Re: [gmx-users] 2019.2 build warnings

[Alex]

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  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  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  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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Re: [gmx-users] 2019.2 build warnings

[Alex]

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  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  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  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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Re: [gmx-users] 2019.2 build warnings

[Alex]

Oh, cool -- thanks! I guess we will be replacing the older builds, then.

Funny enough, you may not recall it, but the hardware for particular box 
was purchased with your own advice, which served us very well up until 
now. :)


Again, thank you.

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  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  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  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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Re: [gmx-users] 2019.2 build warnings

[Szilárd Páll]

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  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  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  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
> >
> >
> >
> >
>  --
>  Gromacs Users mailing list
> 
>  * Please search the archive at
>  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>  posting!
> 
>  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
>  * For (un)subscribe requests visit
>  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>  send a mail to gmx-users-requ...@gromacs.org.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
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> >> send a mail to gmx-users-requ...@gromacs.org.
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> posting!
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Re: [gmx-users] 2019.2 build warnings

[Szilárd Páll]

Thanks, will look at it shortly.

BTW, the regressiontests output indicates which test failed, e.g. from your
earlier email:

FAILED. Check mdrun.out, md.log file(s) in distance_restraints for
distance_restraints




--
Szilárd


On Mon, Apr 29, 2019 at 6:47 PM Alex  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  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  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
> >
> >
> >
> >
>  --
>  Gromacs Users mailing list
> 
>  * Please search the archive at
>  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>  posting!
> 
>  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
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>  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>  send a mail to gmx-users-requ...@gromacs.org.
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
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Re: [gmx-users] 2019.2 build warnings

[Alex]

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  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  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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Re: [gmx-users] 2019.2 build warnings

[Szilárd Páll]

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  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  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
> >>>
> >>>
> >>>
> >>>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> --
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>
> * Please search the archive at
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> posting!
>
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>
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Re: [gmx-users] 2019.2 build warnings

[Alex]

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  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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Re: [gmx-users] 2019.2 build warnings

[Szilárd Páll]

Hi Alex,

On Wed, Apr 24, 2019 at 9:59 PM Alex  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
> >
> >
> >
> >
> >>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] 2019.2 build warnings

[Alex]

Hi Szilárd,

We are using neither Ubuntu 18.04, nor glibc 2.27, but the problem is 
most certainly there. 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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Re: [gmx-users] 2019.2 build warnings

[Szilárd Páll]

What OS are you using? There are some known issues with the Ubuntu 18.04 +
glibc 2.27 which could explain the errors.
--
Szilárd


On Wed, Apr 17, 2019 at 2:32 AM Alex  wrote:

> Okay, more interesting things are happening.
> At the end of 'make' I get a bunch of things like
>
> .. nbnxn_cuda.cu(373): warning: variable "dim_grid" was
> declared but never referenced
> -bash: syntax error near unexpected token `373'
>
> More errors during 'make check' right after " Building NVCC (Device) object
>
> src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o"
> then continues as if nothing happened.
>
> Finally, fails test #42 with what appears to be sarcasm:
> "...
> Thanx for Using GROMACS - Have a Nice Day
>
> Mdrun cannot use the requested (or automatic) number of ranks, retrying
> with 8.
>
> Abnormal return value for ' gmx mdrun-nb cpu   -notunepme >mdrun.out
> 2>&1' was 1
> Retrying mdrun with better settings...
>
> Abnormal return value for ' gmx mdrun -ntmpi 1  -notunepme >mdrun.out
> 2>&1' was -1
> FAILED. Check mdrun.out, md.log file(s) in distance_restraints for
> distance_restraints
>
> Abnormal return value for ' gmx mdrun -ntmpi 6  -notunepme >mdrun.out
> 2>&1' was 1
> Retrying mdrun with better settings...
>
> Abnormal return value for ' gmx mdrun   -notunepme >mdrun.out 2>&1' was
> -1
> FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
> Re-running orientation-restraints using CPU-based PME
>
> Abnormal return value for ' gmx mdrun -ntmpi 1  -pme cpu-notunepme
> >mdrun.out 2>&1' was -1
> FAILED. Check mdrun.out, md.log file(s) in orientation-restraints/pme-cpu
> for orientation-restraints-pme-cpu
> Re-running pull_geometry_angle using CPU-based PME
> Re-running pull_geometry_angle-axis using CPU-based PME
> Re-running pull_geometry_dihedral using CPU-based PME
> 3 out of 55 complex tests FAILED"
>
> Then finally quits for good. Your suggestions will be highly appreciated.
>
> Thank you,
>
> Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] 2019.2 build warnings

[Szilárd Páll]

The warning are harmless, something happened in the build infrastructure
which emits some new warnings that we've not caught before the release.
--
Szilárd


On Wed, Apr 17, 2019 at 1:43 AM Alex  wrote:

> Hi all,
>
> I am building the 2019.2 version, latest CUDA libs (older 2018 version
> works fine). While building, I am getting a ton of warnings as shown below,
> while the build does not terminate. Is this okay, or do we need to do
> anything at this point?
>
> Thanks,
>
> Alex
>
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_grid" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_block" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_grid" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_block" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_grid" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_block" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_grid" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_block" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_grid" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_block" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_grid" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_block" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_grid" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_block" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_grid" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_block" was declared but never referenced
>
> localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
> variable "dim_grid" was declared but never referenced
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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Re: [gmx-users] 2019.2 build warnings

[Alex]

Hi Mark,

Here you are:

 :-) GROMACS - gmx, 2019.2 (-:

    GROMACS is written by:
 Emile Apol  Rossen Apostolov  Paul Bauer Herman J.C. 
Berendsen

    Par Bjelkmar  Christian Blau   Viacheslav Bolnykh Kevin Boyd
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Alan Gray
  Gerrit Groenhof Anca Hamuraru    Vincent Hindriksen  M. Eric Irrgang
  Aleksei Iupinov   Christoph Junghans Joe Jordan Dimitrios Karkoulis
    Peter Kasson    Jiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg Erik Marklund
    Pascal Merz Pieter Meulenhoff    Teemu Murtola Szilard Pall
    Sander Pronk  Roland Schulz  Michael Shirts    Alexey Shvetsov
   Alfons Sijbers Peter Tieleman  Jon Vincent  Teemu 
Virolainen

 Christian Wennberg    Maarten Wolf
   and the project leaders:
    Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx, version 2019.2
Executable: redacted/gmx2019.2_gpu/gromacs-2019.2/build/bin/./gmx
Data prefix:  redacted/gmx2019.2_gpu/gromacs-2019.2 (source tree)
Working dir:  redacted/gmx2019.2_gpu/gromacs-2019.2/build/bin
Command line:
  gmx -version

GROMACS version:    2019.2
Precision:  single
Memory model:   64 bit
MPI library:    thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:    CUDA
SIMD instructions:  AVX2_256
FFT library:    fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:    enabled
Hwloc support:  hwloc-1.11.0
Tracing support:    disabled
C compiler: /usr/bin/cc GNU 5.4.0
C compiler flags:    -mavx2 -mfma -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast

C++ compiler:   /usr/bin/c++ GNU 5.4.0
C++ compiler flags:  -mavx2 -mfma    -std=c++11   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast
CUDA compiler:  /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda 
compiler driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on 
Fri_Feb__8_19:08:17_PST_2019;Cuda compilation tools, release 10.1, V10.1.105
CUDA compiler 
flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;; 
;-mavx2;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;

CUDA driver:    10.10
CUDA runtime:   10.10


On 4/20/2019 12:38 PM, Mark Abraham wrote:

Hi,

Your experience looks unusual. What does gmx -version report?

Mark

On Fri., 19 Apr. 2019, 03:02 Alex,  wrote:


Can someone please confirm that my emails indeed reach this board? :)
Thank you.

On 4/16/2019 6:31 PM, Alex wrote:

Okay, more interesting things are happening.
At the end of 'make' I get a bunch of things like

.. nbnxn_cuda.cu (373): warning:
variable "dim_grid" was declared but never referenced
-bash: syntax error near unexpected token `373'

More errors during 'make check' right after " Building NVCC (Device)
object


src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o"

then continues as if nothing happened.

Finally, fails test #42 with what appears to be sarcasm:
"...
Thanx for Using GROMACS - Have a Nice Day

Mdrun cannot use the requested (or automatic) number of ranks,
retrying with 8.

Abnormal return value for ' gmx mdrun-nb cpu  -notunepme

mdrun.out 2>&1' was 1

Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 1   -notunepme >mdrun.out
2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in distance_restraints for
distance_restraints

Abnormal return value for ' gmx mdrun -ntmpi 6   -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun  -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
Re-running orientation-restraints using CPU-based PME

Abnormal return value for ' gmx mdrun -ntmpi 1 -pme cpu-notunepme

mdrun.out 2>&1' was -1

FAILED. Check mdrun.out, md.log file(s) in
orientation-restraints/pme-cpu for 

Re: [gmx-users] 2019.2 build warnings

[Mark Abraham]

Hi,

Your experience looks unusual. What does gmx -version report?

Mark

On Fri., 19 Apr. 2019, 03:02 Alex,  wrote:

> Can someone please confirm that my emails indeed reach this board? :)
> Thank you.
>
> On 4/16/2019 6:31 PM, Alex wrote:
> > Okay, more interesting things are happening.
> > At the end of 'make' I get a bunch of things like
> >
> > .. nbnxn_cuda.cu (373): warning:
> > variable "dim_grid" was declared but never referenced
> > -bash: syntax error near unexpected token `373'
> >
> > More errors during 'make check' right after " Building NVCC (Device)
> > object
> >
> src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o"
> > then continues as if nothing happened.
> >
> > Finally, fails test #42 with what appears to be sarcasm:
> > "...
> > Thanx for Using GROMACS - Have a Nice Day
> >
> > Mdrun cannot use the requested (or automatic) number of ranks,
> > retrying with 8.
> >
> > Abnormal return value for ' gmx mdrun-nb cpu  -notunepme
> > >mdrun.out 2>&1' was 1
> > Retrying mdrun with better settings...
> >
> > Abnormal return value for ' gmx mdrun -ntmpi 1   -notunepme >mdrun.out
> > 2>&1' was -1
> > FAILED. Check mdrun.out, md.log file(s) in distance_restraints for
> > distance_restraints
> >
> > Abnormal return value for ' gmx mdrun -ntmpi 6   -notunepme >mdrun.out
> > 2>&1' was 1
> > Retrying mdrun with better settings...
> >
> > Abnormal return value for ' gmx mdrun  -notunepme >mdrun.out 2>&1' was -1
> > FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
> > Re-running orientation-restraints using CPU-based PME
> >
> > Abnormal return value for ' gmx mdrun -ntmpi 1 -pme cpu-notunepme
> > >mdrun.out 2>&1' was -1
> > FAILED. Check mdrun.out, md.log file(s) in
> > orientation-restraints/pme-cpu for orientation-restraints-pme-cpu
> > Re-running pull_geometry_angle using CPU-based PME
> > Re-running pull_geometry_angle-axis using CPU-based PME
> > Re-running pull_geometry_dihedral using CPU-based PME
> > 3 out of 55 complex tests FAILED"
> >
> > Then finally quits for good. Your suggestions will be highly appreciated.
> >
> > Thank you,
> >
> > Alex
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Re: [gmx-users] 2019.2 build warnings

[Alex]

Can someone please confirm that my emails indeed reach this board? :) 
Thank you.


On 4/16/2019 6:31 PM, Alex wrote:

Okay, more interesting things are happening.
At the end of 'make' I get a bunch of things like

.. nbnxn_cuda.cu (373): warning: 
variable "dim_grid" was declared but never referenced

-bash: syntax error near unexpected token `373'

More errors during 'make check' right after " Building NVCC (Device) 
object 
src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o"

then continues as if nothing happened.

Finally, fails test #42 with what appears to be sarcasm:
"...
Thanx for Using GROMACS - Have a Nice Day

Mdrun cannot use the requested (or automatic) number of ranks, 
retrying with 8.


Abnormal return value for ' gmx mdrun    -nb cpu  -notunepme 
>mdrun.out 2>&1' was 1

Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 1   -notunepme >mdrun.out 
2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in distance_restraints for 
distance_restraints


Abnormal return value for ' gmx mdrun -ntmpi 6   -notunepme >mdrun.out 
2>&1' was 1

Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun  -notunepme >mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
Re-running orientation-restraints using CPU-based PME

Abnormal return value for ' gmx mdrun -ntmpi 1 -pme cpu    -notunepme 
>mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in 
orientation-restraints/pme-cpu for orientation-restraints-pme-cpu

Re-running pull_geometry_angle using CPU-based PME
Re-running pull_geometry_angle-axis using CPU-based PME
Re-running pull_geometry_dihedral using CPU-based PME
3 out of 55 complex tests FAILED"

Then finally quits for good. Your suggestions will be highly appreciated.

Thank you,

Alex

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Re: [gmx-users] 2019.2 build warnings

[Alex]

Okay, more interesting things are happening.
At the end of 'make' I get a bunch of things like

.. nbnxn_cuda.cu(373): warning: variable "dim_grid" was
declared but never referenced
-bash: syntax error near unexpected token `373'

More errors during 'make check' right after " Building NVCC (Device) object
src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda.cu.o"
then continues as if nothing happened.

Finally, fails test #42 with what appears to be sarcasm:
"...
Thanx for Using GROMACS - Have a Nice Day

Mdrun cannot use the requested (or automatic) number of ranks, retrying
with 8.

Abnormal return value for ' gmx mdrun-nb cpu   -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun -ntmpi 1  -notunepme >mdrun.out
2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in distance_restraints for
distance_restraints

Abnormal return value for ' gmx mdrun -ntmpi 6  -notunepme >mdrun.out
2>&1' was 1
Retrying mdrun with better settings...

Abnormal return value for ' gmx mdrun   -notunepme >mdrun.out 2>&1' was
-1
FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron
Re-running orientation-restraints using CPU-based PME

Abnormal return value for ' gmx mdrun -ntmpi 1  -pme cpu-notunepme
>mdrun.out 2>&1' was -1
FAILED. Check mdrun.out, md.log file(s) in orientation-restraints/pme-cpu
for orientation-restraints-pme-cpu
Re-running pull_geometry_angle using CPU-based PME
Re-running pull_geometry_angle-axis using CPU-based PME
Re-running pull_geometry_dihedral using CPU-based PME
3 out of 55 complex tests FAILED"

Then finally quits for good. Your suggestions will be highly appreciated.

Thank you,

Alex
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[gmx-users] 2019.2 build warnings

[Alex]

Hi all,

I am building the 2019.2 version, latest CUDA libs (older 2018 version
works fine). While building, I am getting a ton of warnings as shown below,
while the build does not terminate. Is this okay, or do we need to do
anything at this point?

Thanks,

Alex


localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_grid" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_block" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_grid" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_block" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_grid" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_block" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_grid" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_block" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_grid" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_block" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_grid" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_block" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_grid" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_block" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_grid" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_block" was declared but never referenced

localstuff/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu(373): warning:
variable "dim_grid" was declared but never referenced
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