Just to update: we rolled back to 2018.1 due to a new simulation, which
is running perfectly fine on the older version.
The only difference between this simulation and everything we've tried
so far is that each charge value in the topology (for about 3000 atoms)
has something like five digits -- directly copied from a DFT output. On
all machines running 2018.1 the initial dynamic relaxation initially
hiccuped at 400% CPU load (instead of normal 2000%) doing something for
a few minutes, but then always recovered and continued to run normally.
2019.2 ended up throwing errors about pressure scaling on one try and
quietly segfaulted on another. On the same machine, rolling back to
2018.1 resulted in normal operation.
I can provide the input if needed (including the batch sh file), but I
don't think we'll be using 2019.2 in the near future, though I kept a
backup of the build.
Alex
On 5/2/2019 12:42 AM, Alex wrote:
Hi Szilárd,
Thanks a bunch. I have upgraded to 2019.2 and a fairly large
"production" test seems to be running without any issues.
Alex
On 5/1/2019 5:07 AM, Szilárd Páll wrote:
Hi,
You can safely ignore the errors as these are caused by properties of
your
hardware that the test scripts are not dealing well enough -- though
admittedly, two of the three errors should be avoided along a message
similar to this
"Mdrun cannot use the requested (or automatic) number of OpenMP threads,
retrying with 8."
(which is what I get when I run the tests on a similar machine).
If you need the tests to pass on the node in question, let me know, I
can
suggest workarounds.
Cheers,
--
Szilárd
On Mon, Apr 29, 2019 at 6:47 PM Alex <nedoma...@gmail.com> wrote:
Hi Szilárd,
Since I don't know which directory inside /complex corresponds to which
tests (at least one of the tests that failed was #42), here's a tarball
of the entire /complex directory per location you specified below:
https://www.dropbox.com/s/44uluopkdan2417/regression_complex_2019.2.tar.gz?dl=0
If you can help us figure this out, it will be great!
Thanks,
Alex
On 4/29/2019 4:25 AM, Szilárd Páll wrote:
Hi,
I assume you used -DREGRESSIONTEST_DOWNLOAD=ON case in which the tests
are
downloaded and unpacked under
BUILD_TREE/tests/regressiontests-release-2019-[SUFFIX]/
In that directory you find the usual regressiontests tree, from there
under
complex/ you'll find the tests in question.
Cheers,
--
Szilárd
On Fri, Apr 26, 2019 at 7:00 PM Alex <nedoma...@gmail.com> wrote:
Hi Szilárd,
I am at a conference right now, but will do my best to upload the
requested data first thing on Monday. In the meantime, could you
please
tell me where the stuff of interest would be located within the local
gromacs build directory? I mean, I could make the entire directory a
tarball, but not sure it's all that necessary. I don't remember which
tests
failed, unfortunately...
Thank you!
Alex
On 4/25/2019 2:54 AM, Szilárd Páll wrote:
Hi Alex,
On Wed, Apr 24, 2019 at 9:59 PM Alex <nedoma...@gmail.com> wrote:
Hi Szilárd,
We are using neither Ubuntu 18.04, nor glibc 2.27, but the
problem is
most certainly there.
OK.
Can you please post the content of the directories of tests that
failed?
It
would be useful to know the exact software configuration
(reported in
the
log) and the details of the errors (reported in the mdrun.out).
Thanks,
--
Szilárd
Until the issue is solved one way or another, we
will be staying with 2018.1, i guess.
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 16.04.6 LTS
Release: 16.04
Codename: xenial
Ubuntu GLIBC 2.23-0ubuntu11
On 4/24/2019 4:57 AM, Szilárd Páll wrote:
What OS are you using? There are some known issues with the Ubuntu
18.04
+
glibc 2.27 which could explain the errors.
--
Szilárd
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