ED2 met process failing

[serbinsh]

I'm trying to setup runs at NOBS (1850 burn site, Manitoba Canada) and running into issues using the FLUXNET drivers

> # Write pecan.CHECKED.xml
> PEcAn.settings::write.settings(settings, outputfile = "pecan.CHECKED.xml")
[1] "/data/Model_Output/pecan.output/PEcAn_2000000723/pecan.CHECKED.xml"
> 
> # start from scratch if no continue is passed in
> statusFile <- file.path(settings$outdir, "STATUS")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
> if (length(which(commandArgs() == "--continue")) == 0 && file.exists(statusFile)) {
+   file.remove(statusFile)
+ }
>   
> # Do conversions
> settings <- PEcAn.utils::do_conversions(settings)
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
2017-10-30 15:34:00 DEBUG  [PEcAn.utils::do_conversions] : 
   do.conversion outdir /data/Model_Output/pecan.output/dbfiles 
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
2017-10-30 15:34:00 INFO   [PEcAn.utils::do_conversions] : PROCESSING:  met 
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
2017-10-30 15:34:00 INFO   [PEcAn.utils::do_conversions] : 
   calling met.process: 
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
  scale  format.id           format.name format.mimetype format.inputtype
1  site 5000000001 FLUXNET2015_SUBSET_HH        text/csv              csv
$download.raw
[1] TRUE

$met2cf
[1] TRUE

$standardize
[1] TRUE

$met2model
[1] TRUE

Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
2017-10-30 15:34:00 DEBUG  [PEcAn.utils::convert.input] : 
   Convert.Inputs download.Fluxnet2015 NA localhost 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_site_0-506 
   FLUXNET2015_SUBSET_HH text/csv 506 1995/01/01 2007/12/31 
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
2017-10-30 15:34:00 INFO   [PEcAn.utils::convert.input] : 
   start CHECK Convert.Inputs download.Fluxnet2015 NA localhost 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_site_0-506/ 
   FLUXNET2015_SUBSET_HH text/csv 506 1995/01/01 2007/12/31 
2017-10-30 15:34:00 WARN   [PEcAn.DB::dbfile.input.check] : 
   Found possible matching input. Checking if its associate files are on 
   host machine 
          id site_id notes          created_at          updated_at start_date
1 1000013675     506       2017-10-12 12:38:40 2017-10-30 18:58:58 1990-01-01
    end_date                   name parent_id user_id access_level raw
1 2008-12-31 Fluxnet2015_site_0-506        NA      NA            4  NA
  format_id
1     5e+09
2017-10-30 15:34:00 DEBUG  [PEcAn.utils::convert.input] : 
   File id = 2000018835 File name = 
   FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3 File path = 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_site_0-506 Input id 
   = 1000013675 10 
2017-10-30 15:34:00 INFO   [PEcAn.utils::convert.input] : 
   end CHECK for existing input record. 
2017-10-30 15:34:00 INFO   [PEcAn.utils::convert.input] : 
   Skipping this input conversion because files are already available. 
2017-10-30 15:34:00 INFO   [.met2cf.module] : 
   Begin change to CF Standards 
2017-10-30 15:34:01 DEBUG  [PEcAn.utils::convert.input] : 
   Convert.Inputs met2CF.csv 1000013675 localhost 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_site_0-506 CF 
   Meteorology application/x-netcdf 506 1995/01/01 2007/12/31 
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
2017-10-30 15:34:01 INFO   [PEcAn.utils::convert.input] : 
   start CHECK Convert.Inputs met2CF.csv 1000013675 localhost 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_site_0-506/ CF 
   Meteorology application/x-netcdf 506 1995/01/01 2007/12/31 
2017-10-30 15:34:01 WARN   [PEcAn.DB::dbfile.input.check] : 
   Found possible matching input. Checking if its associate files are on 
   host machine 
          id site_id notes          created_at          updated_at start_date
1 1000013676     506       2017-10-12 12:39:17 2017-10-12 12:39:17 1995-01-01
    end_date                      name  parent_id user_id access_level raw
1 2008-12-31 Fluxnet2015_CF_site_0-506 1000013675      NA            4  NA
  format_id
1        33
2017-10-30 15:34:01 DEBUG  [PEcAn.utils::convert.input] : 
   File id = 2000018836 File name = 
   FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3 File path = 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_site_0-506 Input 
   id = 1000013676 10 
2017-10-30 15:34:01 INFO   [PEcAn.utils::convert.input] : 
   end CHECK for existing input record. 
2017-10-30 15:34:01 INFO   [PEcAn.utils::convert.input] : 
   Skipping this input conversion because files are already available. 
2017-10-30 15:34:01 INFO   [.met2cf.module] : 
   Finished change to CF Standards 
2017-10-30 15:34:01 INFO   [.metgapfill.module] : Gapfilling 
No geonamesUsername set. See http://geonames.wordpress.com/2010/03/16/ddos-part-ii/ and set one with options(geonamesUsername="foo") for some services to work
2017-10-30 15:34:01 DEBUG  [PEcAn.utils::convert.input] : 
   Convert.Inputs metgapfill 1000013676 localhost 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_gapfill_site_0-506 
   CF Meteorology application/x-netcdf 506 1995/01/01 2007/12/31 
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
2017-10-30 15:34:01 INFO   [PEcAn.utils::convert.input] : 
   start CHECK Convert.Inputs metgapfill 1000013676 localhost 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_gapfill_site_0-506/ 
   CF Meteorology application/x-netcdf 506 1995/01/01 2007/12/31 
2017-10-30 15:34:01 WARN   [PEcAn.DB::dbfile.input.check] : 
   Found possible matching input. Checking if its associate files are on 
   host machine 
          id site_id notes          created_at          updated_at start_date
1 1000013677     506       2017-10-12 12:40:52 2017-10-12 12:40:52 1995-01-01
    end_date                              name  parent_id user_id access_level
1 2008-12-31 Fluxnet2015_CF_gapfill_site_0-506 1000013676      NA            4
  raw format_id
1  NA        33
2017-10-30 15:34:01 DEBUG  [PEcAn.utils::convert.input] : 
   File id = 2000018837 File name = 
   FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3 File path = 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_gapfill_site_0-506 
   Input id = 1000013677 10 
2017-10-30 15:34:01 INFO   [PEcAn.utils::convert.input] : 
   end CHECK for existing input record. 
2017-10-30 15:34:01 INFO   [PEcAn.utils::convert.input] : 
   Skipping this input conversion because files are already available. 
$input.id
[1] 1000013677

$dbfile.id
[1] 2000018837

2017-10-30 15:34:01 INFO   [.metgapfill.module] : 
   Finished Gapfilling Met 
2017-10-30 15:34:01 INFO   [.met2model.module] : 
   Begin Model Specific Conversion 
[1] "Convert to model format"
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
2017-10-30 15:34:01 DEBUG  [PEcAn.utils::convert.input] : 
   Convert.Inputs met2model.ED2 1000013677 localhost 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_ED2_site_0-506 
   ed.met_driver_header files format text/plain 506 1995/01/01 2007/12/31 
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
2017-10-30 15:34:01 INFO   [PEcAn.utils::convert.input] : 
   start CHECK Convert.Inputs met2model.ED2 1000013677 localhost 
   /data/Model_Output/pecan.output/dbfiles/Fluxnet2015_ED2_site_0-506/ 
   ed.met_driver_header files format text/plain 506 1995/01/01 2007/12/31 
2017-10-30 15:34:02 DEBUG  [PEcAn.utils::convert.input] : 
   File id = File name = File path = Input id = 10 
2017-10-30 15:34:02 INFO   [PEcAn.utils::convert.input] : 
   end CHECK for existing input record. 
2017-10-30 15:34:02 DEBUG  [PEcAn.utils::convert.input] : 
   convert.input executing the following function: 
   PEcAn.ED2::met2model.ED2(lst=-6, lat=55.8796, lon=-98.4808, 
   spin_nyear=NULL, spin_nsample=NULL, spin_resample=NULL, overwrite=FALSE, 
   in.path='/data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_gapfill_site_0-506', 
   in.prefix='FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3', 
   outfolder='/data/Model_Output/pecan.output/dbfiles/Fluxnet2015_ED2_site_0-506/', 
   start_date='1995/01/01', end_date='2007/12/31') 

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> remotefunc <- function() {PEcAn.ED2::met2model.ED2(lst=-6, lat=55.8796, lon=-98.4808, spin_nyear=NULL, spin_nsample=NULL, spin_resample=NULL, overwrite=FALSE, in.path='/data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_gapfill_site_0-506', in.prefix='FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3', outfolder='/data/Model_Output/pecan.output/dbfiles/Fluxnet2015_ED2_site_0-506/', start_date='1995/01/01', end_date='2007/12/31')}
> remoteout <- remotefunc()
2017-10-30 15:34:03 WARN   [PEcAn.ED2::met2model.ED2] : 
   The file already exists! Moving to next month! 
Error in UseMethod("h5write") : 
  no applicable method for 'h5write' applied to an object of class "c('array', 'double', 'numeric')"
Calls: remotefunc -> <Anonymous> -> <Anonymous>
Execution halted
[1] 1
2017-10-30 15:34:03 INFO   [PEcAn.utils::convert.input] : 
   RESULTS: Convert.Input 
2017-10-30 15:34:03 INFO   [PEcAn.utils::convert.input] : 1 
2017-10-30 15:34:03 INFO   [PEcAn.utils::convert.input] :  
2017-10-30 15:34:03 DEBUG  [PEcAn.utils::convert.input] : 
   Processing data failed, please check validity of args:lst=-6, 
   lat=55.8796, lon=-98.4808, spin_nyear=NULL, spin_nsample=NULL, 
   spin_resample=NULL, overwrite=FALSE, 
   in.path='/data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_gapfill_site_0-506', 
   in.prefix='FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3', 
   outfolder='/data/Model_Output/pecan.output/dbfiles/Fluxnet2015_ED2_site_0-506/', 
   start_date='1995/01/01', end_date='2007/12/31' 
2017-10-30 15:34:03 SEVERE [PEcAn.utils::convert.input] : 
   Unable to process data using this function:met2model.ED2 
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
Warning: '$.SafeList' is deprecated.
Use 'PEcAn.settings::$.SafeList' instead.
See help("Deprecated")
> proc.time()
   user  system elapsed 
  7.973   0.680   9.580 
The PEcAn project is supported by the National Science Foundation (ABI #1062547, ABI #1458021, DIBBS #1261582, ARC #1023477, EF #1318164, EF #1241894, EF #1241891), NASA Terrestrial Ecosystems, the Energy Biosciences Institute, and an Amazon AWS in Education Grant.

[serbinsh]

The FLUXNET download a previous time and seemed to work but it appears to be crashing on met2model using h5 libs OR something is wrong with the data format?

[serbinsh]

drwxr-sr-x.   2 apache  test  4096 Oct 30 15:02 Fluxnet2015_CF_site_0-506
drwxr-sr-x.   2 apache  test    52 Oct 30 15:34 Fluxnet2015_ED2_site_0-506

Generated nc files

[sserbin@modex Fluxnet2015_CF_site_0-506]$ ll
total 12504
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.1995.nc
-rw-r--r--. 1 apache test 915012 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.1996.nc
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.1997.nc
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.1998.nc
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.1999.nc
-rw-r--r--. 1 apache test 915012 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.2000.nc
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.2001.nc
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.2002.nc
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.2003.nc
-rw-r--r--. 1 apache test 915012 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.2004.nc
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.2005.nc
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.2006.nc
-rw-r--r--. 1 apache test 912516 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.2007.nc
-rw-r--r--. 1 apache test 915012 Oct 30 15:02 FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.2008.nc

Looks accurate

[sserbin@modex Fluxnet2015_CF_site_0-506]$ ncdump -h FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.1995.nc
netcdf FLX_CA-Man_FLUXNET2015_SUBSET_HH_1994-2008_1-3.1995 {
dimensions:
	longitude = 1 ;
	latitude = 1 ;
	time = 17520 ;
variables:
	double longitude(longitude) ;
		longitude:units = "degrees_east" ;
		longitude:long_name = "longitude" ;
	double latitude(latitude) ;
		latitude:units = "degrees_north" ;
		latitude:long_name = "latitude" ;
	double time(time) ;
		time:units = "days since 1700-01-01" ;
		time:long_name = "time" ;
	float air_temperature(time, latitude, longitude) ;
		air_temperature:units = "K" ;
	float air_pressure(time, latitude, longitude) ;
		air_pressure:units = "Pa" ;
	float mole_fraction_of_carbon_dioxide_in_air(time, latitude, longitude) ;
		mole_fraction_of_carbon_dioxide_in_air:units = "mol mol-1" ;
	float soil_temperature(time, latitude, longitude) ;
		soil_temperature:units = "K" ;
	float water_vapor_saturation_deficit(time, latitude, longitude) ;
		water_vapor_saturation_deficit:units = "Pa" ;
	float surface_downwelling_longwave_flux_in_air(time, latitude, longitude) ;
		surface_downwelling_longwave_flux_in_air:units = "W m-2" ;
	float surface_downwelling_shortwave_flux_in_air(time, latitude, longitude) ;
		surface_downwelling_shortwave_flux_in_air:units = "W m-2" ;
	float surface_downwelling_photosynthetic_photon_flux_in_air(time, latitude, longitude) ;
		surface_downwelling_photosynthetic_photon_flux_in_air:units = "mol m-2 s-1" ;
	float precipitation_flux(time, latitude, longitude) ;
		precipitation_flux:units = "kg m-2 s-1" ;
	float eastward_wind(time, latitude, longitude) ;
		eastward_wind:units = "m s-1" ;
	float northward_wind(time, latitude, longitude) ;
		northward_wind:units = "m s-1" ;
}

data:

 longitude = -98.4808 ;
}

  250.381,
  250.823,
  251.171,
  251.769,
  251.874,
  252.485,
  252.681,
  253.005,
  253.166,
  253.166,
  253.325,
  252.681,
  252.188,
  251.938,
  251.854,
  252.316,
  252.325,
  252.333,
  252.342,
  252.351,
  252.359,
  252.367,
  252.376,
  252.105,
  252.271,
  252.271,
  252.105 ;
}

[serbinsh]

Just two ED2 files?

[sserbin@modex Fluxnet2015_ED2_site_0-506]$ ll
total 8
-rw-r--r--. 1 apache test 195 Oct 30 15:34 1995FEB.h5
-rw-r--r--. 1 apache test 195 Oct 30 15:04 1995JAN.h5

[sserbin@modex Fluxnet2015_ED2_site_0-506]$ h5dump 1995FEB.h5
HDF5 "1995FEB.h5" {
GROUP "/" {
}
}

[serbinsh]

[sserbin@modex Fluxnet2015_ED2_site_0-506]$ h5dump -H 1995FEB.h5
HDF5 "1995FEB.h5" {
GROUP "/" {
}
}

Seem just to be empty?

[serbinsh]

Also a problem because the previous failed file exists but is empty so it moved to the next month. Which means once this works, it may skip these two months, where are actually invalid. I will need to run this function and force re-build to purge these two bad files. Another option?

[ankurdesai]

I had a similar problem that was fixed by updating the hdf5 R package (which required a bunch of other updates too). Yes, also had to manually delete empty .h5 files during crashes like this.

[serbinsh]

Thanks @ankurdesai I will give that a shot!

[serbinsh]

Following these instructions for update: https://www.bioconductor.org/packages/devel/bioc/vignettes/rhdf5/inst/doc/rhdf5.pdf

My problem is that it ins't using the HDF5 version that is loaded in my modules but instead finding an old HDF system lib....so that may cause me all sorts of problems.

[serbinsh]

Yeah, trying to run again or manually causes me problems

> remoteout <- remotefunc()
Error in UseMethod("h5write") :
  no applicable method for 'h5write' applied to an object of class "c('array', 'double', 'numeric')"

I think I need to try and install rhdf5 using the more up-to-date HDF5 I have installed but as a module. Its not yet clear how to get bioclite to install using a different lib location. I don't see any flags to do this. Perhaps there is a way to build from source?

[ankurdesai]

Here's what I did in rstudio:
source("https://bioconductor.org/biocLite.R")
biocLite("rhdf5",lib="/usr/local/lib/R/site-library")

Then this worked:
met2model.ED2(lst=-6, lat=46.0765, lon=-89.9742, spin_nyear=NULL, spin_nsample=NULL, spin_resample=NULL, overwrite=FALSE, in.path='/home/carya/output/dbfiles/Fluxnet2015_CF_gapfill_site_0-679', in.prefix='FLX_US-Los_FLUXNET2015_SUBSET_HH_2000-2014_2-3', outfolder='/home/carya/output/dbfiles/Fluxnet2015_ED2_site_0-679/', start_date='2000/01/01', end_date='2008/12/31')

[serbinsh]

@ankurdesai I did the same, still fails. Part of my issue (I think)

chmod: cannot access `tools/misc/h5cc': No such file or directory
	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
		   HDF5 Version: 1.8.7
		  Configured on: Mon Oct 30 16:20:42 EDT 2017
		  Configured by: sserbin@modex
		 Configure mode: production
		    Host system: x86_64-unknown-linux-gnu
	      Uname information: Linux modex 2.6.32-696.3.2.el6.x86_64 #1 SMP Mon Jun 19 11:23:31 CDT 2017 x86_64 x86_64 x86_64 GNU/Linux
		       Byte sex: little-endian
		      Libraries:
	     Installation point: /tmp/RtmpvIF1wd/R.INSTALL988e709a866a/rhdf5/src/hdf5/hdf5

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /data/software/gcc/gcc-5.4.0/bin/gcc -m64 -std=gnu99 ( gcc (GCC) 5.4.0)
                         CFLAGS:
                      H5_CFLAGS:   -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -w -O -fomit-frame-pointer -finline-functions
                      AM_CFLAGS:
                       CPPFLAGS:
                    H5_CPPFLAGS: -D_POSIX_SOURCE   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE

Thats the wrong HDF5 and I am trying to get it to use the correct one....so far failing to use a different HDF5 lib location

I really hate this bioconductor / HDF5 dependency for ED2

[serbinsh]

Or is that somehow the HDF5 that ships with rhdf5?

[serbinsh]

> remotefunc <- function() {PEcAn.ED2::met2model.ED2(lst=-6, lat=55.8796, lon=-98.4808, spin_nyear=NULL, spin_nsample=NULL, spin_resa> le=NULL, overwrite=FALSE, in.path='/data/Model_Output/pecan.output/dbfiles/Fluxnet2015_CF_gapfill_site_0-506', in.prefix='FLX_CA-Ma> FLUXNET2015_SUBSET_HH_1994-2008_1-3', outfolder='/data/Model_Output/pecan.output/dbfiles/Fluxnet2015_ED2_site_0-506/', start_date='> 95/01/01', end_date='2007/12/31')}

> remoteout <- remotefunc()
Error in UseMethod("h5write") :
  no applicable method for 'h5write' applied to an object of class "c('array', 'double', 'numeric')"

That was my own attempt at running that by "hand" after installing rhdf5 again