Potential issue with write.configs.ed

serbinsh commented 8 years ago

From ED2 log

  Local host: modex
--------------------------------------------------------------------------
+---------------- MPI parallel info: --------------------+
+  - Machnum  =      0
+  - Machsize =      1
+---------------- OMP parallel info: --------------------+
+  - thread  use:       1
+  - threads max:       1
+  - cpu     use:       1
+  - cpus    max:       1
+  Note: Max vals are for node, not sockets.
+--------------------------------------------------------+
Reading namelist information
Copying namelist
+------------------------------------------------------------+
|           Ecosystem Demography Model, version 2.2
+------------------------------------------------------------+
|  Input namelist filename is ED2IN
|
|  Single process execution on INITIAL run.
+------------------------------------------------------------+
  => Generating the land/sea mask.
/data/Model_Data/oge2OLD/OGE2_HEADER
 -> Getting file: /data/Model_Data/oge2OLD/OGE2_30N090W.h5...
 + Work allocation, node     1;
 + Polygon array allocation, node     1;
 + Memory successfully allocated on none     1;
 [+] Load_Ed_Ecosystem_Params...
----------------------------------------
  Treefall disturbance parameters:
  - LAMBDA_REF  =  0.00000E+00
  - LAMBDA_EFF  =  0.00000E+00
  - TIME2CANOPY =  3.40282E+38
----------------------------------------
 [+] Checking for XML config...
 count xml pft : /data/Model_Output/pecan.output/PEcAn_2000000123/run/2000008364/config.xml
 ERROR STOP IN LINKLIST: YOU CAN NOT CLOSE THIS TAG: root_turnover_rate
 (line           24 )!

Looks like tags might not be properly formatted in the output XML files @ashiklom

serbinsh commented 8 years ago

Yup, I see a formatting issue in the config.xml files in the /run directory See below:

<?xml version="1.0"?>
<!DOCTYPE config SYSTEM "ed.dtd">
<config>
 <radiation>
  <lai_min>0.01</lai_min>
 </radiation>
 <ed_misc>
  <output_month>12</output_month>
 </ed_misc>
 <pft>
  <mort2>21.2444414302888</mort2>
  <water_conductance>0.00905342726288212</water_conductance>
  <leaf_width>0.076136269934124</leaf_width>
  <quantum_efficiency>0.0575484763032695</quantum_efficiency>
  <root_respiration_factor>4.16613736482945</root_respiration_factor>
  <nonlocal_dispersal>0.233909023396279</nonlocal_dispersal>
  <stomatal_slope>7.0395171352017</stomatal_slope>
  <q>1.25777912974105</q>
  <dark_respiration_factor>0.00875202096264409</dark_respiration_factor>
  <r_fract>0.0937204161351622</r_fract>
  <growth_resp_factor>0.439013127650706</growth_resp_factor>
  <leaf_turnover_rate>3.22441508730999</leaf_turnover_rate>
  <>0.934159581163508</>
  <root_turnover_rate>0.450609889438809</root_turnover_rate>
  <storage_turnover_rate>0.484614816938773</storage_turnover_rate>
  <Vm0>62.3327774951103</Vm0>
  <SLA>19.4535332678829</SLA>
  <num>1</num>
  <name>tempconif</name>
 </pft>
</config>

THere is an orphan with no tag? @ashiklom

serbinsh commented 8 years ago

Looks like this may only happen for some PFTs. Maybe when there is a variable that PEcAn doesn't recognize? Happened for me with the tempconif PFT when running ED2 at Sylvania from the web interface

ashiklom commented 8 years ago

@serbinsh My pull request (#747) hasn't been reviewed or merged yet, so don't look at me! In fact, that workflow may fix this bug. Maybe check out the branch in that pull request and see if you get the same error? If it fixes it, add a :+1: to my pull request :smile:

serbinsh commented 8 years ago

OK, will check. Pointed to you just in case you had any ideas based on changes, but as you say they haven't been merged yet ;)

mdietze commented 8 years ago

Looking through the prior list, the issue was that there was a prior on leafN, which isn't an ED2 parameter. Removed the prior.

As an aside, I don't know who made this PFT and for what purpose. The temperate.* PFTs are the "standard" ED2 pfts (eg NorthernPine and LateConifer). Is anybody using this PFT for something or can I delete it?

PecanProject / pecan

Potential issue with write.configs.ed #752