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kevin218 / Eureka

Eureka! is a data reduction and analysis pipeline intended for time-series observations with JWST.
https://eurekadocs.readthedocs.io/
MIT License
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Stage 2: (FATAL) CRDS server connection and cache load FAILED #548

Closed Spacegirl123 closed 1 year ago

Spacegirl123 commented 1 year ago

Instrument

NIRSpec (Stages 1-3)

What happened?

Hello,

I was running stage 2 of the Eureka! Pipeline when I got the following error: CRDS - ERROR - (FATAL) CRDS server connection and cache load FAILED. Cannot continue.

Tried installing CRDS, but the problem persisted.

Any suggestions on how to solve this would be very welcome.

Best regards, Arushi

Error traceback output

2023-07-06 18:26:10,242 - stpipe - WARNING - Using NumPy C-API based implementation for BLAS functions. WARNING: Unable to find an output metadata file from Eureka!'s S1 in the folder: "D:\Desktop\Eureka\Stage1\" Assuming this S1 data was produced by the JWST pipeline instead.

Starting Stage 2 Reduction Input directory: D:\Desktop\Eureka\Stage1\ Output directory: D:\Desktop\Eureka\Stage2\S2_2023-07-06_nirspec_fs_template_run6\ Copying S2 control file

Found 1 data file(s) ending in rateints.fits 2023-07-06 18:26:11,303 - stpipe.EurekaSpec2Pipeline - INFO - EurekaSpec2Pipeline instance created. 2023-07-06 18:26:11,305 - stpipe.EurekaSpec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created. 2023-07-06 18:26:11,307 - stpipe.EurekaSpec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created. 2023-07-06 18:26:11,308 - stpipe.EurekaSpec2Pipeline.imprint_subtract - INFO - ImprintStep instance created. 2023-07-06 18:26:11,309 - stpipe.EurekaSpec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created. 2023-07-06 18:26:11,310 - stpipe.EurekaSpec2Pipeline.extract_2d - INFO - Extract2dStep instance created. 2023-07-06 18:26:11,314 - stpipe.EurekaSpec2Pipeline.master_background_mos - INFO - MasterBackgroundMosStep instance created. 2023-07-06 18:26:11,315 - stpipe.EurekaSpec2Pipeline.master_background_mos.flat_field - INFO - FlatFieldStep instance created. 2023-07-06 18:26:11,316 - stpipe.EurekaSpec2Pipeline.master_background_mos.pathloss - INFO - PathLossStep instance created. 2023-07-06 18:26:11,317 - stpipe.EurekaSpec2Pipeline.master_background_mos.barshadow - INFO - BarShadowStep instance created. 2023-07-06 18:26:11,318 - stpipe.EurekaSpec2Pipeline.master_background_mos.photom - INFO - PhotomStep instance created. 2023-07-06 18:26:11,320 - stpipe.EurekaSpec2Pipeline.wavecorr - INFO - WavecorrStep instance created. 2023-07-06 18:26:11,321 - stpipe.EurekaSpec2Pipeline.flat_field - INFO - FlatFieldStep instance created. 2023-07-06 18:26:11,322 - stpipe.EurekaSpec2Pipeline.srctype - INFO - SourceTypeStep instance created. 2023-07-06 18:26:11,323 - stpipe.EurekaSpec2Pipeline.straylight - INFO - StraylightStep instance created. 2023-07-06 18:26:11,324 - stpipe.EurekaSpec2Pipeline.fringe - INFO - FringeStep instance created. 2023-07-06 18:26:11,325 - stpipe.EurekaSpec2Pipeline.residual_fringe - INFO - ResidualFringeStep instance created. 2023-07-06 18:26:11,326 - stpipe.EurekaSpec2Pipeline.pathloss - INFO - PathLossStep instance created. 2023-07-06 18:26:11,327 - stpipe.EurekaSpec2Pipeline.barshadow - INFO - BarShadowStep instance created. 2023-07-06 18:26:11,329 - stpipe.EurekaSpec2Pipeline.wfss_contam - INFO - WfssContamStep instance created. 2023-07-06 18:26:11,330 - stpipe.EurekaSpec2Pipeline.photom - INFO - PhotomStep instance created. 2023-07-06 18:26:11,331 - stpipe.EurekaSpec2Pipeline.pixel_replace - INFO - PixelReplaceStep instance created. 2023-07-06 18:26:11,332 - stpipe.EurekaSpec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created. 2023-07-06 18:26:11,335 - stpipe.EurekaSpec2Pipeline.cube_build - INFO - CubeBuildStep instance created. 2023-07-06 18:26:11,336 - stpipe.EurekaSpec2Pipeline.extract_1d - INFO - Extract1dStep instance created. Starting file 1 of 1 Running the Spec2Pipeline

2023-07-06 18:26:11,429 - stpipe.EurekaSpec2Pipeline - INFO - Step EurekaSpec2Pipeline running with args ('D:\Desktop\Eureka\Stage1\rateints.fits',). 2023-07-06 18:26:11,449 - stpipe.EurekaSpec2Pipeline - INFO - Step EurekaSpec2Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': 'D:\Desktop\Eureka\Stage2\S2_2023-07-06_nirspec_fs_template_run6\', 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': True, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_bsub': False, 'fail_on_exception': True, 'save_wfss_esec': False, 'steps': {'bkg_subtract': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_combined_background': False, 'sigma': 3.0, 'maxiters': None, 'wfss_mmag_extract': None}, 'assign_wcs': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.1, 'sip_degree': None, 'sip_max_inv_pix_error': 0.1, 'sip_inv_degree': None, 'sip_npoints': 12, 'slit_y_low': -1, 'slit_y_high': 50}, 'imprint_subtract': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'msa_flagging': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'extract_2d': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'slit_name': None, 'extract_orders': None, 'grism_objects': None, 'tsgrism_extract_height': None, 'wfss_extract_half_height': 5, 'wfss_mmag_extract': None, 'wfss_nbright': 1000}, 'master_background_mos': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'force_subtract': False, 'save_background': False, 'user_background': None, 'inverse': False, 'steps': {'flat_field': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}, 'pathloss': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'barshadow': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'photom': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None, 'mrs_time_correction': True}}}, 'wavecorr': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'flat_field': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}, 'srctype': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'source_type': None}, 'straylight': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'fringe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'residual_fringe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': 'residual_fringe', 'search_output_file': False, 'input_dir': '', 'save_intermediate_results': False, 'ignore_region_min': None, 'ignore_region_max': None}, 'pathloss': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'barshadow': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}, 'wfss_contam': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_simulated_image': False, 'save_contam_images': False, 'maximum_cores': 'none'}, 'photom': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None, 'mrs_time_correction': True}, 'pixel_replace': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'algorithm': 'fit_profile', 'n_adjacent_cols': 3}, 'resample_spec': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'pixfrac': 1.0, 'kernel': 'square', 'fillval': 'INDEF', 'weight_type': 'ivm', 'output_shape': None, 'crpix': None, 'crval': None, 'rotation': None, 'pixel_scale_ratio': 1.0, 'pixel_scale': None, 'output_wcs': '', 'single': False, 'blendheaders': True, 'allowed_memory': None, 'in_memory': True}, 'cube_build': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': True, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': 's3d', 'search_output_file': False, 'input_dir': '', 'channel': 'all', 'band': 'all', 'grating': 'all', 'filter': 'all', 'output_type': 'band', 'scale1': 0.0, 'scale2': 0.0, 'scalew': 0.0, 'weighting': 'drizzle', 'coord_system': 'skyalign', 'rois': 0.0, 'roiw': 0.0, 'weight_power': 2.0, 'wavemin': None, 'wavemax': None, 'single': False, 'skip_dqflagging': False}, 'extract_1d': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'smoothing_length': None, 'bkg_fit': None, 'bkg_order': None, 'bkg_sigma_clip': 3.0, 'log_increment': 50, 'subtract_background': None, 'use_source_posn': None, 'center_xy': None, 'apply_apcorr': True, 'ifu_autocen': False, 'ifu_rfcorr': False, 'soss_atoca': True, 'soss_threshold': 0.01, 'soss_n_os': 2, 'soss_wave_grid_in': None, 'soss_wave_grid_out': None, 'soss_estimate': None, 'soss_rtol': 0.0001, 'soss_max_grid_size': 20000, 'soss_transform': None, 'soss_tikfac': None, 'soss_width': 40.0, 'soss_bad_pix': 'masking', 'soss_modelname': None}}} 2023-07-06 18:26:12,477 - stpipe.EurekaSpec2Pipeline - INFO - Prefetching reference files for dataset: 'rateints.fits' reftypes = ['apcorr', 'camera', 'collimator', 'disperser', 'distortion', 'extract1d', 'filteroffset', 'fore', 'fpa', 'ifufore', 'ifupost', 'ifuslicer', 'msa', 'ote', 'regions', 'speckernel', 'specprofile', 'spectrace', 'specwcs', 'wavecorr', 'wavelengthrange', 'wavemap'] 2023-07-06 18:26:12,479 - CRDS - ERROR - (FATAL) CRDS server connection and cache load FAILED. Cannot continue. See https://hst-crds.stsci.edu/docs/cmdline_bestrefs/ or https://jwst-crds.stsci.edu/docs/cmdline_bestrefs/ for more information on configuring CRDS, particularly CRDS_PATH and CRDS_SERVER_URL. : [Errno 2] No such file or directory: '/grp/crds/cache\config\jwst\server_config'

What operating system are you using?

Windows 10

What version of Python are you running?

Python 3.9.7

What Python packages do you have installed?

aesara-theano-fallback 0.1.0 pypi_0 pypi alabaster 0.7.13 pyhd8ed1ab_0 conda-forge aom 3.5.0 h63175ca_0 conda-forge arviz 0.12.1 pypi_0 pypi asciitree 0.3.3 py_2 conda-forge asdf 2.15.0 pyhd8ed1ab_0 conda-forge asdf-astropy 0.4.0 pyhd8ed1ab_1 conda-forge asdf-coordinates-schemas 0.2.0 pyhd8ed1ab_1 conda-forge asdf-standard 1.0.3 pyhd8ed1ab_0 conda-forge asdf-transform-schemas 0.3.0 pyhd8ed1ab_0 conda-forge asdf-unit-schemas 0.1.0 pyhd8ed1ab_0 conda-forge asdf-wcs-schemas 0.1.1 pyhd8ed1ab_0 conda-forge asteval 0.9.30 pyhd8ed1ab_0 conda-forge astra-toolbox 2.1.1 py39he6999da_0 astra-toolbox astraeus 0.3 pypi_0 pypi astropy 5.3 py39hbaa61f9_0 conda-forge astropy-healpix 0.7 py39hc266a54_2 conda-forge astroquery 0.4.6 pypi_0 pypi astroscrappy 1.1.0 py39hc266a54_2 conda-forge asttokens 2.2.1 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge aws-c-auth 0.7.0 h04ea561_0 conda-forge aws-c-cal 0.6.0 h6ba3258_0 conda-forge aws-c-common 0.8.23 hcfcfb64_0 conda-forge aws-c-compression 0.2.17 h420beca_1 conda-forge aws-c-event-stream 0.3.1 h32a1ef9_0 conda-forge aws-c-http 0.7.10 he907102_2 conda-forge aws-c-io 0.13.27 ha35c040_0 conda-forge aws-c-mqtt 0.8.13 hd8b9713_5 conda-forge aws-c-s3 0.3.12 he99ab17_2 conda-forge aws-c-sdkutils 0.1.11 h420beca_1 conda-forge aws-checksums 0.1.16 h420beca_1 conda-forge aws-crt-cpp 0.20.2 h152936e_18 conda-forge aws-sdk-cpp 1.10.57 h90d02da_16 conda-forge babel 2.12.1 pyhd8ed1ab_1 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.5 pyhd8ed1ab_0 conda-forge backports.zoneinfo 0.2.1 py39hcbf5309_7 conda-forge batman-package 2.4.9 py39hc266a54_1 conda-forge bayesicfitting 3.1.1 pypi_0 pypi beautifulsoup4 4.12.2 pyha770c72_0 conda-forge blas 1.0 mkl bleach 6.0.0 pyhd8ed1ab_0 conda-forge blosc 1.21.4 hdccc3a2_0 conda-forge bokeh 2.4.3 pyhd8ed1ab_3 conda-forge bottleneck 1.3.7 py39hc266a54_0 conda-forge brotli 1.0.9 hcfcfb64_9 conda-forge brotli-bin 1.0.9 hcfcfb64_9 conda-forge brotli-python 1.0.9 py39h99910a6_9 conda-forge bzip2 1.0.8 h8ffe710_4 conda-forge c-ares 1.19.1 hcfcfb64_0 conda-forge c-blosc2 2.10.0 h183a6f4_0 conda-forge ca-certificates 2023.05.30 haa95532_0 cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.3.1 pypi_0 pypi ccdproc 2.4.1 pyhd8ed1ab_0 conda-forge celerite 0.4.2 py39h2ba5b7c_3 conda-forge certifi 2023.5.7 py39haa95532_0 cfitsio 4.2.0 h9ebe7e4_0 conda-forge cftime 1.6.2 pypi_0 pypi charls 2.4.2 h1537add_0 conda-forge charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge click 8.1.3 win_pyhd8ed1ab_2 conda-forge cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge contourpy 1.1.0 py39h1f6ef14_0 conda-forge corner 2.2.2 pyhd8ed1ab_0 conda-forge coverage 7.2.7 py39ha55989b_0 conda-forge crds 11.17.2 pypi_0 pypi cudatoolkit 11.3.1 h59b6b97_2 cycler 0.11.0 pyhd8ed1ab_0 conda-forge cython 0.29.36 py39h99910a6_0 conda-forge cytoolz 0.12.0 py39ha55989b_1 conda-forge dask 2022.6.0 pypi_0 pypi dav1d 1.2.1 hcfcfb64_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge deprecat 2.1.1 pypi_0 pypi dill 0.3.6 pypi_0 pypi distributed 2023.6.1 pyhd8ed1ab_0 conda-forge docutils 0.20.1 py39hcbf5309_0 conda-forge drizzle 1.13.8.dev26+gfd2a32d pypi_0 pypi dynesty 2.1.2 pyhd8ed1ab_0 conda-forge emcee 3.1.4 pyhd8ed1ab_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge eureka 0.9 pypi_0 pypi exceptiongroup 1.1.2 pyhd8ed1ab_0 conda-forge executing 1.2.0 pyhd8ed1ab_0 conda-forge exoplanet 0.5.3 pypi_0 pypi exoplanet-core 0.1.2 pypi_0 pypi exotic-ld 3.0.0 pypi_0 pypi fasteners 0.17.3 pyhd8ed1ab_0 conda-forge fastprogress 1.0.3 pypi_0 pypi filelock 3.12.2 pypi_0 pypi fonttools 4.40.0 py39ha55989b_0 conda-forge freetype 2.12.1 h546665d_1 conda-forge fsspec 2023.6.0 pyh1a96a4e_0 conda-forge future 0.18.3 pyhd8ed1ab_0 conda-forge george 0.4.0 py39h2ba5b7c_5 conda-forge gettext 0.21.1 h5728263_0 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Code of Conduct

taylorbell57 commented 1 year ago

It looks to me like you haven't followed the CRDS-related instructions here. I see we forgot to put in those instructions that once you've made that edit, you will need to close your terminal and reopen it so that the changes are applied

Spacegirl123 commented 1 year ago

Thanks for the tip. But even after following those instructions and re-opening my terminal, the same error still pops up.

taylorbell57 commented 1 year ago

If you open a terminal and type the following two commands, what results do you get for each?

echo $CRDS_PATH
echo $CRDS_SERVER_URL
Spacegirl123 commented 1 year ago

Both come up empty. I tried re-setting those environment variables, and the echo seemed to give the correct output. But once I re-started the terminal they came out empty again.

taylorbell57 commented 1 year ago

Please re-read those instructions I linked above (especially the text above the code) - those export commands are supposed to be inside your "~/.bashrc"-like file (depending on your operating system)

Spacegirl123 commented 1 year ago

Hi, sorry for my late response. I restarted my computer, and the error seems to be solved. Thanks for your help.