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isce-framework / isce2

InSAR Scientific Computing Environment version 2
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ISCE2 installation not working using latest python nor using older pythons #692

Closed falkamelung closed 1 year ago

falkamelung commented 1 year ago

When trying to install isce2 using mamba and the latest python (3.10.10) I am getting error messages regarding cfitsio,kealib,libpng and freetype (full message below). A few months ago (January) it worked fine. I have a working ISCE version installed using python3.10.8. I tried to install using older pythons (3.8, 3.9) and got similar errors (but partly for different packages) (I could not figure out how to force using python3.10.8).

Installation using conda stopped working for me a while ago. I gave up after solving for 6 hours.

Any suggestions are appreciated 

../tools/miniconda3/bin/mamba install isce2 -c conda-forge --yes                                                                                                                                

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        mamba (1.4.2) supported by @QuantStack                                                                                                                                                                          

        GitHub:  https://github.com/mamba-org/mamba                                                                                                                                                                     
        Twitter: https://twitter.com/QuantStack                                                                                                                                                                         

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Looking for: ['isce2']                                                                                                                                                                                                  

warning  libmamba Cache file "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/pkgs/cache/497deca9.json" was modified by another program
warning  libmamba Cache file "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/pkgs/cache/09cdf8bf.json" was modified by another program
warning  libmamba Cache file "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/pkgs/cache/47929eba.json" was modified by another program
warning  libmamba Cache file "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/pkgs/cache/3e39a7aa.json" was modified by another program
warning  libmamba Cache file "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/pkgs/cache/2ce54b42.json" was modified by another program
warning  libmamba Cache file "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/pkgs/cache/4ea078d6.json" was modified by another program
pkgs/main/noarch                                   821.1kB @   1.7MB/s  0.5s
pkgs/r/linux-64                                      1.4MB @   2.4MB/s  0.7s
pkgs/r/noarch                                        1.3MB @   1.6MB/s  0.3s
pkgs/main/linux-64                                   5.5MB @   4.0MB/s  1.6s
conda-forge/noarch                                  11.8MB @   4.0MB/s  3.2s
conda-forge/linux-64                                30.7MB @   5.3MB/s  6.7s

Pinned packages:
  - python 3.10.*

Transaction

  Prefix: /work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3

  Updating specs:

   - isce2
   - ca-certificates
   - certifi
   - openssl

  Package                        Version  Build                    Channel                    Size
────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────────────────────────

  + aom                            3.5.0  h27087fc_0               conda-forge/linux-64        3MB
  + attr                           2.5.1  h166bdaf_1               conda-forge/linux-64       71kB
  + blosc                         1.21.3  hafa529b_0               conda-forge/linux-64       40kB
  + boost-cpp                     1.78.0  h5adbc97_2               conda-forge/linux-64       16MB
  + brotli                         1.0.9  h166bdaf_8               conda-forge/linux-64       19kB
  + brotli-bin                     1.0.9  h166bdaf_8               conda-forge/linux-64       20kB
  + brunsli                          0.1  h9c3ff4c_0               conda-forge/linux-64      205kB
  + c-blosc2                       2.8.0  hf91038e_1               conda-forge/linux-64      284kB
  + cached-property                1.5.2  hd8ed1ab_1               conda-forge/noarch          4kB
  + cached_property                1.5.2  pyha770c72_1             conda-forge/noarch         11kB
  + cairo                         1.16.0  ha61ee94_1014            conda-forge/linux-64        2MB
  + cfitsio                        4.2.0  hd9d235c_0               conda-forge/linux-64      848kB
  + charls                         2.4.1  hcb278e6_0               conda-forge/linux-64      141kB
  + click                          8.1.3  unix_pyhd8ed1ab_2        conda-forge/noarch         76kB
  + cloudpickle                    2.2.1  pyhd8ed1ab_0             conda-forge/noarch         28kB
  + curl                          7.88.1  hdc1c0ab_1               conda-forge/linux-64       88kB
  + cytoolz                       0.12.0  py310h5764c6d_1          conda-forge/linux-64      398kB
  + dask-core                   2023.3.2  pyhd8ed1ab_0             conda-forge/noarch        842kB
  + dav1d                          1.0.0  h166bdaf_1               conda-forge/linux-64      842kB
  + expat                          2.5.0  hcb278e6_1               conda-forge/linux-64      137kB
  + fftw                          3.3.10  nompi_hf0379b8_106       conda-forge/linux-64        2MB
  + font-ttf-dejavu-sans-mono       2.37  hab24e00_0               conda-forge/noarch        397kB
  + font-ttf-inconsolata           3.000  h77eed37_0               conda-forge/noarch         97kB
  + font-ttf-source-code-pro       2.038  h77eed37_0               conda-forge/noarch        701kB
  + font-ttf-ubuntu                 0.83  hab24e00_0               conda-forge/noarch          2MB
  + fontconfig                    2.14.2  h14ed4e7_0               conda-forge/linux-64      272kB
  + fonts-conda-ecosystem              1  0                        conda-forge/noarch          4kB
  + fonts-conda-forge                  1  0                        conda-forge/noarch          4kB
  + freetype                      2.12.1  hca18f0e_1               conda-forge/linux-64      626kB
  + freexl                         1.0.6  h166bdaf_1               conda-forge/linux-64       50kB
  + fsspec                      2023.3.0  pyhd8ed1ab_1             conda-forge/noarch        111kB
  + gdal                           3.6.2  py310hc1b7723_9          conda-forge/linux-64        1MB
  + geos                          3.11.1  h27087fc_0               conda-forge/linux-64        2MB
  + geotiff                        1.7.1  h7a142b4_6               conda-forge/linux-64      259kB
  + gettext                       0.21.1  h27087fc_0               conda-forge/linux-64        4MB
  + giflib                         5.2.1  h0b41bf4_3               conda-forge/linux-64       77kB
  + h5py                           3.8.0  nompi_py310h0311031_100  conda-forge/linux-64        1MB
  + hdf4                          4.2.15  h9772cbc_5               conda-forge/linux-64      974kB
  + hdf5                          1.12.2  nompi_h4df4325_101       conda-forge/linux-64        3MB
  + imagecodecs                2023.1.23  py310ha3ed6a1_0          conda-forge/linux-64        2MB
  + imageio                       2.27.0  pyh24c5eb1_0             conda-forge/noarch          3MB
  + importlib-metadata             6.1.0  pyha770c72_0             conda-forge/noarch         25kB
  + importlib_metadata             6.1.0  hd8ed1ab_0               conda-forge/noarch          9kB
  + isce2                          2.6.2  py310h04680ef_0          conda-forge/linux-64        6MB
  + jpeg                              9e  h0b41bf4_3               conda-forge/linux-64      240kB
  + json-c                          0.16  hc379101_0               conda-forge/linux-64      281kB
  + jxrlib                           1.1  h7f98852_2               conda-forge/linux-64      241kB
  + kealib                         1.5.0  ha7026e8_0               conda-forge/linux-64      164kB
  + lazy_loader                      0.2  pyhd8ed1ab_0             conda-forge/noarch         14kB
  + lcms2                           2.15  hfd0df8a_0               conda-forge/linux-64      241kB
  + lerc                           4.0.0  h27087fc_0               conda-forge/linux-64      282kB
  + libacl                         2.3.1  ha37c62d_1               conda-forge/linux-64      114kB
  + pywavelets                     1.4.1  py310h0a54255_0          conda-forge/linux-64        4MB
  + pyyaml                           6.0  py310h5764c6d_5          conda-forge/linux-64      176kB
  + scikit-image                  0.20.0  py310h9b08913_0          conda-forge/linux-64       10MB
  + scipy                         1.10.1  py310h8deb116_0          conda-forge/linux-64       25MB
  + snappy                        1.1.10  h9fff704_0               conda-forge/linux-64       39kB
  + sqlite                        3.40.0  h4ff8645_0               conda-forge/linux-64      820kB
  + tifffile                   2023.3.21  pyhd8ed1ab_0             conda-forge/noarch        174kB
  + tiledb                        2.13.2  hd532e3d_0               conda-forge/linux-64        5MB
  + typing-extensions              4.5.0  hd8ed1ab_0               conda-forge/noarch         10kB
  + typing_extensions              4.5.0  pyha770c72_0             conda-forge/noarch         31kB
  + tzcode                         2023c  h0b41bf4_0               conda-forge/linux-64       69kB
  + xerces-c                       3.2.4  h55805fa_1               conda-forge/linux-64        2MB
  + xorg-kbproto                   1.0.7  h7f98852_1002            conda-forge/linux-64       27kB
  + xorg-libice                   1.0.10  h7f98852_0               conda-forge/linux-64       59kB
  + xorg-libsm                     1.2.3  hd9c2040_1000            conda-forge/linux-64       26kB
  + xorg-libx11                   1.6.12  h36c2ea0_0               conda-forge/linux-64      941kB
  + xorg-libxau                    1.0.9  h7f98852_0               conda-forge/linux-64       13kB
  + xorg-libxdmcp                  1.1.3  h7f98852_0               conda-forge/linux-64       19kB
  + xorg-libxext                   1.3.4  h516909a_0               conda-forge/linux-64       53kB
  + xorg-libxft                    2.3.4  hc534e41_1               conda-forge/linux-64       55kB
  + xorg-libxmu                    1.1.3  h516909a_0               conda-forge/linux-64       92kB
  + xorg-libxp                     1.0.3  0                        conda-forge/linux-64       29kB
  + xorg-libxrender               0.9.10  h516909a_1002            conda-forge/linux-64       32kB
  + xorg-libxt                     1.1.5  h516909a_1003            conda-forge/linux-64      376kB
  + xorg-renderproto              0.11.1  h7f98852_1002            conda-forge/linux-64       10kB
  + xorg-xextproto                 7.3.0  h0b41bf4_1003            conda-forge/linux-64       30kB
  + xorg-xproto                   7.0.31  h7f98852_1007            conda-forge/linux-64       75kB
  + yaml                           0.2.5  h7f98852_2               conda-forge/linux-64       89kB
  + zfp                            1.0.0  h27087fc_3               conda-forge/linux-64      292kB
  + zipp                          3.15.0  pyhd8ed1ab_0             conda-forge/noarch         17kB
  + zlib                          1.2.13  h166bdaf_4               conda-forge/linux-64     Cached
  + zlib-ng                        2.0.7  h0b41bf4_0               conda-forge/linux-64       95kB

  Change:
────────────────────────────────────────────────────────────────────────────────────────────────────

  - libxml2                       2.10.3  hfdac1af_6               conda-forge                    
  + libxml2                       2.10.3  hca2bb57_4               conda-forge/linux-64      714kB

  Downgrade:
────────────────────────────────────────────────────────────────────────────────────────────────────

  - icu                             72.1  hcb278e6_0               conda-forge                    
  + icu                             70.1  h27087fc_0               conda-forge/linux-64       14MB

  Summary:

  Install: 128 packages
  Change: 1 packages
  Downgrade: 1 packages

  Total download: 251MB

────────────────────────────────────────────────────────────────────────────────────────────────────

lerc                                               281.8kB @   1.6MB/s  0.2s
libpq                                                2.5MB @  10.9MB/s  0.2s
nspr                                               226.8kB @   1.0MB/s  0.1s
geos                                                 1.7MB @   6.4MB/s  0.3s
libexpat                                            78.0kB @ 291.0kB/s  0.1s
freexl                                              49.6kB @ 184.4kB/s  0.1s
pcre2                                                2.4MB @   6.1MB/s  0.4s
xorg-libxau                                         13.4kB @  32.9kB/s  0.1s
xorg-xextproto                                      30.3kB @  74.1kB/s  0.1s
libgfortran5                                         1.8MB @   3.9MB/s  0.2s
pthread-stubs                                        5.6kB @  11.9kB/s  0.1s
xorg-libxdmcp                                       19.1kB @  40.2kB/s  0.1s
attr                                                71.0kB @ 148.9kB/s  0.1s
libzip                                              99.4kB @ 171.0kB/s  0.1s
jxrlib                                             240.9kB @ 413.4kB/s  0.1s
libbrotlicommon                                     67.2kB @ 115.1kB/s  0.1s
libzopfli                                          168.1kB @ 277.1kB/s  0.1s
librttopo                                          241.9kB @ 336.6kB/s  0.1s
hdf4                                               973.8kB @   1.3MB/s  0.1s
xorg-libsm                                          26.4kB @  33.2kB/s  0.1s
libbrotlidec                                        34.2kB @  43.0kB/s  0.1s
libglib                                              3.3MB @   3.9MB/s  0.3s
openjpeg                                           352.0kB @ 412.5kB/s  0.1s
lcms2                                              240.8kB @ 281.7kB/s  0.1s
tiledb                                               5.1MB @   5.6MB/s  0.3s
cfitsio                                            848.0kB @ 930.1kB/s  0.1s
xorg-libx11                                        940.8kB @ 997.4kB/s  0.1s
icu                                                 14.2MB @  14.5MB/s  1.0s
fftw                                                 2.2MB @   2.3MB/s  0.2s
font-ttf-inconsolata                                96.5kB @  88.0kB/s  0.1s
font-ttf-source-code-pro                           700.8kB @ 634.7kB/s  0.1s
cached_property                                     11.1kB @   9.9kB/s  0.1s
font-ttf-ubuntu                                      2.0MB @   1.7MB/s  0.1s
partd                                               18.7kB @  16.4kB/s  0.0s
cached-property                                      4.1kB @   3.6kB/s  0.0s
typing-extensions                                    9.7kB @   8.4kB/s  0.0s
fonts-conda-forge                                    4.1kB @   3.5kB/s  0.0s
pooch                                               50.9kB @  44.0kB/s  0.0s
gdal                                                 1.4MB @   1.2MB/s  0.0s
libpng                                             282.6kB @ 230.6kB/s  0.1s
giflib                                              77.4kB @  63.2kB/s  0.0s
snappy                                              38.9kB @  31.0kB/s  0.0s
xorg-xproto                                         74.9kB @  59.2kB/s  0.1s
libaec                                              34.4kB @  27.2kB/s  0.1s
libgdal                                             10.2MB @   8.2MB/s  0.1s
zlib-ng                                             94.6kB @  73.2kB/s  0.0s
sqlite                                             820.2kB @ 632.0kB/s  0.1s
dav1d                                              842.3kB @ 648.4kB/s  0.0s
nss                                                  2.0MB @   1.5MB/s  0.0s
libgfortran-ng                                      22.9kB @  17.3kB/s  0.0s
libacl                                             113.5kB @  85.7kB/s  0.0s
libxcb                                             399.9kB @ 300.4kB/s  0.0s
proj                                                 2.9MB @   2.1MB/s  0.1s
libspatialite                                        4.1MB @   2.9MB/s  0.1s
brotli                                              18.9kB @  13.3kB/s  0.1s
poppler                                             15.6MB @  11.0MB/s  0.3s
xorg-libxmu                                         91.9kB @  63.0kB/s  0.0s
libopenblas                                         10.6MB @   7.2MB/s  0.2s
poppler-data                                         2.3MB @   1.5MB/s  0.1s
typing_extensions                                   31.3kB @  20.5kB/s  0.1s
fsspec                                             111.2kB @  72.6kB/s  0.1s
numpy                                                6.7MB @   4.2MB/s  0.2s
tifffile                                           173.9kB @ 109.9kB/s  0.1s
importlib-metadata                                  24.9kB @  15.7kB/s  0.1s
imageio                                              3.3MB @   2.0MB/s  0.1s
libdeflate                                          65.0kB @  38.9kB/s  0.1s
xorg-renderproto                                     9.6kB @   5.6kB/s  0.1s
openmotif                                            7.3MB @   4.3MB/s  0.1s
cytoolz                                            397.8kB @ 225.1kB/s  0.1s
scikit-image                                        10.4MB @   6.0MB/s  0.2s
zfp                                                292.1kB @ 163.2kB/s  0.1s
freetype                                           625.7kB @ 344.3kB/s  0.1s
libbrotlienc                                       295.2kB @ 162.6kB/s  0.0s
pyyaml                                             176.3kB @  95.5kB/s  0.0s
geotiff                                            258.9kB @ 136.4kB/s  0.1s
scipy                                               24.7MB @  13.0MB/s  0.3s
postgresql                                           5.1MB @   2.7MB/s  0.1s
pillow                                              46.5MB @  24.2MB/s  0.6s
xorg-libxext                                        52.6kB @  27.3kB/s  0.0s
boost-cpp                                           15.9MB @   8.2MB/s  0.2s
liblapack                                           12.8kB @   6.6kB/s  0.0s
locket                                               8.2kB @   4.2kB/s  0.0s
importlib_metadata                                   9.3kB @   4.8kB/s  0.0s
imagecodecs                                          1.9MB @ 987.0kB/s  0.1s
pywavelets                                           3.7MB @   1.9MB/s  0.1s
cairo                                                1.6MB @ 792.0kB/s  0.0s
xorg-libice                                         59.4kB @  29.3kB/s  0.0s
gettext                                              4.3MB @   2.1MB/s  0.1s
pixman                                             642.5kB @ 313.4kB/s  0.1s
libtiff                                            406.7kB @ 198.3kB/s  0.0s
libxml2                                            713.9kB @ 346.4kB/s  0.0s
brotli-bin                                          20.1kB @   9.7kB/s  0.0s
libkml                                             624.7kB @ 301.0kB/s  0.1s
libcblas                                            12.8kB @   6.2kB/s  0.0s
cloudpickle                                         27.9kB @  13.4kB/s  0.0s
isce2                                                6.2MB @   3.0MB/s  0.1s
zipp                                                17.2kB @   8.2kB/s  0.0s
platformdirs                                        17.9kB @   8.6kB/s  0.0s
dask-core                                          842.4kB @ 401.9kB/s  0.0s
charls                                             141.4kB @  66.3kB/s  0.0s
expat                                              136.8kB @  63.8kB/s  0.0s
libwebp-base                                       356.8kB @ 165.2kB/s  0.1s
font-ttf-dejavu-sans-mono                          397.4kB @ 185.1kB/s  0.0s
xerces-c                                             1.8MB @ 844.7kB/s  0.1s
click                                               76.0kB @  35.2kB/s  0.0s
hdf5                                                 3.3MB @   1.5MB/s  0.1s
xorg-libxft                                         55.4kB @  25.5kB/s  0.0s
h5py                                                 1.1MB @ 523.4kB/s  0.0s
yaml                                                89.1kB @  40.4kB/s  0.0s
libblas                                             12.9kB @   5.8kB/s  0.0s
aom                                                  2.9MB @   1.3MB/s  0.0s
tzcode                                              68.6kB @  30.5kB/s  0.0s
xorg-kbproto                                        27.3kB @  12.2kB/s  0.0s
networkx                                             1.5MB @ 656.5kB/s  0.0s
libavif                                            104.9kB @  46.6kB/s  0.0s
fontconfig                                         272.0kB @ 120.8kB/s  0.0s
jpeg                                               240.4kB @ 105.3kB/s  0.0s
blosc                                               40.3kB @  17.8kB/s  0.0s
curl                                                88.1kB @  38.5kB/s  0.0s
lazy_loader                                         13.8kB @   6.1kB/s  0.0s
c-blosc2                                           284.1kB @ 124.2kB/s  0.0s
xorg-libxrender                                     31.9kB @  13.9kB/s  0.0s
json-c                                             281.4kB @ 121.7kB/s  0.0s
fonts-conda-ecosystem                                3.7kB @   1.6kB/s  0.0s
[+] 18.7s
Downloading       ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 251.4MB / 251.4MB                            2.3s
cfitsio-4.2.0-hd9d235c_0.conda extraction failed
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kealib-1.5.0-ha7026e8_0.conda extraction failed
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libpng-1.6.39-h753d276_0.conda extraction failed
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freetype-2.12.1-hca18f0e_1.conda extraction failed
Found incorrect download: libpng. Aborting

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1132, in __call__
        return func(*args, **kwargs)
      File "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/mamba/mamba.py", line 941, in exception_converter
        raise e
      File "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/mamba/mamba.py", line 934, in exception_converter
        exit_code = _wrapped_main(*args, **kwargs)
      File "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/mamba/mamba.py", line 892, in _wrapped_main
        result = do_call(parsed_args, p)
      File "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/mamba/mamba.py", line 754, in do_call
        exit_code = install(args, parser, "install")
      File "/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/mamba/mamba.py", line 588, in install
        transaction.fetch_extract_packages()
    RuntimeError: Found incorrect download: libpng. Aborting

`$ ../tools/miniconda3/bin/mamba install isce2 -c conda-forge --yes`

  environment variables:
                 CIO_TEST=<not set>
               CONDA_ROOT=/work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3
           CURL_CA_BUNDLE=<not set>
                    FPATH=/opt/apps/lmod/lmod/init/ksh_funcs
               LD_PRELOAD=<not set>
                  MANPATH=::
               MODULEPATH=/opt/apps/modulefiles
                     PATH=/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
__LMOD_REF_COUNT_MODULEPATH=/opt/apps/modulefiles:1
    __LMOD_REF_COUNT_PATH=/usr/lib64/qt-
                          3.3/bin:1;/usr/local/bin:1;/bin:1;/usr/bin:1;/opt/dell/srvadmin/bin:1
         __LMOD_SET_FPATH=1

     active environment : None
       user config file : /home1/05861/tg851601/.condarc
 populated config files : /home1/05861/tg851601/.condarc
          conda version : 23.3.1
    conda-build version : not installed
         python version : 3.10.10.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.17=0
                          __linux=3.10.0=0
                          __unix=0=0
       base environment : /work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3  (writable)
      conda av data dir : /work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/pkgs
                          /home1/05861/tg851601/.conda/pkgs
       envs directories : /work2/05861/tg851601/stampede2/code2/rsmas_insar/tools/miniconda3/envs
                          /home1/05861/tg851601/.conda/envs
               platform : linux-64
             user-agent : conda/23.3.1 requests/2.28.2 CPython/3.10.10 Linux/3.10.0-1160.53.1.el7.x86_64 centos/7.9.2009 glibc/2.17
                UID:GID : 851601:820134
             netrc file : /home1/05861/tg851601/.netrc
           offline mode : False

An unexpected error has occurred. Conda has prepared the above report.

To add to the confusion, if I just run the same mamba command again it runs through but then I receive an ISCE error

 File "/work2/05861/tg851601/stampede2/code1/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/isce/components/iscesys/ImageApi/DataAccessorPy.py", line 31, in <module>
    from iscesys.ImageApi import DataAccessor as DA
ImportError: /work2/05861/tg851601/stampede2/code1/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/isce/components/iscesys/ImageApi/../../../../../.././libspatialite.so.7: undefined symbol: sqlite3_strlike
hariiirs commented 1 year ago

I was also working fine with isce2 in February 2023, but now suddenly it stops and showing errors here and there. I followed the process as -

1) Installed anaconda3 2) Created a new environment (First Time with specific version of Python 3.7 and repeated for 3.9, 3.11 too; second time without any specific version of python) 3) Activated the newly created environment 4) Installed isce2 as $conda install -c conda-forge isce2 5) Exported the PATHs of topsStack, prepStackToStaMPS, Applications etc. 6) run stackSentinel.py -h

Now it is showing same error in almost all the above trials -

Screenshot from 2023-04-21 14-55-28

Although the same process was followed earlier and it was working fine.

yunjunz commented 1 year ago

@hariiirs that is a change introduced in the stack processor. You need to set up the $PYTHONPATH as well now, in addition to the $PATH, since version 2.6.2, as described here: https://github.com/isce-framework/isce2/blob/main/contrib/stack/README.md#2-setup-paths-for-stack-processors.

falkamelung commented 1 year ago

Hopefully this resolves @hariiirs issue but not my issue. If somebody is successful with the installation please let me know.

EJFielding commented 1 year ago

Version 2.6.3 was released, which should work better with Python 3.10 and 3.11.

falkamelung commented 1 year ago

It does not solve the problem, unfortunately. With the latest miniconda3 (python 3.10.11) mamba install isce2 -c conda-forge --yes gives me nearly the same errors as before (see above).

If I first install MintPy (as I usually do):

../tools/miniconda3/bin/conda install --yes --file ../tools/MintPy/requirements.txt
../tools/miniconda3/bin/mamba install isce2 -c conda-forge --yes

the ISCE installation works, but it gives am import error for sqlite3_strlike (same as previously):

miniconda3[1056] ./share/isce2/topsStack/stackSentinel.py --help
Traceback (most recent call last):
  File "/work2/05861/tg851601/stampede2/codetn/rsmas_insar/tools/miniconda3/./share/isce2/topsStack/stackSentinel.py", line 16, in <module>
    from isceobj.Sensor.TOPS.Sentinel1 import Sentinel1
  File "/work2/05861/tg851601/stampede2/codetn/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/isce/components/isceobj/Sensor/TOPS/Sentinel1.py", line 39, in <module>
    from .BurstSLC import BurstSLC
  File "/work2/05861/tg851601/stampede2/codetn/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/isce/components/isceobj/Sensor/TOPS/BurstSLC.py", line 8, in <module>
    from isceobj.Image.Image import Image
  File "/work2/05861/tg851601/stampede2/codetn/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/isce/components/isceobj/Image/Image.py", line 38, in <module>
    from iscesys.ImageApi.DataAccessorPy import DataAccessor
  File "/work2/05861/tg851601/stampede2/codetn/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/isce/components/iscesys/ImageApi/DataAccessorPy.py", line 31, in <module>
    from iscesys.ImageApi import DataAccessor as DA
ImportError: /work2/05861/tg851601/stampede2/codetn/rsmas_insar/tools/miniconda3/lib/python3.10/site-packages/isce/components/iscesys/ImageApi/../../../../../.././libspatialite.so.7: undefined symbol: sqlite3_strlike

I use the same environment that worked previously:

export ISCE_HOME=${RSMASINSAR_HOME}/tools/miniconda3/lib/$python_version/site-packages/isce
export ISCE_STACK=${RSMASINSAR_HOME}/tools/miniconda3/share/isce2
export PYTHONPATH=${PYTHONPATH}:${ISCE_HOME}:${ISCE_HOME}/components:${ISCE_STACK}
yunjunz commented 1 year ago

I would recommend installing mintpy dependencies and isce2 in one command line, such as below, so that conda/mamba could resolve the dependencies at once. I just tried it recently in a fresh environment, and it worked for me with python 3.10 and 3.11.

mamba install --file MintPy/requirements.txt isce2 --yes
falkamelung commented 1 year ago

It turns out that if I omit running

mamba update mamba --yes

it works fine.

Uff! So updating mamba introduces a problem.

I noticed when I reinstalled miniconda on my Mac (there was a pysqlite2 and sqlite import error). At least something good coming out of my Mac dying!

Closing this and hope to never have to reopen again.