Can I still use "-cpi -append" for a new run in Version 2020?

User discussions
1

GROMACS version:2020.1
GROMACS modification: Yes/No
Here post your question

I used to use mdrun_mpi -deffnm md_0_1 -cpi -append
for a MD production run, whether it is a new run, or continue run. This works in older version (e.g. 2019.3), indicating: No previous checkpoint file present with -cpi option, assuming this is a new run

However, at Version 2020.1, I was told:
Could not do a restart with appending because the checkpoint file was not
found. Either supply the name of the right checkpoint file or do not use
-append

This means that, I need to remove -cpi -append in a new run, then add -cpi -append in its following continuing runs.

Would it still be possible to have -cpi -append in a new run in Version 2020.1?

2

Hi,

Three scenarios are possible with -cpi :

* no files with matching names are present: new output files are written

* all files are present with names and checksums matching those stored in the checkpoint file: files are appended

* otherwise no files are modified and a fatal error is generated

Maybe the first two fullfill your needs.
Alessandra

3

Hi I agree with what you have said, but it seems to only work in the old version.

In the new version, e.g. 2020.1, adding -cpi -append will throw an error when no checkpoint files exist.

4

The problem is that there is no checkpoint file. The -cpi option is going to look for md_0_1.cpt, which according to the error message, does not exist. This is not something that should have changed between versions.

5

Hi Justin, yes, it is a new run, so there is no checkpoint file.

But why the Version 2020.1 could not regard it as a new run? I was told:
Could not do a restart with appending because the checkpoint file was not
found. Either supply the name of the right checkpoint file or do not use
-append

6

mdrun is trying to be smarter by not simply bypassing things that the user may not have intended to do. If it’s a new run, don’t supply mdrun with irrelevant command-line options.

7

Yes, that is what I found in the Version 2020.1.

In Version 2019.3, using mdrun_mpi -deffnm md_0_1 -cpi -append for a new run has no problems. This change seems to be not convenient.

Thank you Justin!

8

The change was made to prevent possible loss of data and certainly loss of time. While mdrun has always warned about this issue, now it prevents the user from potentially overwriting existing data or thinking that their extension is running when in fact it is not.

9

Sure, thanks!