verdurin/dorado-0.6.1-foss-2023a-CUDA-12.1.1_partial.log

## dorado-0.6.1-foss-2023a-CUDA-12.1.1_partial.log
dorado/dorado/utils/tty_utils.h
dorado/dorado/utils/types.cpp
dorado/dorado/utils/types.h
dorado/dorado/utils/uuid_utils.cpp
dorado/dorado/utils/uuid_utils.h
dorado/tests/
dorado/tests/AdapterDetectorTest.cpp
dorado/tests/AlignerTest.cpp
dorado/tests/AsyncQueueTest.cpp
dorado/tests/BamReaderTest.cpp
dorado/tests/BamUtilsTest.cpp
dorado/tests/BamWriterTest.cpp
dorado/tests/BarcodeClassifierSelectorTest.cpp
dorado/tests/BarcodeClassifierTest.cpp
dorado/tests/BarcodeDemuxerNodeTest.cpp
dorado/tests/BedFileTest.cpp
dorado/tests/CMakeLists.txt
dorado/tests/CRFModelConfigTest.cpp
dorado/tests/CliUtilsTest.cpp
dorado/tests/CustomBarcodeParserTest.cpp
dorado/tests/DuplexReadTaggingNodeTest.cpp
dorado/tests/DuplexSplitTest.cpp
dorado/tests/Fast5DataLoaderTest.cpp
dorado/tests/IndexFileAccessTest.cpp
dorado/tests/MathUtilsTest.cpp
dorado/tests/MessageSinkUtils.h
dorado/tests/MetalLinearTest.cpp
dorado/tests/Minimap2IndexTest.cpp
dorado/tests/ModBaseEncoderTest.cpp
dorado/tests/ModelFinderTest.cpp
dorado/tests/ModelKitsTest.cpp
dorado/tests/ModelMetadataTest.cpp
dorado/tests/ModelUtilsTest.cpp
dorado/tests/MotifMatcherTest.cpp
dorado/tests/NodeSmokeTest.cpp
dorado/tests/PairingNodeTest.cpp
dorado/tests/PipelineTest.cpp
dorado/tests/Pod5DataLoaderTest.cpp
dorado/tests/PolyACalculatorTest.cpp
dorado/tests/PostConditionTest.cpp
dorado/tests/RNASplitTest.cpp
dorado/tests/ReadFilterNodeTest.cpp
dorado/tests/ReadForwarderNodeTest.cpp
dorado/tests/ReadTest.cpp
dorado/tests/RealignMovesTest.cpp
dorado/tests/ResumeLoaderTest.cpp
dorado/tests/SampleSheetTests.cpp
dorado/tests/SequenceUtilsTest.cpp
dorado/tests/StereoDuplexTest.cpp
dorado/tests/StitchTest.cpp
dorado/tests/StringUtilsTest.cpp
dorado/tests/TensorUtilsTest.cpp
dorado/tests/TestUtils.cpp
dorado/tests/TestUtils.h
dorado/tests/TimeUtilsTest.cpp
dorado/tests/TrimRapidAdapterTest.cpp
dorado/tests/TrimTest.cpp
dorado/tests/alignment_processing_items_test.cpp
dorado/tests/cuda_utils_test.cpp
dorado/tests/data/
dorado/tests/data/adapter_trim/
dorado/tests/data/adapter_trim/custom_primers.fasta
dorado/tests/data/adapter_trim/lsk109_single_read.fastq
dorado/tests/data/aligner_test/
dorado/tests/data/aligner_test/basecall.sam
dorado/tests/data/aligner_test/basecall_target.fa
dorado/tests/data/aligner_test/dataset.fastq
dorado/tests/data/aligner_test/lambda_ecoli.fasta
dorado/tests/data/aligner_test/long_target.fa
dorado/tests/data/aligner_test/query.fa
dorado/tests/data/aligner_test/rev_target.fq
dorado/tests/data/aligner_test/supplementary_aln_query.fa
dorado/tests/data/aligner_test/supplementary_aln_target.fa
dorado/tests/data/aligner_test/supplementary_basecall_target.fa
dorado/tests/data/aligner_test/target.bed
dorado/tests/data/aligner_test/target.fq
dorado/tests/data/alignment_processing_items/
dorado/tests/data/alignment_processing_items/input/
dorado/tests/data/alignment_processing_items/input/bam.bam
dorado/tests/data/alignment_processing_items/input/duplicates/
dorado/tests/data/alignment_processing_items/input/duplicates/duplicate
dorado/tests/data/alignment_processing_items/input/duplicates/duplicate.bam
dorado/tests/data/alignment_processing_items/input/duplicates/duplicate.fa
dorado/tests/data/alignment_processing_items/input/duplicates/duplicate.fastq
dorado/tests/data/alignment_processing_items/input/duplicates/duplicate.fq
dorado/tests/data/alignment_processing_items/input/duplicates/duplicate.sam
dorado/tests/data/alignment_processing_items/input/fa.fa
dorado/tests/data/alignment_processing_items/input/fastq.fastq
dorado/tests/data/alignment_processing_items/input/fq.fq
dorado/tests/data/alignment_processing_items/input/no_extension
dorado/tests/data/alignment_processing_items/input/no_extension_gz.gz
dorado/tests/data/alignment_processing_items/input/non_hts_file.txt
dorado/tests/data/alignment_processing_items/input/sam.sam
dorado/tests/data/alignment_processing_items/input/sam_gz.sam.gz
dorado/tests/data/alignment_processing_items/input/sam_gzip.gzip
dorado/tests/data/bam_reader/
dorado/tests/data/bam_reader/fastq_with_tags.fq
dorado/tests/data/bam_reader/input.fa
dorado/tests/data/bam_reader/small.sam
dorado/tests/data/bam_utils/
dorado/tests/data/bam_utils/aligned_record.bam
dorado/tests/data/bam_utils/test.sam
dorado/tests/data/barcode_demux/
dorado/tests/data/barcode_demux/custom_barcodes/
dorado/tests/data/barcode_demux/custom_barcodes/RPB004.toml
dorado/tests/data/barcode_demux/custom_barcodes/RPB004_sequences.fasta
dorado/tests/data/barcode_demux/custom_barcodes/bad_double_ended_kit.toml
dorado/tests/data/barcode_demux/custom_barcodes/bad_double_ended_kit_not_all_params_set.toml
dorado/tests/data/barcode_demux/custom_barcodes/flank_free_arrangement.toml
dorado/tests/data/barcode_demux/custom_barcodes/scoring_params.toml
dorado/tests/data/barcode_demux/custom_barcodes/test_kit_double_ended.toml
dorado/tests/data/barcode_demux/custom_barcodes/test_kit_ends_different_barcodes.toml
dorado/tests/data/barcode_demux/custom_barcodes/test_kit_ends_different_flanks.toml
dorado/tests/data/barcode_demux/custom_barcodes/test_kit_single_ended.toml
dorado/tests/data/barcode_demux/custom_barcodes/test_sequences.fasta
dorado/tests/data/barcode_demux/double_end/
dorado/tests/data/barcode_demux/double_end/SQK-RPB004_BC01.fastq
dorado/tests/data/barcode_demux/double_end/SQK-RPB004_BC05.fastq
dorado/tests/data/barcode_demux/double_end/SQK-RPB004_BC11.fastq
dorado/tests/data/barcode_demux/double_end/unclassified.fastq
dorado/tests/data/barcode_demux/double_end_variant/
dorado/tests/data/barcode_demux/double_end_variant/EXP-PBC096_BC04.fastq
dorado/tests/data/barcode_demux/double_end_variant/EXP-PBC096_BC37.fastq
dorado/tests/data/barcode_demux/double_end_variant/EXP-PBC096_BC83.fastq
dorado/tests/data/barcode_demux/double_end_variant/EXP-PBC096_barcode_both_ends_fail.fastq
dorado/tests/data/barcode_demux/double_end_variant/EXP-PBC096_barcode_both_ends_pass.fastq
dorado/tests/data/barcode_demux/double_end_variant/unclassified.fastq
dorado/tests/data/barcode_demux/no_trim_expected.fastq
dorado/tests/data/barcode_demux/read_group_test/
dorado/tests/data/barcode_demux/read_group_test/SQK-RBK114_BC01_BC04_unclassified.pod5
dorado/tests/data/barcode_demux/sample_sheet.csv
dorado/tests/data/barcode_demux/simple_mapped_reads.sam
dorado/tests/data/barcode_demux/single_end/
dorado/tests/data/barcode_demux/single_end/SQK-RBK114-96_BC01.fastq
dorado/tests/data/barcode_demux/single_end/SQK-RBK114-96_BC92.fastq
dorado/tests/data/barcode_demux/single_end/SQK-RBK114-96_RBK39.fastq
dorado/tests/data/barcode_demux/single_end/unclassified.fastq
dorado/tests/data/basespace/
dorado/tests/data/basespace/pairs.bam
dorado/tests/data/basespace/pairs.txt
dorado/tests/data/bedfile_test/
dorado/tests/data/bedfile_test/test_bed.bed
dorado/tests/data/duplex/
dorado/tests/data/duplex/pairs.txt
dorado/tests/data/duplex/pod5/
dorado/tests/data/duplex/pod5/duplex.pod5
dorado/tests/data/fast5/
dorado/tests/data/fast5/single_read.fast5
dorado/tests/data/model_configs/
dorado/tests/data/model_configs/dna_r10.4.1_e8.2_260bps_fast@v4.0.0/
dorado/tests/data/model_configs/dna_r10.4.1_e8.2_260bps_fast@v4.0.0/config.toml
dorado/tests/data/model_configs/dna_r10.4.1_e8.2_400bps_hac@v4.2.0/
dorado/tests/data/model_configs/dna_r10.4.1_e8.2_400bps_hac@v4.2.0/config.toml
dorado/tests/data/model_configs/dna_r10.4.1_e8.2_400bps_hac@v4.3.0/
dorado/tests/data/model_configs/dna_r10.4.1_e8.2_400bps_hac@v4.3.0/config.toml
dorado/tests/data/model_configs/dna_r10.4.1_e8.2_400bps_hac@v4.3.0_quantile/
dorado/tests/data/model_configs/dna_r10.4.1_e8.2_400bps_hac@v4.3.0_quantile/config.toml
dorado/tests/data/model_configs/dna_r9.4.1_e8_hac@v3.3/
dorado/tests/data/model_configs/dna_r9.4.1_e8_hac@v3.3/config.toml
dorado/tests/data/model_configs/rna002_70bps_fast@v3/
dorado/tests/data/model_configs/rna002_70bps_fast@v3/config.toml
dorado/tests/data/model_configs/rna004_130bps_sup@v3.0.1/
dorado/tests/data/model_configs/rna004_130bps_sup@v3.0.1/config.toml
dorado/tests/data/multi_read_pod5/
dorado/tests/data/multi_read_pod5/filtered.pod5
dorado/tests/data/nested_pod5_folder/
dorado/tests/data/nested_pod5_folder/subfolder/
dorado/tests/data/nested_pod5_folder/subfolder/single_na24385.pod5
dorado/tests/data/pod5/
dorado/tests/data/pod5/dna_r10.4.1_e8.2_260bps/
dorado/tests/data/pod5/dna_r10.4.1_e8.2_260bps/dna_r10.4.1_e8.2_260bps-FLO_PRO114-SQK_NBD114_96_260-4000.pod5
dorado/tests/data/pod5/dna_r10.4.1_e8.2_260bps/dna_r10.4.1_e8.2_260bps-FLO_PRO114M-SQK_RPB114_24_260-4000.pod5
dorado/tests/data/pod5/dna_r10.4.1_e8.2_400bps_4khz/
dorado/tests/data/pod5/dna_r10.4.1_e8.2_400bps_4khz/dna_r10.4.1_e8.2_400bps_4khz-FLO_FLG114-SQK_PCB114_24-4000.pod5
dorado/tests/data/pod5/dna_r10.4.1_e8.2_400bps_4khz/dna_r10.4.1_e8.2_400bps_4khz-FLO_MIN114-SQK_NBD114_96-4000.pod5
dorado/tests/data/pod5/dna_r10.4.1_e8.2_400bps_4khz/dna_r10.4.1_e8.2_400bps_4khz-FLO_PRO114M-SQK_PCS114-4000.pod5
dorado/tests/data/pod5/dna_r10.4.1_e8.2_400bps_5khz/
dorado/tests/data/pod5/dna_r10.4.1_e8.2_400bps_5khz/dna_r10.4.1_e8.2_400bps_5khz-FLO_PRO114M-SQK_LSK114_XL-5000.pod5
dorado/tests/data/pod5/dna_r10.4.1_e8.2_400bps_5khz/dna_r10.4.1_e8.2_400bps_5khz-FLO_PRO114M-SQK_MLK114_96_XL-5000.pod5
dorado/tests/data/pod5/dna_r10.4.1_e8.2_400bps_5khz/dna_r10.4.1_e8.2_400bps_5khz-FLO_PRO114M-SQK_RAD114-5000.pod5
dorado/tests/data/pod5/dna_r9.4.1_e8/
dorado/tests/data/pod5/dna_r9.4.1_e8/dna_r9.4.1_e8-FLO_FLG001-SQK_RAB204-4000.pod5
dorado/tests/data/pod5/dna_r9.4.1_e8/dna_r9.4.1_e8-FLO_PRO002M-SQK_LSK108-4000.pod5
dorado/tests/data/pod5/dna_r9.4.1_e8/dna_r9.4.1_e8-FLO_PRO002M-SQK_RAB201-4000.pod5
dorado/tests/data/pod5/mixed/
dorado/tests/data/pod5/mixed/dna_r10.4.1_e8.2_260bps-FLO_PRO114M-SQK_MLK114_96_XL_260-4000.pod5
dorado/tests/data/pod5/mixed/dna_r10.4.1_e8.2_400bps_5khz-FLO_FLG114HD-SQK_LSK114_XL-5000.pod5
dorado/tests/data/pod5/rna002_70bps/
dorado/tests/data/pod5/rna002_70bps/rna002_70bps-FLO_MIN106-SQK_RNA002-3000.pod5
dorado/tests/data/pod5/rna002_70bps/rna002_70bps-FLO_MINSP6-SQK_RNA002-3000.pod5
dorado/tests/data/pod5/rna002_70bps/rna002_70bps-FLO_PRO002_ECO-SQK_RNA002-3000.pod5
dorado/tests/data/pod5/rna004_130bps/
dorado/tests/data/pod5/rna004_130bps/rna004_130bps-FLO_MIN004RA-SQK_RNA004-4000.pod5
dorado/tests/data/pod5/rna004_130bps/rna004_130bps-FLO_PRO004RA-SQK_RNA004-4000.pod5
dorado/tests/data/pod5/single_na24385.pod5
dorado/tests/data/poly_a/
dorado/tests/data/poly_a/configs/
dorado/tests/data/poly_a/configs/polya.toml
dorado/tests/data/poly_a/r10_cdna_pod5/
dorado/tests/data/poly_a/r10_cdna_pod5/cDNA_r10_test.pod5
dorado/tests/data/poly_a/r10_fwd_cdna/
dorado/tests/data/poly_a/r10_fwd_cdna/moves.bin
dorado/tests/data/poly_a/r10_fwd_cdna/seq.txt
dorado/tests/data/poly_a/r10_fwd_cdna/signal.tensor
dorado/tests/data/poly_a/r9_rev_cdna/
dorado/tests/data/poly_a/r9_rev_cdna/moves.bin
dorado/tests/data/poly_a/r9_rev_cdna/seq.txt
dorado/tests/data/poly_a/r9_rev_cdna/signal.tensor
dorado/tests/data/poly_a/rna002/
dorado/tests/data/poly_a/rna002/moves.bin
dorado/tests/data/poly_a/rna002/seq.txt
dorado/tests/data/poly_a/rna002/signal.tensor
dorado/tests/data/poly_a/rna004/
dorado/tests/data/poly_a/rna004/moves.bin
dorado/tests/data/poly_a/rna004/seq.txt
dorado/tests/data/poly_a/rna004/signal.tensor
dorado/tests/data/poly_a/rna004_pod5/
dorado/tests/data/poly_a/rna004_pod5/rna004_pt_50.pod5
dorado/tests/data/resume_loader/
dorado/tests/data/resume_loader/basecall.sam
dorado/tests/data/rna_split/
dorado/tests/data/rna_split/signal.tensor
dorado/tests/data/sample_sheets/
dorado/tests/data/sample_sheets/invalid.csv
dorado/tests/data/sample_sheets/no_barcode.csv
dorado/tests/data/sample_sheets/single_barcode.csv
dorado/tests/data/sample_sheets/valid_but_weird.csv
dorado/tests/data/single_channel_multi_read_pod5/
dorado/tests/data/single_channel_multi_read_pod5/filtered.pod5
dorado/tests/data/split/
dorado/tests/data/split/moves
dorado/tests/data/split/one_subread_split/
dorado/tests/data/split/one_subread_split/moves
dorado/tests/data/split/one_subread_split/qstring
dorado/tests/data/split/one_subread_split/raw.tensor
dorado/tests/data/split/one_subread_split/seq
dorado/tests/data/split/qstring
dorado/tests/data/split/raw.tensor
dorado/tests/data/split/seq
dorado/tests/data/stereo/
dorado/tests/data/stereo/complement_moves
dorado/tests/data/stereo/complement_qstring
dorado/tests/data/stereo/complement_raw_data.tensor
dorado/tests/data/stereo/complement_seq
dorado/tests/data/stereo/stereo_raw_data.tensor
dorado/tests/data/stereo/template_moves
dorado/tests/data/stereo/template_qstring
dorado/tests/data/stereo/template_raw_data.tensor
dorado/tests/data/stereo/template_seq
dorado/tests/data/trimmer/
dorado/tests/data/trimmer/reverse_strand_record.bam
dorado/tests/gpu_monitor_test.cpp
dorado/tests/main.cpp
dorado/tests/myers_test.cpp
dorado/tests/run_ios_test.py
dorado/tests/symbol_test.cpp
dorado/tests/test_expected_logging.sh
dorado/tests/test_model_download.py
dorado/tests/test_simple_auto_basecaller_execution.sh
dorado/tests/test_simple_basecaller_execution.bat
dorado/tests/test_simple_basecaller_execution.sh

== 2024-07-10 22:50:10,011 filetools.py:398 INFO Removing 1 files & directories
== 2024-07-10 22:50:10,315 filetools.py:383 INFO Path /tmp/eb-_xxxemsh/tmpgdp_5vq0 successfully removed.
== 2024-07-10 22:50:10,317 easyblock.py:452 DEBUG File /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz found for source dorado-0.6.1.tar.gz
== 2024-07-10 22:50:10,317 easyblock.py:496 INFO Added sources: [{'name': 'dorado-0.6.1.tar.gz', 'path': '/apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz', 'cmd': None, 'checksum': None, 'finalpath': '/dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1'}]
== 2024-07-10 22:50:10,324 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for dorado-0.6.1_include-fstream.patch: /tmp/eb-_xxxemsh/files_pr20444/d/dorado
== 2024-07-10 22:50:10,325 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /home/software/venvs/eb/bin/eb
== 2024-07-10 22:50:10,326 tools.py:288 INFO Also considering installation prefix /home/software/venvs/eb (determined via path to 'eb' script)...
== 2024-07-10 22:50:10,326 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/src/easybuild/local/easybuild/easyconfigs
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== 2024-07-10 22:50:10,327 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/venvs/eb/easybuild/easyconfigs/easybuild/easyconfigs
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== 2024-07-10 22:50:10,328 tools.py:303 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
== 2024-07-10 22:50:10,328 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/venvs/eb/lib64/python3.6/site-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-07-10 22:50:10,328 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python36.zip/easybuild/easyconfigs
== 2024-07-10 22:50:10,328 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/easybuild/easyconfigs
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== 2024-07-10 22:50:10,328 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/venvs/eb/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-07-10 22:50:10,328 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/venvs/eb/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-07-10 22:50:10,329 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/venvs/eb/lib64/python3.6/site-packages/gitdb/ext/smmap/easybuild/easyconfigs
== 2024-07-10 22:50:10,329 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/venvs/eb/easybuild/easyconfigs
== 2024-07-10 22:50:10,329 tools.py:307 DEBUG Added /home/software/venvs/eb/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-07-10 22:50:10,329 easyblock.py:851 INFO Found file dorado-0.6.1_include-fstream.patch at /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch
== 2024-07-10 22:50:10,329 easyblock.py:520 DEBUG File /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch found for patch dorado-0.6.1_include-fstream.patch
== 2024-07-10 22:50:10,329 easyblock.py:535 INFO Added patches: [{'name': 'dorado-0.6.1_include-fstream.patch', 'postinstall': False, 'path': '/tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch', 'checksum': 'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377'}]
== 2024-07-10 22:50:10,330 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-07-10 22:50:10,440 easyblock.py:2411 INFO md5 checksum for /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz: d195000519e706d0b6dc4afbbf2c5afb
== 2024-07-10 22:50:10,441 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-07-10 22:50:10,564 easyblock.py:2411 INFO sha256 checksum for /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz: e092538055fce10d9c7f6ddb0fa58594e42e6e7a52026fb4c8501cb325bcddd4
== 2024-07-10 22:50:10,564 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-07-10 22:50:10,564 easyblock.py:2411 INFO md5 checksum for /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch: a06364489f58ce9faf5e03c7c5c3909a
== 2024-07-10 22:50:10,565 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-07-10 22:50:10,565 easyblock.py:2411 INFO sha256 checksum for /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch: a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377
== 2024-07-10 22:50:10,598 easyconfig.py:2642 DEBUG Determining full module name for dorado EasyConfig @ /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb (force_visible: False)
== 2024-07-10 22:50:10,599 easyconfig.py:2619 DEBUG No alternative software name specified to determine module name with
== 2024-07-10 22:50:10,599 utilities.py:115 DEBUG Module name dorado/0.6.1-foss-2023a-CUDA-12.1.1 validated
== 2024-07-10 22:50:10,599 easyconfig.py:2650 DEBUG Obtained valid full module name dorado/0.6.1-foss-2023a-CUDA-12.1.1
== 2024-07-10 22:50:10,600 config.py:700 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /apps/eb/el8/upstream/modules
== 2024-07-10 22:50:10,600 easyblock.py:2446 INFO Checking dirs that need to be created: ['/apps/eb/el8/upstream/software/dorado/0.6.1-foss-2023a-CUDA-12.1.1', '/apps/eb/el8/upstream/modules/all/dorado', '/apps/eb/el8/upstream/modules/bio/dorado']
== 2024-07-10 22:50:10,602 filetools.py:1912 INFO Creating directory /apps/eb/el8/upstream/software/dorado/0.6.1-foss-2023a-CUDA-12.1.1 (parents: True, set_gid: False, sticky: False)
== 2024-07-10 22:50:10,608 filetools.py:1912 INFO Creating directory /apps/eb/el8/upstream/modules/all/dorado (parents: True, set_gid: False, sticky: False)
== 2024-07-10 22:50:10,612 filetools.py:1912 INFO Creating directory /apps/eb/el8/upstream/modules/bio/dorado (parents: True, set_gid: False, sticky: False)
== 2024-07-10 22:50:10,622 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-07-10 22:50:10,624 configuremake.py:96 INFO config.guess version: 2018-08-29 (last updated: 2024-06-18T12:07:40.627381, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c)
== 2024-07-10 22:50:10,625 configuremake.py:151 INFO Found config.guess at /apps/eb/el8/upstream/sources/generic/eb_v4.9.2/ConfigureMake/config.guess
== 2024-07-10 22:50:10,625 build_log.py:267 INFO ... (took 43 secs)
== 2024-07-10 22:50:10,633 easyblock.py:3942 DEBUG Not skipping ready step (skippable: False, skip: None, skipsteps: [], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False)
== 2024-07-10 22:50:10,633 build_log.py:267 INFO creating build dir, resetting environment...
== 2024-07-10 22:50:10,641 easyblock.py:3950 INFO Starting ready step
== 2024-07-10 22:50:10,641 easyconfig.py:1702 INFO Generating template values...
== 2024-07-10 22:50:10,641 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-07-10 22:50:10,642 templates.py:231 DEBUG version found in easyconfig is 0.6.1
== 2024-07-10 22:50:10,644 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-07-10 22:50:10,644 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-07-10 22:50:10,644 templates.py:333 DEBUG name: name, config: dorado
== 2024-07-10 22:50:10,644 templates.py:333 DEBUG name: parallel, config: None
== 2024-07-10 22:50:10,644 templates.py:333 DEBUG name: version, config: 0.6.1
== 2024-07-10 22:50:10,644 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-07-10 22:50:10,644 templates.py:333 DEBUG name: versionprefix, config:
== 2024-07-10 22:50:10,645 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-07-10 22:50:10,645 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-07-10 22:50:10,645 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', builddir='/dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1', cudamajver='12', cudaminver='1', cudashortver='12.1', cudaver='12.1.1', github_account='dorado', installdir='/apps/eb/el8/upstream/software/dorado/0.6.1-foss-2023a-CUDA-12.1.1', module_name='dorado/0.6.1-foss-2023a-CUDA-12.1.1', mpi_cmd_prefix='mpirun -n 1', name='dorado', nameletter='d', nameletterlower='d', namelower='dorado', start_dir='None', sysroot='', toolchain_name='foss', toolchain_version='2023a', version='0.6.1', version_major='0', version_major_minor='0.6', version_minor='6', versionprefix='', versionsuffix='-CUDA-12.1.1'
== 2024-07-10 22:50:10,645 easyblock.py:3958 INFO Running method check_readiness_step part of step ready
== 2024-07-10 22:50:10,646 easyblock.py:2246 DEBUG Desired parallelism specified via 'parallel' build option: None
== 2024-07-10 22:50:10,646 easyblock.py:2255 INFO Setting parallelism: 8
== 2024-07-10 22:50:10,647 modules.py:814 DEBUG Current MODULEPATH: /apps/eb/el8/upstream/modules/all:/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
== 2024-07-10 22:50:10,647 modules.py:828 DEBUG Running module command '/usr/share/lmod/lmod/libexec/lmod python --terse list' from /home/software
== 2024-07-10 22:50:10,713 modules.py:835 DEBUG Output of module command '/usr/share/lmod/lmod/libexec/lmod python --terse list': stdout: import os
os.environ["MODULEPATH"] = "/apps/eb/el8/upstream/modules/all:/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core";
os.environ["_ModuleTable001_"] = "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";
os.environ["_ModuleTable002_"] = "L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsCn0K";
os.environ["_ModuleTable_Sz_"] = "2";
_mlstatus = True
; stderr: No modules loaded

== 2024-07-10 22:50:10,714 modules.py:1471 DEBUG Output found in stdout, seems like '/usr/share/lmod/lmod/libexec/lmod python --terse list' ran fine
== 2024-07-10 22:50:10,719 easyblock.py:3958 INFO Running method make_builddir part of step ready
== 2024-07-10 22:50:10,720 easyblock.py:1066 DEBUG Creating the build directory /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1 (cleanup: True)
== 2024-07-10 22:50:10,720 filetools.py:1912 INFO Creating directory /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1 (parents: True, set_gid: False, sticky: False)
== 2024-07-10 22:50:10,733 easyblock.py:3958 INFO Running method reset_env part of step ready
== 2024-07-10 22:50:10,733 easyblock.py:3958 INFO Running method handle_iterate_opts part of step ready
== 2024-07-10 22:50:10,734 easyconfig.py:1702 INFO Generating template values...
== 2024-07-10 22:50:10,734 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-07-10 22:50:10,734 templates.py:231 DEBUG version found in easyconfig is 0.6.1
== 2024-07-10 22:50:10,735 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-07-10 22:50:10,735 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-07-10 22:50:10,735 templates.py:333 DEBUG name: name, config: dorado
== 2024-07-10 22:50:10,735 templates.py:333 DEBUG name: parallel, config: 8
== 2024-07-10 22:50:10,735 templates.py:333 DEBUG name: version, config: 0.6.1
== 2024-07-10 22:50:10,735 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-07-10 22:50:10,735 templates.py:333 DEBUG name: versionprefix, config:
== 2024-07-10 22:50:10,735 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-07-10 22:50:10,736 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-07-10 22:50:10,736 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', builddir='/dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1', cudamajver='12', cudaminver='1', cudashortver='12.1', cudaver='12.1.1', github_account='dorado', installdir='/apps/eb/el8/upstream/software/dorado/0.6.1-foss-2023a-CUDA-12.1.1', module_name='dorado/0.6.1-foss-2023a-CUDA-12.1.1', mpi_cmd_prefix='mpirun -n 1', name='dorado', nameletter='d', nameletterlower='d', namelower='dorado', parallel='8', start_dir='None', sysroot='', toolchain_name='foss', toolchain_version='2023a', version='0.6.1', version_major='0', version_major_minor='0.6', version_minor='6', versionprefix='', versionsuffix='-CUDA-12.1.1'
== 2024-07-10 22:50:10,736 build_log.py:267 INFO ... (took < 1 sec)
== 2024-07-10 22:50:10,743 easyblock.py:3942 DEBUG Not skipping source step (skippable: True, skip: None, skipsteps: [], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False)
== 2024-07-10 22:50:10,744 build_log.py:267 INFO unpacking...
== 2024-07-10 22:50:10,751 easyblock.py:3950 INFO Starting source step
== 2024-07-10 22:50:10,751 easyconfig.py:1702 INFO Generating template values...
== 2024-07-10 22:50:10,751 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-07-10 22:50:10,751 templates.py:231 DEBUG version found in easyconfig is 0.6.1
== 2024-07-10 22:50:10,752 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-07-10 22:50:10,752 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-07-10 22:50:10,752 templates.py:333 DEBUG name: name, config: dorado
== 2024-07-10 22:50:10,752 templates.py:333 DEBUG name: parallel, config: 8
== 2024-07-10 22:50:10,752 templates.py:333 DEBUG name: version, config: 0.6.1
== 2024-07-10 22:50:10,752 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-07-10 22:50:10,752 templates.py:333 DEBUG name: versionprefix, config:
== 2024-07-10 22:50:10,752 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-07-10 22:50:10,752 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-07-10 22:50:10,752 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', builddir='/dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1', cudamajver='12', cudaminver='1', cudashortver='12.1', cudaver='12.1.1', github_account='dorado', installdir='/apps/eb/el8/upstream/software/dorado/0.6.1-foss-2023a-CUDA-12.1.1', module_name='dorado/0.6.1-foss-2023a-CUDA-12.1.1', mpi_cmd_prefix='mpirun -n 1', name='dorado', nameletter='d', nameletterlower='d', namelower='dorado', parallel='8', start_dir='None', sysroot='', toolchain_name='foss', toolchain_version='2023a', version='0.6.1', version_major='0', version_major_minor='0.6', version_minor='6', versionprefix='', versionsuffix='-CUDA-12.1.1'
== 2024-07-10 22:50:10,753 easyblock.py:3958 INFO Running method checksum_step part of step source
== 2024-07-10 22:50:10,753 easyblock.py:2464 INFO Checksum verification for /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz using None passed.
== 2024-07-10 22:50:10,753 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum
== 2024-07-10 22:50:10,754 filetools.py:1307 DEBUG Computed sha256 checksum for /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch: a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377 (correct checksum: a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377)
== 2024-07-10 22:50:10,754 easyblock.py:2464 INFO Checksum verification for /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch using a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377 passed.
== 2024-07-10 22:50:10,754 easyblock.py:3958 INFO Running method extract_step part of step source
== 2024-07-10 22:50:10,754 easyblock.py:2576 INFO Unpacking source dorado-0.6.1.tar.gz
== 2024-07-10 22:50:10,754 filetools.py:1931 DEBUG Not creating existing path /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1
== 2024-07-10 22:50:10,754 filetools.py:459 DEBUG Unpacking /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz in directory /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1
== 2024-07-10 22:50:10,755 filetools.py:468 DEBUG Using command derived from file extension to unpack /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz: tar xzf /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz
== 2024-07-10 22:50:10,755 run.py:180 DEBUG run_cmd: Output of "tar xzf /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz" will be logged to /tmp/eb-_xxxemsh/easybuild-run_cmd-3n9mgcb7.log
== 2024-07-10 22:50:10,763 run.py:221 DEBUG run_cmd: running cmd tar xzf /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz (in /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1)
== 2024-07-10 22:50:10,763 run.py:247 INFO running cmd: tar xzf /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz
== 2024-07-10 22:50:11,530 run.py:689 DEBUG cmd "tar xzf /apps/eb/el8/upstream/sources/d/dorado/dorado-0.6.1.tar.gz" exited with exit code 0 and output:

== 2024-07-10 22:50:11,533 run.py:725 DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w)
== 2024-07-10 22:50:11,534 filetools.py:1361 DEBUG Last dir list ['tests', 'dorado', 'documentation', 'cmake', 'benchmark', 'README.md', 'LICENCE.txt', 'DEV.md', 'CMakeLists.txt', 'CHANGELOG.md']
== 2024-07-10 22:50:11,534 filetools.py:1362 DEBUG Possible new dir /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1/dorado found
== 2024-07-10 22:50:11,534 build_log.py:267 INFO ... (took < 1 sec)
== 2024-07-10 22:50:11,547 easyblock.py:3942 DEBUG Not skipping patch step (skippable: True, skip: None, skipsteps: [], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False)
== 2024-07-10 22:50:11,547 build_log.py:267 INFO patching...
== 2024-07-10 22:50:11,554 easyblock.py:3950 INFO Starting patch step
== 2024-07-10 22:50:11,555 easyconfig.py:1702 INFO Generating template values...
== 2024-07-10 22:50:11,555 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-07-10 22:50:11,556 templates.py:231 DEBUG version found in easyconfig is 0.6.1
== 2024-07-10 22:50:11,556 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-07-10 22:50:11,556 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-07-10 22:50:11,556 templates.py:333 DEBUG name: name, config: dorado
== 2024-07-10 22:50:11,556 templates.py:333 DEBUG name: parallel, config: 8
== 2024-07-10 22:50:11,556 templates.py:333 DEBUG name: version, config: 0.6.1
== 2024-07-10 22:50:11,556 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-07-10 22:50:11,556 templates.py:333 DEBUG name: versionprefix, config:
== 2024-07-10 22:50:11,557 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-07-10 22:50:11,557 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-07-10 22:50:11,558 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', builddir='/dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1', cudamajver='12', cudaminver='1', cudashortver='12.1', cudaver='12.1.1', github_account='dorado', installdir='/apps/eb/el8/upstream/software/dorado/0.6.1-foss-2023a-CUDA-12.1.1', module_name='dorado/0.6.1-foss-2023a-CUDA-12.1.1', mpi_cmd_prefix='mpirun -n 1', name='dorado', nameletter='d', nameletterlower='d', namelower='dorado', parallel='8', start_dir='None', sysroot='', toolchain_name='foss', toolchain_version='2023a', version='0.6.1', version_major='0', version_major_minor='0.6', version_minor='6', versionprefix='', versionsuffix='-CUDA-12.1.1'
== 2024-07-10 22:50:11,558 easyblock.py:3958 INFO Running method patch_step part of step patch
== 2024-07-10 22:50:11,558 easyblock.py:2594 INFO Applying patch dorado-0.6.1_include-fstream.patch
== 2024-07-10 22:50:11,565 easyblock.py:2607 DEBUG Source index: 0; patch level: None; source path suffix: ; copy patch: False
== 2024-07-10 22:50:11,565 easyblock.py:2612 DEBUG Determine begin path for patch dorado-0.6.1_include-fstream.patch: /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1/dorado
== 2024-07-10 22:50:11,565 easyblock.py:2621 DEBUG Applying patch {'name': 'dorado-0.6.1_include-fstream.patch', 'postinstall': False, 'path': '/tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch', 'checksum': 'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377', 'md5': 'a06364489f58ce9faf5e03c7c5c3909a', 'sha256': 'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377'} in path /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1/dorado
== 2024-07-10 22:50:11,569 filetools.py:1619 DEBUG Guessed patch level 1 for patch /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch
== 2024-07-10 22:50:11,569 run.py:221 DEBUG run_cmd: running cmd patch -p1 -i /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch (in /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1/dorado)
== 2024-07-10 22:50:11,569 run.py:247 INFO running cmd: patch -p1 -i /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch
== 2024-07-10 22:50:11,592 run.py:689 DEBUG cmd "patch -p1 -i /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1_include-fstream.patch" exited with exit code 0 and output:
patching file dorado/cli/duplex.cpp
patching file dorado/cli/demux.cpp

== 2024-07-10 22:50:11,593 run.py:725 DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w)
== 2024-07-10 22:50:11,594 build_log.py:267 INFO ... (took < 1 sec)
== 2024-07-10 22:50:11,613 easyblock.py:3942 DEBUG Not skipping prepare step (skippable: False, skip: None, skipsteps: [], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False)
== 2024-07-10 22:50:11,613 build_log.py:267 INFO preparing...
== 2024-07-10 22:50:11,621 easyblock.py:3950 INFO Starting prepare step
== 2024-07-10 22:50:11,621 easyconfig.py:1702 INFO Generating template values...
== 2024-07-10 22:50:11,621 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-07-10 22:50:11,622 templates.py:231 DEBUG version found in easyconfig is 0.6.1
== 2024-07-10 22:50:11,622 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-07-10 22:50:11,622 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-07-10 22:50:11,622 templates.py:333 DEBUG name: name, config: dorado
== 2024-07-10 22:50:11,622 templates.py:333 DEBUG name: parallel, config: 8
== 2024-07-10 22:50:11,622 templates.py:333 DEBUG name: version, config: 0.6.1
== 2024-07-10 22:50:11,622 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-07-10 22:50:11,622 templates.py:333 DEBUG name: versionprefix, config:
== 2024-07-10 22:50:11,622 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-07-10 22:50:11,623 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-07-10 22:50:11,623 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', builddir='/dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1', cudamajver='12', cudaminver='1', cudashortver='12.1', cudaver='12.1.1', github_account='dorado', installdir='/apps/eb/el8/upstream/software/dorado/0.6.1-foss-2023a-CUDA-12.1.1', module_name='dorado/0.6.1-foss-2023a-CUDA-12.1.1', mpi_cmd_prefix='mpirun -n 1', name='dorado', nameletter='d', nameletterlower='d', namelower='dorado', parallel='8', start_dir='None', sysroot='', toolchain_name='foss', toolchain_version='2023a', version='0.6.1', version_major='0', version_major_minor='0.6', version_minor='6', versionprefix='', versionsuffix='-CUDA-12.1.1'
== 2024-07-10 22:50:11,623 easyblock.py:3958 INFO Running method prepare_step part of step prepare
== 2024-07-10 22:50:11,623 easyconfig.py:2710 DEBUG Determining initial module paths for dorado EasyConfig @ /tmp/eb-_xxxemsh/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-07-10 22:50:11,623 easyconfig.py:2712 DEBUG Obtained initial module paths: []
== 2024-07-10 22:50:11,625 easyconfig.py:1135 DEBUG Dependencies BEFORE filtering: [{'full_mod_name': 'binutils/2.40-GCCcore-12.3.0', 'short_mod_name': 'binutils/2.40-GCCcore-12.3.0', 'name': 'binutils', 'version': '2.40', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'CMake/3.26.3-GCCcore-12.3.0', 'short_mod_name': 'CMake/3.26.3-GCCcore-12.3.0', 'name': 'CMake', 'version': '3.26.3', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'CUDA/12.1.1', 'short_mod_name': 'CUDA/12.1.1', 'name': 'CUDA', 'version': '12.1.1', 'versionsuffix': '', 'toolchain': {'name': 'system', 'version': 'system'}, 'toolchain_inherited': False, 'system': True, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'OpenSSL/1.1', 'short_mod_name': 'OpenSSL/1.1', 'name': 'OpenSSL', 'version': '1.1', 'versionsuffix': '', 'toolchain': {'name': 'system', 'version': 'system'}, 'toolchain_inherited': False, 'system': True, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'PyTorch/2.1.2-foss-2023a-CUDA-12.1.1', 'short_mod_name': 'PyTorch/2.1.2-foss-2023a-CUDA-12.1.1', 'name': 'PyTorch', 'version': '2.1.2', 'versionsuffix': '-CUDA-12.1.1', 'toolchain': {'name': 'foss', 'version': '2023a'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'HDF5/1.14.0-gompi-2023a', 'short_mod_name': 'HDF5/1.14.0-gompi-2023a', 'name': 'HDF5', 'version': '1.14.0', 'versionsuffix': '', 'toolchain': {'name': 'gompi', 'version': '2023a'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'zstd/1.5.5-GCCcore-12.3.0', 'short_mod_name': 'zstd/1.5.5-GCCcore-12.3.0', 'name': 'zstd', 'version': '1.5.5', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'HTSlib/1.18-GCC-12.3.0', 'short_mod_name': 'HTSlib/1.18-GCC-12.3.0', 'name': 'HTSlib', 'version': '1.18', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'kineto/0.4.0-GCC-12.3.0', 'short_mod_name': 'kineto/0.4.0-GCC-12.3.0', 'name': 'kineto', 'version': '0.4.0', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'libaec/1.0.6-GCCcore-12.3.0', 'short_mod_name': 'libaec/1.0.6-GCCcore-12.3.0', 'name': 'libaec', 'version': '1.0.6', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}]
== 2024-07-10 22:50:11,625 easyconfig.py:1138 DEBUG Dependencies AFTER filtering: [{'full_mod_name': 'binutils/2.40-GCCcore-12.3.0', 'short_mod_name': 'binutils/2.40-GCCcore-12.3.0', 'name': 'binutils', 'version': '2.40', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'CMake/3.26.3-GCCcore-12.3.0', 'short_mod_name': 'CMake/3.26.3-GCCcore-12.3.0', 'name': 'CMake', 'version': '3.26.3', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'CUDA/12.1.1', 'short_mod_name': 'CUDA/12.1.1', 'name': 'CUDA', 'version': '12.1.1', 'versionsuffix': '', 'toolchain': {'name': 'system', 'version': 'system'}, 'toolchain_inherited': False, 'system': True, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'OpenSSL/1.1', 'short_mod_name': 'OpenSSL/1.1', 'name': 'OpenSSL', 'version': '1.1', 'versionsuffix': '', 'toolchain': {'name': 'system', 'version': 'system'}, 'toolchain_inherited': False, 'system': True, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'PyTorch/2.1.2-foss-2023a-CUDA-12.1.1', 'short_mod_name': 'PyTorch/2.1.2-foss-2023a-CUDA-12.1.1', 'name': 'PyTorch', 'version': '2.1.2', 'versionsuffix': '-CUDA-12.1.1', 'toolchain': {'name': 'foss', 'version': '2023a'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'HDF5/1.14.0-gompi-2023a', 'short_mod_name': 'HDF5/1.14.0-gompi-2023a', 'name': 'HDF5', 'version': '1.14.0', 'versionsuffix': '', 'toolchain': {'name': 'gompi', 'version': '2023a'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'zstd/1.5.5-GCCcore-12.3.0', 'short_mod_name': 'zstd/1.5.5-GCCcore-12.3.0', 'name': 'zstd', 'version': '1.5.5', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'HTSlib/1.18-GCC-12.3.0', 'short_mod_name': 'HTSlib/1.18-GCC-12.3.0', 'name': 'HTSlib', 'version': '1.18', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'kineto/0.4.0-GCC-12.3.0', 'short_mod_name': 'kineto/0.4.0-GCC-12.3.0', 'name': 'kineto', 'version': '0.4.0', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'libaec/1.0.6-GCCcore-12.3.0', 'short_mod_name': 'libaec/1.0.6-GCCcore-12.3.0', 'name': 'libaec', 'version': '1.0.6', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}]
== 2024-07-10 22:50:11,626 toolchain.py:527 DEBUG _check_dependencies: adding toolchain dependencies [{'full_mod_name': 'binutils/2.40-GCCcore-12.3.0', 'short_mod_name': 'binutils/2.40-GCCcore-12.3.0', 'name': 'binutils', 'version': '2.40', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'CMake/3.26.3-GCCcore-12.3.0', 'short_mod_name': 'CMake/3.26.3-GCCcore-12.3.0', 'name': 'CMake', 'version': '3.26.3', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'CUDA/12.1.1', 'short_mod_name': 'CUDA/12.1.1', 'name': 'CUDA', 'version': '12.1.1', 'versionsuffix': '', 'toolchain': {'name': 'system', 'version': 'system'}, 'toolchain_inherited': False, 'system': True, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'OpenSSL/1.1', 'short_mod_name': 'OpenSSL/1.1', 'name': 'OpenSSL', 'version': '1.1', 'versionsuffix': '', 'toolchain': {'name': 'system', 'version': 'system'}, 'toolchain_inherited': False, 'system': True, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'PyTorch/2.1.2-foss-2023a-CUDA-12.1.1', 'short_mod_name': 'PyTorch/2.1.2-foss-2023a-CUDA-12.1.1', 'name': 'PyTorch', 'version': '2.1.2', 'versionsuffix': '-CUDA-12.1.1', 'toolchain': {'name': 'foss', 'version': '2023a'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'HDF5/1.14.0-gompi-2023a', 'short_mod_name': 'HDF5/1.14.0-gompi-2023a', 'name': 'HDF5', 'version': '1.14.0', 'versionsuffix': '', 'toolchain': {'name': 'gompi', 'version': '2023a'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'zstd/1.5.5-GCCcore-12.3.0', 'short_mod_name': 'zstd/1.5.5-GCCcore-12.3.0', 'name': 'zstd', 'version': '1.5.5', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'HTSlib/1.18-GCC-12.3.0', 'short_mod_name': 'HTSlib/1.18-GCC-12.3.0', 'name': 'HTSlib', 'version': '1.18', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'kineto/0.4.0-GCC-12.3.0', 'short_mod_name': 'kineto/0.4.0-GCC-12.3.0', 'name': 'kineto', 'version': '0.4.0', 'versionsuffix': '', 'toolchain': {'name': 'GCC', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}, {'full_mod_name': 'libaec/1.0.6-GCCcore-12.3.0', 'short_mod_name': 'libaec/1.0.6-GCCcore-12.3.0', 'name': 'libaec', 'version': '1.0.6', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '12.3.0'}, 'toolchain_inherited': False, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}]
== 2024-07-10 22:50:11,627 toolchain.py:537 DEBUG _check_dependencies: MODULEPATH: /apps/eb/el8/upstream/modules/all:/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
== 2024-07-10 22:50:11,627 modules.py:492 DEBUG Found cached result for 'module avail' with key '('MODULEPATH=/apps/eb/el8/upstream/modules/all:/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core', 'lmod', '--show-hidden')': ['Abseil/20230125.3-GCCcore-12.3.0', 'Autoconf/2.71-GCCcore-11.2.0', 'Autoconf/2.71-GCCcore-11.3.0', 'Autoconf/2.71-GCCcore-12.2.0', 'Autoconf/2.71-GCCcore-12.3.0', 'Autoconf/2.71-GCCcore-13.2.0', 'Autoconf/2.72-GCCcore-13.3.0', 'Automake/1.16.4-GCCcore-11.2.0', 'Automake/1.16.5-GCCcore-11.3.0', 'Automake/1.16.5-GCCcore-12.2.0', 'Automake/1.16.5-GCCcore-12.3.0', 'Automake/1.16.5-GCCcore-13.2.0', 'Automake/1.16.5-GCCcore-13.3.0', 'Autotools/20210726-GCCcore-11.2.0', 'Autotools/20220317-GCCcore-11.3.0', 'Autotools/20220317-GCCcore-12.2.0', 'Autotools/20220317-GCCcore-12.3.0', 'Autotools/20220317-GCCcore-13.2.0', 'Autotools/20231222-GCCcore-13.3.0', 'BLIS/0.9.0-GCC-12.3.0', 'Bison/3.7.6-GCCcore-11.2.0', 'Bison/3.8.2', 'Bison/3.8.2-GCCcore-11.3.0', 'Bison/3.8.2-GCCcore-12.2.0', 'Bison/3.8.2-GCCcore-12.3.0', 'Bison/3.8.2-GCCcore-13.2.0', 'Bison/3.8.2-GCCcore-13.3.0', 'Brotli/1.0.9-GCCcore-12.3.0', 'Brotli/1.1.0-GCCcore-13.3.0', 'CMake/3.26.3-GCCcore-12.3.0', 'CMake/3.29.3-GCCcore-13.3.0', 'CUDA/12.1.1', 'Catch2/2.13.9-GCCcore-12.3.0', 'DB/18.1.40-GCCcore-11.2.0', 'DB/18.1.40-GCCcore-11.3.0', 'DB/18.1.40-GCCcore-12.2.0', 'Doxygen/1.11.0-GCCcore-13.3.0', 'Doxygen/1.9.7-GCCcore-12.3.0', 'Eigen/3.4.0-GCCcore-12.3.0', 'FFTW.MPI/3.3.10-gompi-2023a', 'FFTW/3.3.10-GCC-12.3.0', 'FFmpeg/6.0-GCCcore-12.3.0', 'FlexiBLAS/3.3.1-GCC-12.3.0', 'FriBidi/1.0.12-GCCcore-12.3.0', 'GCC/12.3.0', 'GCCcore/11.2.0', 'GCCcore/11.3.0', 'GCCcore/12.2.0', 'GCCcore/12.3.0', 'GCCcore/13.2.0', 'GCCcore/13.3.0', 'GDRCopy/2.3.1-GCCcore-12.3.0', 'GMP/6.2.1-GCCcore-12.3.0', 'Go/1.22.1', 'HDF5/1.14.0-gompi-2023a', 'HTSlib/1.18-GCC-12.3.0', 'LAME/3.100-GCCcore-11.2.0', 'LAME/3.100-GCCcore-11.3.0', 'LAME/3.100-GCCcore-12.2.0', 'LAME/3.100-GCCcore-12.3.0', 'LAME/3.100-GCCcore-13.2.0', 'LibTIFF/4.5.0-GCCcore-12.3.0', 'LittleCMS/2.15-GCCcore-12.3.0', 'M4/1.4.19', 'M4/1.4.19-GCCcore-11.2.0', 'M4/1.4.19-GCCcore-11.3.0', 'M4/1.4.19-GCCcore-12.2.0', 'M4/1.4.19-GCCcore-12.3.0', 'M4/1.4.19-GCCcore-13.2.0', 'M4/1.4.19-GCCcore-13.3.0', 'MPC/1.3.1-GCCcore-12.3.0', 'MPFR/4.2.0-GCCcore-12.3.0', 'Meson/1.1.1-GCCcore-12.3.0', 'Meson/1.4.0-GCCcore-13.3.0', 'NASM/2.16.01-GCCcore-12.3.0', 'NCCL/2.18.3-GCCcore-12.3.0-CUDA-12.1.1', 'Ninja/1.11.1-GCCcore-12.3.0', 'Ninja/1.12.1-GCCcore-13.3.0', 'OpenBLAS/0.3.23-GCC-12.3.0', 'OpenJPEG/2.5.0-GCCcore-12.3.0', 'OpenMPI/4.1.5-GCC-12.3.0', 'OpenSSL/1.1', 'OpenSSL/3', 'PMIx/4.2.4-GCCcore-12.3.0', 'Perl-bundle-CPAN/5.36.1-GCCcore-12.3.0', 'Perl-bundle-CPAN/5.38.2-GCCcore-13.3.0', 'Perl/5.34.0-GCCcore-11.2.0', 'Perl/5.34.1-GCCcore-11.3.0', 'Perl/5.36.0-GCCcore-12.2.0', 'Perl/5.36.1-GCCcore-12.3.0', 'Perl/5.38.0', 'Perl/5.38.0-GCCcore-13.2.0', 'Perl/5.38.2-GCCcore-13.3.0', 'Pillow/10.0.0-GCCcore-12.3.0', 'PyYAML/6.0-GCCcore-12.3.0', 'Python-bundle-PyPI/2023.06-GCCcore-12.3.0', 'Python/3.11.3-GCCcore-12.3.0', 'Python/3.12.3-GCCcore-13.3.0', 'Rust/1.70.0-GCCcore-12.3.0', 'SDL2/2.28.2-GCCcore-12.3.0', 'SQLite/3.42.0-GCCcore-12.3.0', 'SQLite/3.45.3-GCCcore-13.3.0', 'ScaLAPACK/2.2.0-gompi-2023a-fb', 'SciPy-bundle/2023.07-gfbf-2023a', 'Szip/2.1.1-GCCcore-12.3.0', 'Tcl/8.6.13-GCCcore-12.3.0', 'Tcl/8.6.14-GCCcore-13.3.0', 'UCC/1.2.0-GCCcore-12.3.0', 'UCX-CUDA/1.14.1-GCCcore-12.3.0-CUDA-12.1.1', 'UCX/1.14.1-GCCcore-12.3.0', 'UnZip/6.0-GCCcore-12.3.0', 'UnZip/6.0-GCCcore-13.3.0', 'Wayland/1.23.0-GCCcore-13.3.0', 'X11/20230603-GCCcore-12.3.0', 'X11/20240607-GCCcore-13.3.0', 'XZ/5.4.2-GCCcore-12.3.0', 'XZ/5.4.5-GCCcore-13.3.0', 'Yasm/1.3.0-GCCcore-12.3.0', 'Z3/4.12.2-GCCcore-12.3.0', 'binutils/2.37', 'binutils/2.37-GCCcore-11.2.0', 'binutils/2.38', 'binutils/2.38-GCCcore-11.3.0', 'binutils/2.39', 'binutils/2.39-GCCcore-12.2.0', 'binutils/2.40', 'binutils/2.40-GCCcore-12.3.0', 'binutils/2.40-GCCcore-13.2.0', 'binutils/2.42', 'binutils/2.42-GCCcore-13.3.0', 'bzip2/1.0.8-GCCcore-12.3.0', 'bzip2/1.0.8-GCCcore-13.3.0', 'cURL/8.0.1-GCCcore-12.3.0', 'cURL/8.7.1-GCCcore-13.3.0', 'cffi/1.15.1-GCCcore-12.3.0', 'cryptography/41.0.1-GCCcore-12.3.0', 'cuDNN/8.9.2.26-CUDA-12.1.1', 'expat/2.4.1-GCCcore-11.2.0', 'expat/2.4.8-GCCcore-11.3.0', 'expat/2.4.9-GCCcore-12.2.0', 'expat/2.5.0-GCCcore-12.3.0', 'expat/2.6.2-GCCcore-13.3.0', 'expecttest/0.1.5-GCCcore-12.3.0', 'ffnvcodec/12.0.16.0', 'flex/2.6.4', 'flex/2.6.4-GCCcore-11.2.0', 'flex/2.6.4-GCCcore-11.3.0', 'flex/2.6.4-GCCcore-12.2.0', 'flex/2.6.4-GCCcore-12.3.0', 'flex/2.6.4-GCCcore-13.2.0', 'flex/2.6.4-GCCcore-13.3.0', 'flit/3.9.0-GCCcore-12.3.0', 'fontconfig/2.14.2-GCCcore-12.3.0', 'fontconfig/2.15.0-GCCcore-13.3.0', 'foss/2023a', 'freetype/2.13.0-GCCcore-12.3.0', 'freetype/2.13.2-GCCcore-13.3.0', 'gettext/0.21.1', 'gettext/0.21.1-GCCcore-12.3.0', 'gettext/0.22.5', 'gettext/0.22.5-GCCcore-13.3.0', 'gfbf/2023a', 'gh/2.52.0', 'giflib/5.2.1-GCCcore-12.3.0', 'git/2.41.0-GCCcore-12.3.0-nodocs', 'gmpy2/2.1.5-GCC-12.3.0', 'gompi/2023a', 'gperf/3.1-GCCcore-12.3.0', 'gperf/3.1-GCCcore-13.3.0', 'groff/1.22.4-GCCcore-11.2.0', 'groff/1.22.4-GCCcore-11.3.0', 'groff/1.22.4-GCCcore-12.2.0', 'groff/1.22.4-GCCcore-12.3.0', 'groff/1.23.0-GCCcore-13.3.0', 'gzip/1.12-GCCcore-12.3.0', 'hatchling/1.18.0-GCCcore-12.3.0', 'help2man/1.48.3-GCCcore-11.2.0', 'help2man/1.49.2-GCCcore-11.3.0', 'help2man/1.49.2-GCCcore-12.2.0', 'help2man/1.49.3-GCCcore-12.3.0', 'help2man/1.49.3-GCCcore-13.2.0', 'help2man/1.49.3-GCCcore-13.3.0', 'hwloc/2.9.1-GCCcore-12.3.0', 'hypothesis/6.82.0-GCCcore-12.3.0', 'intltool/0.51.0-GCCcore-12.3.0', 'intltool/0.51.0-GCCcore-13.3.0', 'jbigkit/2.1-GCCcore-12.3.0', 'kineto/0.4.0-GCC-12.3.0', 'libaec/1.0.6-GCCcore-12.3.0', 'libarchive/3.6.2-GCCcore-12.3.0', 'libarchive/3.7.4-GCCcore-13.3.0', 'libdeflate/1.18-GCCcore-12.3.0', 'libevent/2.1.12-GCCcore-12.3.0', 'libfabric/1.18.0-GCCcore-12.3.0', 'libffi/3.4.4-GCCcore-12.3.0', 'libffi/3.4.5-GCCcore-13.3.0', 'libiconv/1.17-GCCcore-12.3.0', 'libiconv/1.17-GCCcore-13.3.0', 'libjpeg-turbo/2.1.5.1-GCCcore-12.3.0', 'libpciaccess/0.17-GCCcore-12.3.0', 'libpciaccess/0.18.1-GCCcore-13.3.0', 'libpng/1.6.39-GCCcore-12.3.0', 'libpng/1.6.43-GCCcore-13.3.0', 'libreadline/8.1-GCCcore-11.2.0', 'libreadline/8.1.2-GCCcore-11.3.0', 'libreadline/8.2-GCCcore-12.2.0', 'libreadline/8.2-GCCcore-12.3.0', 'libreadline/8.2-GCCcore-13.3.0', 'libtool/2.4.6-GCCcore-11.2.0', 'libtool/2.4.7-GCCcore-11.3.0', 'libtool/2.4.7-GCCcore-12.2.0', 'libtool/2.4.7-GCCcore-12.3.0', 'libtool/2.4.7-GCCcore-13.2.0', 'libtool/2.4.7-GCCcore-13.3.0', 'libwebp/1.3.1-GCCcore-12.3.0', 'libxml2/2.11.4-GCCcore-12.3.0', 'libxml2/2.12.7-GCCcore-13.3.0', 'libyaml/0.2.5-GCCcore-12.3.0', 'lmod', 'lz4/1.9.4-GCCcore-12.3.0', 'magma/2.7.2-foss-2023a-CUDA-12.1.1', 'make/4.4.1-GCCcore-12.3.0', 'ncurses/6.2-GCCcore-11.2.0', 'ncurses/6.3', 'ncurses/6.3-GCCcore-11.3.0', 'ncurses/6.3-GCCcore-12.2.0', 'ncurses/6.4-GCCcore-12.3.0', 'ncurses/6.4-GCCcore-13.2.0', 'ncurses/6.5', 'ncurses/6.5-GCCcore-13.3.0', 'networkx/3.1-gfbf-2023a', 'numactl/2.0.16-GCCcore-12.3.0', 'patchelf/0.18.0-GCCcore-12.3.0', 'pkgconf/1.8.0', 'pkgconf/1.9.5-GCCcore-12.3.0', 'pkgconf/2.0.3-GCCcore-13.2.0', 'pkgconf/2.2.0-GCCcore-13.3.0', 'poetry/1.5.1-GCCcore-12.3.0', 'protobuf-python/4.24.0-GCCcore-12.3.0', 'protobuf/24.0-GCCcore-12.3.0', 'pybind11/2.11.1-GCCcore-12.3.0', 'pytest-flakefinder/1.1.0-GCCcore-12.3.0', 'pytest-rerunfailures/12.0-GCCcore-12.3.0', 'pytest-shard/0.1.2-GCCcore-12.3.0', 'scikit-build/0.17.6-GCCcore-12.3.0', 'settarg', 'setuptools-rust/1.6.0-GCCcore-12.3.0', 'sympy/1.12-gfbf-2023a', 'util-linux/2.39-GCCcore-12.3.0', 'util-linux/2.40-GCCcore-13.3.0', 'virtualenv/20.23.1-GCCcore-12.3.0', 'x264/20230226-GCCcore-12.3.0', 'x265/3.5-GCCcore-12.3.0', 'xorg-macros/1.20.0-GCCcore-12.3.0', 'xorg-macros/1.20.1-GCCcore-13.3.0', 'zlib/1.2.11', 'zlib/1.2.11-GCCcore-11.2.0', 'zlib/1.2.12', 'zlib/1.2.12-GCCcore-11.3.0', 'zlib/1.2.12-GCCcore-12.2.0', 'zlib/1.2.13', 'zlib/1.2.13-GCCcore-12.3.0', 'zlib/1.2.13-GCCcore-13.2.0', 'zlib/1.3.1', 'zlib/1.3.1-GCCcore-13.3.0', 'zstd/1.5.5-GCCcore-12.3.0']
== 2024-07-10 22:50:11,628 modules.py:628 INFO Checking whether binutils/2.40-GCCcore-12.3.0 exists...
== 2024-07-10 22:50:11,628 modules.py:633 INFO Module binutils/2.40-GCCcore-12.3.0 exists (found in list of available modules)
== 2024-07-10 22:50:11,628 modules.py:656 INFO Result for existence check of binutils/2.40-GCCcore-12.3.0 module: True
== 2024-07-10 22:50:11,628 modules.py:628 INFO Checking whether CMake/3.26.3-GCCcore-12.3.0 exists...
== 2024-07-10 22:50:11,628 modules.py:633 INFO Module CMake/3.26.3-GCCcore-12.3.0 exists (found in list of available modules)
== 2024-07-10 22:50:11,629 modules.py:656 INFO Result for existence check of CMake/3.26.3-GCCcore-12.3.0 module: True
== 2024-07-10 22:50:11,629 modules.py:628 INFO Checking whether CUDA/12.1.1 exists...
== 2024-07-10 22:50:11,629 modules.py:633 INFO Module CUDA/12.1.1 exists (found in list of available modules)
== 2024-07-10 22:50:11,629 modules.py:656 INFO Result for existence check of CUDA/12.1.1 module: True
== 2024-07-10 22:50:11,629 modules.py:628 INFO Checking whether OpenSSL/1.1 exists...
== 2024-07-10 22:50:11,629 modules.py:633 INFO Module OpenSSL/1.1 exists (found in list of available modules)
== 2024-07-10 22:50:11,629 modules.py:656 INFO Result for existence check of OpenSSL/1.1 module: True
== 2024-07-10 22:50:11,629 modules.py:628 INFO Checking whether PyTorch/2.1.2-foss-2023a-CUDA-12.1.1 exists...
== 2024-07-10 22:50:11,629 modules.py:636 INFO Module PyTorch/2.1.2-foss-2023a-CUDA-12.1.1 not found in list of available modules, checking via 'module show'...
== 2024-07-10 22:50:11,629 modules.py:572 DEBUG Checking whether PyTorch/2.1.2-foss-2023a-CUDA-12.1.1 exists based on output of 'module show'
== 2024-07-10 22:50:11,629 modules.py:814 DEBUG Current MODULEPATH: /apps/eb/el8/upstream/modules/all:/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core
== 2024-07-10 22:50:11,630 modules.py:828 DEBUG Running module command '/usr/share/lmod/lmod/libexec/lmod python show PyTorch/2.1.2-foss-2023a-CUDA-12.1.1' from /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1/dorado
== 2024-07-10 22:50:11,821 modules.py:835 DEBUG Output of module command '/usr/share/lmod/lmod/libexec/lmod python show PyTorch/2.1.2-foss-2023a-CUDA-12.1.1': stdout: import os
os.environ["MODULEPATH"] = "/apps/eb/el8/upstream/modules/all:/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core";
os.environ["_ModuleTable001_"] = "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";
os.environ["_ModuleTable002_"] = "L3Vzci9zaGFyZS9tb2R1bGVmaWxlcy9MaW51eDovdXNyL3NoYXJlL21vZHVsZWZpbGVzL0NvcmU6L3Vzci9zaGFyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsCn0K";
os.environ["_ModuleTable_Sz_"] = "2";
_mlstatus = True
; stderr:
== 2024-07-10 22:50:11,822 modules.py:723 DEBUG Cached result for 'module show PyTorch/2.1.2-foss-2023a-CUDA-12.1.1' with key '('MODULEPATH=/apps/eb/el8/upstream/modules/all:/etc/modulefiles:/usr/share/modulefiles:/usr/share/modulefiles/Linux:/usr/share/modulefiles/Core:/usr/share/lmod/lmod/modulefiles/Core', 'lmod', 'PyTorch/2.1.2-foss-2023a-CUDA-12.1.1')':
== 2024-07-10 22:50:11,822 modules.py:582 DEBUG Checking line '' to determine whether PyTorch/2.1.2-foss-2023a-CUDA-12.1.1 exists...
== 2024-07-10 22:50:11,823 modules.py:586 DEBUG Treating line '' as whitespace, so skipping it
== 2024-07-10 22:50:11,823 modules.py:649 INFO Module PyTorch/2.1.2-foss-2023a-CUDA-12.1.1 not found via module avail/show, checking whether it is a wrapper
== 2024-07-10 22:50:11,830 modules.py:656 INFO Result for existence check of PyTorch/2.1.2-foss-2023a-CUDA-12.1.1 module: False
== 2024-07-10 22:50:11,830 modules.py:628 INFO Checking whether HDF5/1.14.0-gompi-2023a exists...
== 2024-07-10 22:50:11,830 modules.py:633 INFO Module HDF5/1.14.0-gompi-2023a exists (found in list of available modules)
== 2024-07-10 22:50:11,831 modules.py:656 INFO Result for existence check of HDF5/1.14.0-gompi-2023a module: True
== 2024-07-10 22:50:11,831 modules.py:628 INFO Checking whether zstd/1.5.5-GCCcore-12.3.0 exists...
== 2024-07-10 22:50:11,831 modules.py:633 INFO Module zstd/1.5.5-GCCcore-12.3.0 exists (found in list of available modules)
== 2024-07-10 22:50:11,831 modules.py:656 INFO Result for existence check of zstd/1.5.5-GCCcore-12.3.0 module: True
== 2024-07-10 22:50:11,831 modules.py:628 INFO Checking whether HTSlib/1.18-GCC-12.3.0 exists...
== 2024-07-10 22:50:11,831 modules.py:633 INFO Module HTSlib/1.18-GCC-12.3.0 exists (found in list of available modules)
== 2024-07-10 22:50:11,831 modules.py:656 INFO Result for existence check of HTSlib/1.18-GCC-12.3.0 module: True
== 2024-07-10 22:50:11,832 modules.py:628 INFO Checking whether kineto/0.4.0-GCC-12.3.0 exists...
== 2024-07-10 22:50:11,832 modules.py:633 INFO Module kineto/0.4.0-GCC-12.3.0 exists (found in list of available modules)
== 2024-07-10 22:50:11,832 modules.py:656 INFO Result for existence check of kineto/0.4.0-GCC-12.3.0 module: True
== 2024-07-10 22:50:11,832 modules.py:628 INFO Checking whether libaec/1.0.6-GCCcore-12.3.0 exists...
== 2024-07-10 22:50:11,832 modules.py:633 INFO Module libaec/1.0.6-GCCcore-12.3.0 exists (found in list of available modules)
== 2024-07-10 22:50:11,832 modules.py:656 INFO Result for existence check of libaec/1.0.6-GCCcore-12.3.0 module: True
== 2024-07-10 22:50:11,843 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): Missing modules for dependencies (use --robot?): PyTorch/2.1.2-foss-2023a-CUDA-12.1.1 (at easybuild/tools/toolchain/toolchain.py:563 in _check_dependencies)
== 2024-07-10 22:50:11,845 build_log.py:267 INFO ... (took < 1 sec)
== 2024-07-10 22:50:11,853 config.py:700 DEBUG software install path as specified by 'installpath' and 'subdir_software': /apps/eb/el8/upstream/software
== 2024-07-10 22:50:11,853 filetools.py:2013 INFO Removing lock /apps/eb/el8/upstream/software/.locks/_apps_eb_el8_upstream_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock...
== 2024-07-10 22:50:11,857 filetools.py:383 INFO Path /apps/eb/el8/upstream/software/.locks/_apps_eb_el8_upstream_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock successfully removed.
== 2024-07-10 22:50:11,858 filetools.py:2017 INFO Lock removed: /apps/eb/el8/upstream/software/.locks/_apps_eb_el8_upstream_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock
== 2024-07-10 22:50:11,858 easyblock.py:4285 WARNING build failed (first 300 chars): Missing modules for dependencies (use --robot?): PyTorch/2.1.2-foss-2023a-CUDA-12.1.1
== 2024-07-10 22:50:11,858 easyblock.py:328 INFO Closing log for application name dorado version 0.6.1