pnetcdf on edison.nersc.gov

[mfwehner@lbl_gov]

Using cesm1_2_2 on edison.nersc.gov

> When I set these variables in env_run.xml
> env_run.xml:
> env_run.xml:
> env_run.xml:
> env_run.xml:
>
> I get a segmentation fault. Has anybody tried parallel i.o in cesm with edison? Are these the correct settings?

Without changing these the code runs fine, albeit slow.
Thanks
Michael

 

[jedwards]

Hi Michael,Something was lost in your post and the variables you set are missing, but for most compsets on edison PIO_TYPENAME=pnetcdf this is a default value which can be overwritten by the component specific values.   Look for the settings actually used near the top of the cpl.log file.     Please include your cesm.log and cpl.log file along with the compset and grid you are trying to use and I'll see if I can be of more help. 

 

[mfwehner@lbl_gov]

sorry about the lost part of the posthere are the settings that fail entry id="ATM_PIO_STRIDE"   value="24" 
entry id="ATM_PIO_ROOT"   value="0"    
entry id="ATM_PIO_NUMTASKS"   value="128" 
entry id="ATM_PIO_TYPENAME"   value="pnetcdf"

 

[jedwards]

Hi Michael,I'm still waiting to see the output logs from your run.   Aliso did you try just setting PIO_TYPENAME=pnetcdf without changing any of the other parameters?   

 

[mfwehner@lbl_gov]

The log file is  /scratch1/scratchdirs/mwehner/seCAM5_test7200x2/run/cesm.log.140818-131355Shows a seg faultPermissions should be readable for that run

 

[jedwards]

I'm not sure if this is an IO problem or not - did you also change the pe-layout for this case?    Can you send me yourcase setup including any user_nl or source modifications?   

 

[jedwards]

I don't think that it's an IO problem.  It looks like a compiler optimization issue.   Add the following to a file called Depends.edison in your case directory and rebuild: cube_mod.o: cube_mod.F90
    $(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O0 $<

 

[mfwehner@lbl_gov]

JimI am doing something wrong with the Depends file.I get the error/scratch1/scratchdirs/mwehner/seCAM5_test7200x2_new/Depends.edison:1: *** multiple target patterns.  Stop.

In the log file /scratch1/scratchdirs/mwehner/seCAM5_test7200x2_new/bld/intel/mpt/nodebug/threads/mct.bldlog.140826-172244

this is what I put in the file. it is just one line.more /scratch1/scratchdirs/mwehner/seCAM5_test7200x2_new/Depends.edison
cube_mod.o: cube_mod.F90     $(FC) -c $(INCLDIR) $(INCS) $(FFLAGS) $(FREEFLAGS) -O0 $<

  

 

[jedwards]

It's Makefile format, you need a new line which begins with a tab:Look in one of the other Depends files in scripts/ccsm_utils/Machines for an example.