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PCMDI tools problem - lats #1949

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durack1 opened this Issue Apr 25, 2016 · 9 comments

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durack1 commented Apr 25, 2016

The following problems are occurring with the PCMDI_tools - lats in particular:

[durack1@oceanonly 150219_AMIPForcingData]$ source /usr/local/uvcdat/2.4.1.rcf_all_pcmdi/bin/setup_runtime.csh
.//.: Permission denied.                                                                                      
Successfully updated your environment to use UVCDAT                                                           
(changes are valid for this session/terminal only)                                                            
Version: v2.5.0-291-g0fc5d7e                                                                                  
Location: /usr/local/uvcdat/2.4.1.rcf_all_pcmdi                                                               
Reset these changes by running: source /usr/local/uvcdat/2.4.1.rcf_all_pcmdi/bin/reset_runtime.csh            
[durack1@oceanonly 150219_AMIPForcingData]$ cl                                                                
[durack1@oceanonly 150219_AMIPForcingData]$ cd77 -ezget -lats mkhurrell1.f -o mkhurrell1 -fcray-pointer -std=legacy
/usr/local/uvcdat/2.4.1.rcf_all_pcmdi/Externals/lib/libgrib2c.a(dec_jpeg2000.o): In function `dec_jpeg2000':
dec_jpeg2000.c:(.text+0x3f): undefined reference to `jas_stream_memopen'
dec_jpeg2000.c:(.text+0x56): undefined reference to `jpc_decode'
dec_jpeg2000.c:(.text+0xe2): undefined reference to `jas_matrix_create'
dec_jpeg2000.c:(.text+0x13a): undefined reference to `jas_image_readcmpt'
dec_jpeg2000.c:(.text+0x1c0): undefined reference to `jas_matrix_destroy'
dec_jpeg2000.c:(.text+0x1cc): undefined reference to `jas_stream_close'
dec_jpeg2000.c:(.text+0x1db): undefined reference to `jas_image_destroy'
/usr/local/uvcdat/2.4.1.rcf_all_pcmdi/Externals/lib/libgrib2c.a(dec_png.o): In function `user_read_data':
dec_png.c:(.text+0x1c): undefined reference to `png_get_io_ptr'
/usr/local/uvcdat/2.4.1.rcf_all_pcmdi/Externals/lib/libgrib2c.a(dec_png.o): In function `dec_png':
dec_png.c:(.text+0xaf): undefined reference to `png_sig_cmp'
dec_png.c:(.text+0xd8): undefined reference to `png_create_read_struct'
dec_png.c:(.text+0xfb): undefined reference to `png_create_info_struct'
dec_png.c:(.text+0x11e): undefined reference to `png_destroy_read_struct'
dec_png.c:(.text+0x134): undefined reference to `png_create_info_struct'
dec_png.c:(.text+0x15c): undefined reference to `png_destroy_read_struct'
dec_png.c:(.text+0x18d): undefined reference to `png_destroy_read_struct'
dec_png.c:(.text+0x1c4): undefined reference to `png_set_read_fn'
dec_png.c:(.text+0x1e1): undefined reference to `png_read_png'
dec_png.c:(.text+0x1f4): undefined reference to `png_get_rows'
dec_png.c:(.text+0x241): undefined reference to `png_get_IHDR'
dec_png.c:(.text+0x333): undefined reference to `png_destroy_read_struct'
collect2: ld returned 1 exit status
[durack1@oceanonly 150219_AMIPForcingData]$

There is also a bug that has crept in that wasn't an issue in earlier releases:

Ok so close, but it doesn’t get the “robust” tag just yet..

It seems that lats (or the cdms relationship with lats) has changed between now and June 2015 when the identical code (run against the identical lats libraries that I compiled myself) that generated the boundary conditions last June.

We’re now getting this error from lats – in addition to not being able to compile mkhurrell1.f as below:
***
 Field written successfully by LATS: sic

      Creating coards           file with LATS:
           /work/durack1/Shared/150219_AMIPForcingData/360x180_v1.0.1/bcinfo_sic_360x180_v1.0.1
 ifreq:            6
     Defining a variable with LATS: sicmax
     Defining a variable with LATS: sicbcsmax
     Defining a variable with LATS: sicmin
     Defining a variable with LATS: sicbcsmin
     Defining a variable with LATS: sicvar
     Defining a variable with LATS: sicbcsvar
 time out:            0           1           0           0
LATS error (lats_write): LATS (lats.c) -->
  Invalid year: 0, file /work/durack1/Shared/150219_AMIPForcingData/360x180_v1.0.1/bcinfo_sic_360x180_v1.0.1.nc year <= 0 NOT Supported
  if climatology use year 2 in lats_write
***

@durack1 durack1 added the Bug label Apr 25, 2016

@durack1 durack1 added this to the 2.6 milestone Apr 25, 2016

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durack1 commented Apr 25, 2016

@doutriaux1 apologies, the file I'm trying to compile is at https://github.com/PCMDI/amipbcs/blob/master/mkhurrell1.f

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doutriaux1 commented Apr 26, 2016

@durack1 this works for me with:
cd77 -ezget -lats -cdms -fcray-pointer mkhurrell1.f -o paul

@doutriaux1 doutriaux1 closed this May 4, 2016

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durack1 commented May 17, 2016

@doutriaux1 I am yet to test this.. Will report and close if/when I have confirmed a compile

@durack1 durack1 reopened this May 17, 2016

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doutriaux1 commented May 17, 2016

I missed you @durack1 😉

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durack1 commented May 17, 2016

@doutriaux1 course you did.. rigorous commentary..

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durack1 commented May 23, 2016

@doutriaux1 thanks for trying, this is where things are now:

(duroenv-robust)duro@ocean:[150219_AMIPForcingData]:[178]> cd77 -ezget -lats -cdms -fcray-pointer mkhurrell1.f -o paul
mkhurrell1.f:4621.72:

          pause 'tridag: rewrite equations'                             
                                                                        1
Warning: Deleted feature: PAUSE statement at (1)
mkhurrell1.f:4631.72:

            pause 'tridag failed'                                       
                                                                        1
Warning: Deleted feature: PAUSE statement at (1)
mkhurrell1.f:4654.72:

      if(n.le.2)pause 'n too small in cyclic'                           
                                                                        1
Warning: Deleted feature: PAUSE statement at (1)
mkhurrell1.f:4655.72:

      if(n.gt.nmax)pause 'nmax too small in cyclic'                     
                                                                        1
Warning: Deleted feature: PAUSE statement at (1)
/usr/bin/ld: warning: libhdf5_hl.so.10, needed by /usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libhdf5.so.10, needed by /usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: libjpeg.so.8, needed by /usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so, not found (try using -rpath or -rpath-link)
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_U16LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libpng.so: undefined reference to `inflateReset2@ZLIB_1.2.3.4'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dset_extent'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pcreate'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_native_type'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aexists'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pfill_value_defined'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_layout'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tis_variable_str'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_std_error@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Oopen'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Acreate1'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_size'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5DSis_scale'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Fflush'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Fopen'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_INT_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5check_version'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_chunk_cache'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5DSdetach_scale'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pget_layout'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_U16BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_I8BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Awrite'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_member_type'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aclose'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Gunlink'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_read_header@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dget_create_plist'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_IEEE_F64LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_set_defaults@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_start_compress@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Idec_ref'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dget_space'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5DSget_scale_name'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Literate'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_I16LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_U64BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_set_quality@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pget_chunk'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Gcreate2'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_stdio_dest@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5P_CLS_DATASET_ACCESS_ID_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_finish_compress@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_member_name'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_CreateDecompress@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_member_value'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Sget_simple_extent_npoints'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_finish_decompress@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Gget_objinfo'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_link_creation_order'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_CreateCompress@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_LLONG_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tenum_insert'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tinsert'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_member_offset'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_obj_track_times'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_SHORT_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dread'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tset_strpad'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pget_chunk_cache'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_UCHAR_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_fclose_degree'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tequal'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_fletcher32'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_deflate'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aopen_by_name'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_I32BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aget_space'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Sget_simple_extent_ndims'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_U32BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_U64LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_IEEE_F64BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tset_size'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Fis_hdf5'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5P_CLS_GROUP_CREATE_ID_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5DSget_num_scales'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_I8LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tarray_create1'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Fget_obj_count'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Adelete'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aget_type'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Fcreate'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pclose'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_I32LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Screate_simple'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_fapl_core'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tcommit1'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pget_nfilters'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Sselect_hyperslab'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5DSset_scale'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5DSattach_scale'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_DOUBLE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_fill_time'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Sget_simple_extent_dims'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_array_dims1'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_read_scanlines@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5P_CLS_DATASET_XFER_ID_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_C_S1_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_U8LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Lexists'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tvlen_create'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dopen2'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tcopy'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dget_type'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_ULLONG_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Screate'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pget_filter2'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_UINT_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_cache'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_IEEE_F32LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_I16BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pget_link_creation_order'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_start_decompress@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_super'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_FLOAT_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_attr_creation_order'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_libver_bounds'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dget_access_plist'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_U8BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_shuffle'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aopen_name'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aread'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_order'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_destroy_compress@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5P_CLS_DATASET_CREATE_ID_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_nmembers'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_I64LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Gget_create_plist'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aget_num_attrs'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Sclose'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_array_ndims'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_fill_value'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_U32LE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Sget_simple_extent_type'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5open'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5DSiterate_scales'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Eset_auto1'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_default_colorspace@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pset_chunk'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Oclose'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5P_CLS_FILE_CREATE_ID_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_destroy_decompress@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Gmove'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tclose'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aopen_idx'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_stdio_src@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_SCHAR_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dcreate1'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Iinc_ref'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Gopen2'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Pget_fill_value'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tenum_create'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_NATIVE_USHORT_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libjasper.so: undefined reference to `jpeg_write_scanlines@LIBJPEG_8.0'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dwrite'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dclose'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_IEEE_F32BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tget_class'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Tcreate'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5P_CLS_FILE_ACCESS_ID_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Fclose'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Gclose'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Dcreate2'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5T_STD_I64BE_g'
/usr/local/anaconda2/envs/duroenv-robust/lib/libnetcdf.so: undefined reference to `H5Aget_name'
collect2: ld returned 1 exit status
(duroenv-robust)duro@ocean:[150219_AMIPForcingData]:[179]>
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durack1 commented May 24, 2016

@doutriaux1 should LD_LIBRARY_PATH be set in cd77 - that way it'll remove another external environment variable dependency for this stuff to work?

@aashish24 aashish24 modified the milestones: 3.0, 2.6 Jun 8, 2016

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durack1 commented Jun 9, 2016

@doutriaux1 I believe this is sorted in the nightly conda channel - did you want to comment and close?

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durack1 commented Jul 5, 2016

@doutriaux1 this is resolved, so closing

@durack1 durack1 closed this Jul 5, 2016

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