Opened 14 years ago

Closed 14 years ago

#69 closed help (fixed)

Empty .pe files

Reported by: H.Luijting@… Owned by: jeff
Component: UM Model Keywords:
Cc: Platform:
UM Version:



I have problems with my run (xclni). It's a 12km run that creates boundary files for my 4 km run. It's a copy of a run that does work, only for a different case study (so starting from a different start dump).

The run compiles, starts running but then nothing happens. It crashes when the computation time (1h) is exceeded. I have had this problem before, but was then able to open the .pe0 file to see what was going wrong. This time all the .pe files are empty, the file size is zero.

How do I find out what's going wrong if none of the files contain data? Can someone have a look at my run and see what's going on? Thanks a lot!

I have attached the job basis file in case you need to have a look at it, and all directories on hpcx are accessible.


PS I had to turn Chang's hand edit off, as there is no RECONA file for this run ( I did the reconfiguration separately)

Attachments (1)

U_xclng.JPG (60.3 KB) - added by hanneke 14 years ago.

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Change History (8)

comment:1 Changed 14 years ago by jeff

  • Owner changed from um_support to jeff
  • Status changed from new to assigned

You need to turn off buffering of the output. In umui window

Sub-Model Independent → Script Inserts and Modifications

You need to add to The "Defined Environment Variables" window. Add Variable name


with value


include the quotes. Now the fort6 files should have some data in them.

It looks like the job is hanging right at the start of the run, I would only use a small amount of CPU time (~300 sec) so you are not wasting it.


comment:2 Changed 14 years ago by jeff

  • Reporter changed from hanneke to H.Luijting@…

Changed 14 years ago by hanneke

comment:3 Changed 14 years ago by hanneke

Thanks Jeff, I now have fort6 files with data in it.

They didn't tell me much however… I realized that there is a problem with my start dump (the one outputted by the reconfiguration run). The fields look strange, I have attached an example.

I first thought it must be caused by the global dump, as I didn't change anything else. But I am also working on other runs and ran into the same problem with one of those, one that is actually using a different global dump. The reconfiguration run is the one you helped me with before (xclng). Do you know what can cause the fields to look like this?


comment:4 Changed 14 years ago by jeff

Hi Hanneke

There is a problem with the 6.1 reconfiguration and it looks like it is effecting your jobs. It seems the compiler update on hpcx has a bug in it, which several people have noticed. I am looking into a work around at the moment, I'll let you know when I have something working.


comment:5 Changed 14 years ago by jeff

Hi Hanneke

I have written a mod which will hopefully fix the problem. You can find the mod here


which should be $PUM_MODS61/recon_fix_6.1.mf90 in the umui, under Modifications for the reconfiguration. Can you test this mod and let me know if you have any problems with it.


comment:6 Changed 14 years ago by hanneke

Hello Jeff,

I am sorry for the late reply! I saw the email about the mod set, so I assume it has been tested now, but just to let you know that this indeed has solved my problem - the start dump looks fine now!

Thanks a lot!

comment:7 Changed 14 years ago by jeff

  • Resolution set to fixed
  • Status changed from assigned to closed
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