Hello,
on most Linux systems there is a virtual ram-disk mounted in /dev/shm
which is read/writeable to all users. If it is not there, just run the
command "mount|grep ^tmpfs" to find its location. I'm not sure it is a
good idea, or appreciated by the system administrators to use it for
your purpose, but it should not break anything to try.
cheers
On 4/27/20 7:28 PM, Baer, Bradly wrote:
Paolo,
I believe there is the capability of creating a local scratch folder
that is deleted on the end of the job. I will try that as a solution as
I don't think I am yet brave enough to go under the hood of QE.
As far as the Ryzen performance, I used the same open source libraries
for both systems (OpenMPI, OpenBLAS, FFTW3). I don't know how to
identify if I have a conflict between MPI and multi threading, but I
will look into using Intel's MKL and see if that solves the performance
issues. I will also keep searching; the mail you referenced reminded me
that there is likely more interest in the performance of epyc rather
than ryzen.
Thanks for the advice.
-Brad
--------------------------------------------------------
Bradly Baer
Graduate Research Assistant, Walker Lab
Interdisciplinary Materials Science
Vanderbilt University
------------------------------------------------------------------------
*From:* users <[email protected]> on behalf of
Paolo Giannozzi <[email protected]>
*Sent:* Saturday, April 25, 2020 10:30 AM
*To:* Quantum ESPRESSO users Forum <[email protected]>
*Subject:* Re: [QE-users] QE Performance on cluster and AMD
On Sat, Apr 25, 2020 at 1:34 AM Baer, Bradly
<[email protected] <mailto:[email protected]>> wrote:
My submitted jobs for phonon calculations keep being canceled
because QE is writing large files to the networked filesystem which
is both very slow and under a fairly tight quota.
don't you have anything else to use for scratch files? in the worst-case
scenario, a local /tmp or /scratch file system, even if not visible to
all processors, may do the job (with some caveats)
Files in the _ph0 directory, and appear to be creating one file
per processor that I request for my job. Is there some way to have
QE load these files in to RAM instead
there is some way, but it requires some work and some understanding of
how the "buffer" machinery used in the self-consistent code works. If
you feel brave enough to work with the latest development version and to
perform some tests, I can explain what to do.
A second question: has anyone had success in using QE on AMD Ryzen
processors? I have a Ryzen system that is struggling to match the
performance of an Intel system that is several years older. Both are
running QE6.5 on Ubuntu. From pw.x output, cegterg is 10x slower
and cdiaghg is 100x slower on the AMD machine. I had hoped that
going from 4 cores to 16 cores would make it faster, not slower!
100x means that something VERY wrong is happening. Are you sure there
isn't some conflict between MPI and multithreading? Please also see the
following message, that contains an important piece of information:
https://www.mail-archive.com/[email protected]/msg37148.html
<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mail-archive.com%2Fusers%40lists.quantum-espresso.org%2Fmsg37148.html&data=02%7C01%7Cbradly.b.baer%40vanderbilt.edu%7Ca98d116614954748e48f08d7e92da395%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637234254548330786&sdata=Y%2FcpGdYuEIi2mb5yJBhvBFM4e1RxSTAkebnAZztzCuY%3D&reserved=0>
Paolo
Thanks,
Bradly Baer
--------------------------------------------------------
Bradly Baer
Graduate Research Assistant, Walker Lab
Interdisciplinary Materials Science
Vanderbilt University
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Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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