Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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:

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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:

Re: [gmx-users] 2019.2 build warnings

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, --

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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 > > ..

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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

Re: [gmx-users] 2019.2 build warnings

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 "

[gmx-users] 2019.2 build warnings

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