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Ticket Resolution Summary Owner Reporter
#1758 answered Error in dump reconfiguartion annette dilshadshawki
Description

Hello Helpdesk,

Your regular UMUI user in need of help again!

After running the job xlzyb, (UKCA 8.4 job), I get the following error in the .rcf.leave file:

/home/dshawk/output/xlzyb000.xlzyb.d15336.t153517.rcf.leave
[NID 00157] 2015-12-02 15:51:09 Exec /projects/ukca-imp/dshawk/xlzyb/bin/qxreconf failed: chdir /work/scratch/jtmp/pbs.326348
.xcm00.x8z No such file or directory
/projects/ukca-imp/dshawk/xlzyb/bin/qsrecon: Error in dump reconfiguration - see OUTPUT

The directory /work/scratch/jtmp…. does not exist! I checked OUTPUT which is lower down but it does not give any useful information:

 ==============================================================================
 =================================== OUTPUT ===================================
 ==============================================================================

 UMUI Namelist output in /projects/ukca-imp/dshawk/xlzyb/xlzyb.umui.nl
 DATAW/DATAM file listing in /projects/ukca-imp/dshawk/xlzyb/xlzyb.list
 STASH output should be in /projects/ukca-imp/dshawk/xlzyb/xlzyb.stash

I have run reconfiguration since I prevented some diagnostics from outputting in the STASH section of the UM, as I thought you need to reconfigure whenever an ancil or stash diagnostic is changed.

Please help!

Dill

#1761 fixed fcm merge for NEMO annette cthomas
Description

Hi,

I have been trying to add a new branch to NEMO for use in a Rose suite on Monsoon. In this case the base version of NEMO is 3.4 but there are already several branches on top of it. My aim is to change two of the .F90 files but leave the rest as they are. On Puma I did the following (just considering one of the files):

fcm branch-create sstbias fcm:nemo-tr@vn3.4 fcm checkout fcm:nemo-br/dev/cthomas/vn3.4_sstbias make the changes to NEMOGCM/NEMO/OPA_SRC/OBS/diaobs.F90 fcm merge fcm:nemo-br/dev/deazer/vn3.4_OBS_NEMOVAR_community_UKMO accept the new changes in diaobs.F90 fcm commit

Then I edited the Rose suite on Monsoon. In the fcm option "extract.location{diff}[nemo]", I removed the line

branches/dev/deazer/vn3.4_OBS_NEMOVAR_community_UKMO@5408

and added

branches/dev/cthomas/vn3.4_sstbias@5459

When compiling, however, I get lots of errors about files missing. It looks like the merge didn't do quite what I wanted. I guess I've missed an important step somewhere - if you had any advice I'd be very grateful. I can make files available somewhere public if that's useful.

Cheers, Chris

#1765 fixed Error in job when changing only STASH diagnostics annette dilshadshawki
Description

Dear Helpdesk,

I have job that I tried to run called xlzyc that I copied from another job xlyta and after changing the STASH diagnostics, the job has some output but then I get the following error message in the following .leave file:

home/dshawk/output/xlzyc000.xlzyc.d15338.t151655.leave
ATP Stack walkback for Rank 131 starting:
  _start@start.S:113
  __libc_start_main@libc-start.c:242
  flumemain_@flumeMain.f90:48
  um_shell_@um_shell.f90:1865
  u_model_@u_model.f90:2688
  atm_step_@atm_step.f90:10120
  atmos_physics2_@atmos_physics2.f90:3965
  ni_conv_ctl_@ni_conv_ctl.f90:2384
  _cray$mt_execute_parallel_with_proc_bind@0x1d7ee64
  _cray$mt_start_one_code_parallel@0x1d7eac9
  ni_conv_ctl__cray$mt$p0001@ni_conv_ctl.f90:2465
  glue_conv$glue_conv_mod_@glue_conv-gconv5a.f90:1838
  ereport64$ereport_mod_@ereport_mod.f90:107
  gc_abort_@gc_abort.F90:136
  mpl_abort_@mpl_abort.F90:46
  pmpi_abort@0x1d89b3c
  MPI_Abort@0x1db3984
  MPID_Abort@0x1ddeea1
  abort@abort.c:92
  raise@pt-raise.c:42
ATP Stack walkback for Rank 131 done
Process died with signal 6: 'Aborted'
Forcing core dumps of ranks 131, 12, 0
View application merged backtrace tree with: stat-view atpMergedBT.dot
You may need to: module load stat

_pmiu_daemon(SIGCHLD): [NID 00092] [c0-0c1s7n0] [Fri Dec  4 16:09:16 2015] PE RANK 95 exit signal Killed
[NID 00092] 2015-12-04 16:09:16 Apid 251553: initiated application termination
_pmiu_daemon(SIGCHLD): [NID 00110] [c0-0c1s11n2] [Fri Dec  4 16:09:16 2015] PE RANK 134 exit signal Killed
xlzyc: Run failed

I then wanted to double check the difference so I made a copy of the original job xlyta (now called xlzyd), and compared it to the modified job, xlzyc and this can be found in puma:

/home/dilshadshawk/umui_jobs/diff.xlzyc.xlzyd

Is there something strange that I am not spotting? I am quite baffled as not much has been changed from one job to the other.

Any help would be much appreciated.

Best wishes, Dill

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