GROMACS development

Today

04:53 PM GROMACS Bug #2947 (Fix uploaded): mdrun segfaults when trying to use membed

10:15 AM GROMACS Bug #2762: incorrect results with Ubuntu 18.04 / glibc 2.27 (?) and >20 threads

For completeness I added the asm files for both the build with a fix, and one where the pragma has been commented out...

05/16/2019

11:52 AM GROMACS Bug #2762: incorrect results with Ubuntu 18.04 / glibc 2.27 (?) and >20 threads

This is what it does according to the gcc manual...

11:51 AM GROMACS Bug #2762: incorrect results with Ubuntu 18.04 / glibc 2.27 (?) and >20 threads

So, spending way too much time on trying optimization flags, I found that...

10:47 AM GROMACS Bug #2762: incorrect results with Ubuntu 18.04 / glibc 2.27 (?) and >20 threads

so, I checked some more and changed the RelWithDebugInfo flags from...

09:36 AM GROMACS Bug #2762: incorrect results with Ubuntu 18.04 / glibc 2.27 (?) and >20 threads

I checked builds both with -O3 and -O2, with the crash only happening with -O3. I could try to see which optimization...

05/15/2019

05:15 PM GROMACS Bug #2954: genion changes residue numbering

can you provide your inputs and command line so I can check this in the debugger? :)

05:06 PM GROMACS Bug #2954: genion changes residue numbering

I see your point and will investigate this.
I quick read through genion did not show anything that would do this, th...

03:50 PM GROMACS Bug #2954: genion changes residue numbering

Is this behaviour different to previous versions of GROMACS? I would see this as expected behaviour, but maybe it sho...

11:28 AM GROMACS Bug #2762: incorrect results with Ubuntu 18.04 / glibc 2.27 (?) and >20 threads

Attached log files for sample run