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Joe Jordan

  • Registered on: 03/01/2018
  • Last connection: 02/15/2019

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01/20/2019

04:07 PM GROMACS Task #2727: Move non-analysis functions out of gmxana
Any script that currently uses make_ndx can trivially be updated by using the -on flag on select. There is a cost to ...

01/14/2019

11:10 AM GROMACS Task #2831: Bump required version numbers of infrastructure for 2020
From a user perspective, I don't think there will be much difference between CUDA 8 or 9. CUDA 9 supports GPUs going ...

01/12/2019

04:19 PM GROMACS Task #2829 (New): mdrun appends when checkpoint specified by -cpi is not found
If I invoke mdrun with all paths correctly specified:
gmx mdrun -s md.part0001.tpr -cpi md.part0001.cpt -noappend
...

01/04/2019

06:00 PM GROMACS Task #2825: reportGpuUsage is misleading
I agree that there is not much value add to cleverly attempting to print back to stderr how mdrun was called. In gene...
05:00 PM GROMACS Task #2825 (Closed): reportGpuUsage is misleading
If I specify a gpu_id to mdrun I will get output to stderr as follows.
> Command line:
> gmx mdrun -deffnm nvt -n...

12/19/2018

08:45 AM GROMACS Bug #2572: 1/viscosity output is wrong in gmx-2018.2, but OK in gmx-5.1.5
Please provide the files and exact command line invocations that you used in the case where it works and where it doe...

12/10/2018

10:00 PM GROMACS Bug #2798: Default mpi rank number fails when there are 16 cores and 3 gpus
I immediately guessed that the issue was a problem of the work not being divisible and was able to just use less reso...
12:02 PM GROMACS Bug #2798 (New): Default mpi rank number fails when there are 16 cores and 3 gpus
Starting mdrun with as follows
srun gmx mdrun -s part.tpr
on a node with 3 gpus gives a domain decomposition error....

11/19/2018

01:15 PM GROMACS Bug #2768 (Resolved): clang 7.0.0 warns about unused variable in gmxapi
Applied in changeset commit:de71ffac62115a3ca4c4f4af1b39e3f5f687f27d.
11:45 AM GROMACS Revision de71ffac: fix unused variable warning from gmxapi compilation
Fixes #2768
Change-Id: I8c77dd19f15df6f365122e25680e9d0a553cb36c

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