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Joe Jordan

  • Registered on: 03/01/2018
  • Last connection: 12/10/2018

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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
09:47 AM GROMACS Bug #2768 (Closed): clang 7.0.0 warns about unused variable in gmxapi
Using cmake 3.12.1 and clang 7.0.0 generates the following warning at compiliation....

11/15/2018

04:26 PM GROMACS Bug #2760 (Rejected): grompp only warns when molecules in .top file are wrong
If you have a conformation file (gro, pdb, etc) and a molecular topology file (top) there are some cases where one sh...
07:38 AM GROMACS Task #2758: Modernize genconf
Wearing my "the devil made me do it" hat, that is a typo because I was not paying attention when I wrote this. I mean...

11/14/2018

04:25 PM GROMACS Task #2758 (New): Modernize genconf
The genconf utility is still cast in the c-style format. It should be migrated to work in the TrajectoryAnalysis fram...

11/12/2018

04:50 PM GROMACS Revision f370e961: Add coolquotes
Change-Id: Ifcbbb45f531612454bd080f91b247817530f78e0

11/09/2018

12:19 PM GROMACS Task #2735: Allow gmx_genrestr to write correct position restraints for molecules after the first molecule
I tested this to make sure that mdrun also works and everything seems fine. I created a slightly more elaborate scrip...

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