[Darshan-users] Using darshan to characterize PHDF characteristics

[Snyder, Shane]

Hi Mahzad,

Thanks again for bringing this to our attention and providing us with info for reproducing the error.

I was able to push a fix for this to Darshan's master branch just now that should resolve this problem and allow you to run darshan-convert and darshan-job-summary tools. I've tested on your log and things all appear to be working fine on my end.

FYI, I also just released the latest version of Darshan (3.1.7), and this bug fix is the last we included in that particular release if you want to use something a bit more stable than master. You can download it here: https://www.mcs.anl.gov/research/projects/darshan/download/

Thanks!
--Shane

On 1/22/19 9:54 AM, Carns, Philip H. via Darshan-users wrote:
Excellent, thanks for sharing the reproducer, Mahzad.  We have confirmed the problem; we have a bug in the darshan-convert utility that should be easy to fix.  Will report back with an update soon.

thanks,
-Phil



On 2019-01-21 21:18:51-05:00 Mahzad Khoshlessan wrote:

Hi Phil,
Yes, darshan-job-summary.pl<http://darshan-job-summary.pl> and darshan-parser work fine.
Sure, I have attached my logfile.
Thanks for the help.
[https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png] mkhoshle_python_id30468_1-21-57554-509712531345...<https://drive.google.com/file/d/1QfNXQ_l31FW38yGJxSEKXuZWgaUio-Py/view?usp=drive_web>[X]

Mahzad Khoshlessan

Research Associate
Arizona State University
Center for Biological Physics and Department of Physics

On Fri, Jan 18, 2019 at 7:55 AM Carns, Philip H. via Darshan-users <darshan-users at lists.mcs.anl.gov<mailto:darshan-users at lists.mcs.anl.gov>> wrote:
Hi Mahzad,

Everything you are doing looks fine to me.  It's possible that we have a bug that is being triggered in darshan-convert (this is a command line utility called within darshan-summary-per-file.sh to help split up the data).

Are you able to run darshan-job-summary.pl<http://darshan-job-summary.pl> and/or darshan-parser on the log file?

Can you share your log file for us to have a look at it and see if we can reproduce?

thanks!
-Phil



On 2019-01-15 19:54:20-05:00 Darshan-users wrote:

Hello all,
I have a python code and I am using parallel hdf5 through h5py.
I compiled darshan with the following options:
 ./configure --prefix=/home/mkhoshle/installs/darshan --with-mem- align=8 --with-log-path=/oasis/scratch/comet/mkhoshle/temp_project/darshan-logs --with-jobid-env=PBS_JOBID --enable-HDF5-post-1.10 CC=mpicc
I set the the environment variable LD_PRELOAD as:
export LD_PRELOAD=/home/mkhoshle/installs/darshan/lib/libdarshan.so:/home/mkhoshle/hdf5/v1.10.1/lib/libhdf5.so
And I am using Darshan 3.1.5.
I can run my code with no error but when I run darshan-summary-per-file.sh I get the following error and I get no output.
darshan-summary-per-file.sh /oasis/scratch/comet/mkhoshle/temp_project/darshan-logs/2019/1/15/mkhoshle_python_id10574_1-15-58292-3565400970146387705_1.darshan /oasis/scratch/comet/mkhoshle/temp_project/darshan/58292
Status: Generating summary for file 1 of 64: __init__.py
=======================================================
/home/mkhoshle/installs/darshan/bin/darshan-summary-per-file.sh: line 63: 27764 Segmentation fault darshan-convert --file $hash $1 $2/$file.darshan
=======================================================
darshan-summary-per-file.sh done. Results can be found in /oasis/scratch/comet/mkhoshle/temp_project/darshan/58292/*.pdf.
Am I doing anything wrong?
Thanks,
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