Opened 5 years ago

Closed 5 years ago

#1938 closed help (fixed)


Reported by: earhg Owned by: um_support
Component: UM Model Keywords:
Cc: Platform: Other
UM Version: 8.4


I am getting some strange looking errors when trying to run a copy of Grenville's job xidem on POLARIS, my job xmvnm, from PUMA for the first time. The .leave file is attached. They look a bit like they might be related to the POLARIS hand edit, but since I am sourcing Grenville's file I don't see how it could cause an issue. Many thanks for any ideas! Hamish

Attachments (1)

xmvnm000.xmvnm.d16221.t150310.leave (9.0 KB) - added by earhg 5 years ago.

Download all attachments as: .zip

Change History (9)

Changed 5 years ago by earhg

comment:1 Changed 5 years ago by ros

Hi Hamish,

I know there has always been something odd with parexe on Polaris, which Grenville managed to fix with some script changes/hand-edits. Unfortunately Grenville is out of the office for another week. I will take a look and see if I can track it down, but it might have to wait until he returns.


comment:2 Changed 5 years ago by earhg

Please could someone look at this again? Sorry to be a pain…
many thanks

comment:3 Changed 5 years ago by grenville


We saw this problem at UM 6.6.3 - the fix at 6.6.3 should work at 8.4.

Please see /home/grenville/um6.6.3/hg6.6.3_polaris_fixes/src/script/control/ — where I commented out the run through the environment variables, namely

# Now run though the environment and, in alphabetical order
# set the variables in print_array
#foreach $key ( sort keys %ENV ){
# $value = $ENV{$key};

# push @print_array, "$key='$value'\n";

The same code appears in the UM 8.4 script (see

You can test the fix by commenting out the lines in your local copy of (Best to make ea branch subsequently.)

The parexe file is useful for UM hackers but not so much for the rest of us.


comment:4 Changed 5 years ago by earhg

hi Grenville,
Thank you very much for looking at this. I swapped in your file but the run failed in roughly the same place with the error here:

/nobackup/earhg/xmvnm/umatmos/bin/xmvnm.exe: error while loading shared libraries: cannot open shared object file: No such file or directory

I tried commenting out the set -a command, but it didn't help. The output from three runs today is at /home/ufaserv1_g/earhg/output/xmvnm000.xmvnm.d16236.t104945.leave

Is this the correct Fortran library? module list gives me Currently Loaded Modulefiles:

1) licenses 2) sge 3) bit/64 4) intel/ 5) mvapich2/1.8 6) leeds 7) user

thanks again for your help

comment:5 Changed 5 years ago by grenville


I'm looking at this - it appears to be a module mismatch. It's been years since we installed 8.4 on Polaris (it's not been used since as far as I know), so it's not surprising that there are some snags.


comment:6 Changed 5 years ago by grenville


I have changed the hand edit polaris_8.4.1 so that it loads the latest mvapich2, and rebuilt gcom for consistency. Doing this worked for my job xidem.

Please do a full rebuild (make sure the modification to you did earlier is there).

I have not rebuilt other gcoms for different mpi implementations, so please try to stick with mvapich2. We can rebuild the others if needed.


comment:7 Changed 5 years ago by earhg

hi Grenville,
Thank you very much for this - I did as you suggested and the job completed nicely just now.
Hopefully it will work just as well when I try to run my customised jobs.

comment:8 Changed 5 years ago by grenville

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