lists.mcs.anl.gov
Subject: Re: [Darshan-users] Darshan trace file creation

Hi Wadud,

Could you try regenerating the summary report, but pass the '--verbose' flag to darshan-job-summary script?

That should create a directory in /tmp that stores all the temporary files used by that script. Included will be a 'summary.log' file that contains the output from each step of generating the summary. Do you happen to see any errors or indication of what went wrong in there? It could be that you are missing some LaTeX or gnuplot prerequisite packages or something like that.

Thanks,
--Shane

On 11/30/2016 05:33 AM, Wadud Miah wrote:
Hi again Shane,

When I try to create the job summary report, the command gets stuck:

[wadud at WM-porlock ~]$ darshan-job-summary.pl pr1ebt05_bt.A.9.mpi_io_full_id2483888_11-29-65132-8929929721473377761_1.darshan
Slowest unique file time: 0.001923
Slowest shared file time: 0.130845
Total bytes read and written by app (may be incorrect): 104858212
Total absolute I/O time: 0.132768
**NOTE: above shared and unique file times calculated using MPI-IO timers if MPI-IO interface used on a given file, POSIX timers otherwise.

This has happened also on my laptop. When I run “top -H” I don’t see the process doing anything. Any help will be appreciated.

Regards,
Wadud.

From: Shane Snyder [mailto:ssnyder at mcs.anl.gov]
Sent: 29 November 2016 20:50
To: Wadud Miah <wadud.miah at nag.co.uk><mailto:wadud.miah at nag.co.uk>; darshan-users at lists.mcs.anl.gov<mailto:darshan-users at lists.mcs.anl.gov>
Subject: Re: [Darshan-users] Darshan trace file creation

Hi Wadud,

I'm assuming this is a Fortran app, right?

If so, I believe this is tied back to a known issue with Intel MPI's Fortran bindings. Long story short, these bindings are calling the PMPI variants of the MPI function calls directly which bypasses any profiling tool that wraps the MPI interface at the C layer (e.g., Darshan). See this post for more details: https://software.intel.com/en-us/forums/intel-clusters-and-hpc-technology/topic/279445

I haven't personally confirmed this on Intel MPI 5.x versions (the post I reference above is regarding a 4.x version of Intel MPI), but I believe other users have reported the problem still exists.

It should be possible to work around the issue by modifying Darshan to provide an additional interface for intercepting Fortran MPI calls natively at the Fortran layer, but we have not undertaken this development effort as of yet. Lacking that, I'm not sure what, if any, other solutions there are, unfortunately.

Thanks,
--Shane
On 11/28/2016 02:58 PM, Wadud Miah wrote:

Hello,

I built Darshan with Intel MPI 5.1.3 and gcc 4.3.4 with the following configure flags:

./configure --prefix=$HOME/darshan-3.1.2-impi --with-mem-align=8 --with-jobid-env=NONE --with-log-path-by-env=DARSHAN_LOGPATH

which built fine. I set DARSHAN_LOGPATH to darshan-trace-dir and I created the directory darshan-trace-dir. I then executed my MPI code which does I/O using:

mpirun -n 9 -env LD_PRELOAD /home/pr1ebt00/pr1ebt05/darshan-3.1.2-impi/lib/libdarshan.so ./bt.A.9.mpi_io_full

in the same directory that has the darshan-trace-dir directory. However, I do not see any tracefile in the directory darshan-trace-dir and no error messages. Any help will be greatly appreciated.

Thanks in advance,

Wadud.

---------------------------------------

Dr. Wadud Miah

Computational Scientist

Numerical Algorithms Group

01865 518035

________________________________

The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is:

Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.

This e-mail has been scanned for all viruses by Microsoft Office 365.

________________________________

_______________________________________________

Darshan-users mailing list

Darshan-users at lists.mcs.anl.gov<mailto:Darshan-users at lists.mcs.anl.gov>

https://lists.mcs.anl.gov/mailman/listinfo/darshan-users

________________________________________________________________________
This e-mail has been scanned for all viruses by Star.
________________________________________________________________________
________________________________

The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is:

Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.

This e-mail has been scanned for all viruses by Microsoft Office 365.

________________________________

________________________________________________________________________
This e-mail has been scanned for all viruses by Star.
________________________________________________________________________
________________________________

The Numerical Algorithms Group Ltd is a company registered in England and Wales with company number 1249803. The registered office is:

Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.

This e-mail has been scanned for all viruses by Microsoft Office 365.

________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/darshan-users/attachments/20161201/91c5da0f/attachment-0001.html>