[gmx-users] 2019.2 build warnings

Szilárd Páll pall.szilard at gmail.com
Wed Apr 24 12:58:31 CEST 2019


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 <nedomacho at gmail.com> 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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