[Darshan-users] Using darshan to characterize PHDF characteristics

[Mahzad Khoshlessan]

Thank you so much. I will check it and will let you know if I have any
problems.

Mahzad Khoshlessan

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


On Tue, Jan 22, 2019 at 1:29 PM Snyder, Shane via Darshan-users <
darshan-users at lists.mcs.anl.gov> wrote:

> 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 and darshan-parser work fine.
> Sure, I have attached my logfile.
> Thanks for the help.
>  mkhoshle_python_id30468_1-21-57554-509712531345...
> <https://drive.google.com/file/d/1QfNXQ_l31FW38yGJxSEKXuZWgaUio-Py/view?usp=drive_web>
>
> 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> 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 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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>
>
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