Dear Galaxy Team, I'm trying to install the repeatexplorer tool https://bitbucket.org/repeatexplorer/ I get the following message that I cannot solve. it does not seem to be releated to the repeatexplorer tool itself since it is not using MPI as far as I can tell although it does not seem to happen with other tools at the galaxy instance. ERROR: ld.so: object '/usr/lib/openmpi/lib/libmpi.so' from LD_PRELOAD cannot be preloaded (wrong ELF class: ELFCLASS64): ignored. note: /usr/lib/openmpi/lib/libmpi.so exists and is a 64 bits lib I've tried unsetting the LD_PRELOAD library for the galaxy user but that did not help,. According to the logs it looks like this error occurs after the job finishes. I would appreciate any clues on how to debug this and to find out where this message comes from. below the snippet from the logfiles: galaxy.jobs DEBUG 2016-04-04 11:22:40,544 (1829) Working directory for job is: /mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829 galaxy.jobs.handler DEBUG 2016-04-04 11:22:40,556 (1829) Dispatching to drmaa runner galaxy.jobs DEBUG 2016-04-04 11:22:40,760 (1829) Persisting job destination (destination id: sge_default) galaxy.jobs.runners DEBUG 2016-04-04 11:22:40,765 Job [1829] queued (207.994 ms) galaxy.jobs.handler INFO 2016-04-04 11:22:40,808 (1829) Job dispatched galaxy.jobs.runners DEBUG 2016-04-04 11:22:41,841 (1829) command is: bash /mnt/data/home/NIOO/galaxy/galaxy-dist/tools/umbr_programs/seqclust/seqclust-main.sh -s /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3137.dat -m 0.01 -o 40 -d Viridiplantae -v /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3173.dat -w /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3174.dat -y /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3175.dat -z RMSKtable -r /mnt/data/home/NIOO/galaxy/galaxy-dist -t /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3176.dat -u '/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/dataset_3176_files' -p false -f 0 -a True -l 55 -x " " -K 10; return_code=$?; python "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/set_metadata_VcdaXP.py" "/tmp/tmpOOJhc4" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/galaxy.json" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2937_ivd_QV,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2937__9U8lt,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2937_zmXF2T,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2937_XHZd2p,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3176.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2937_0_rQHI" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2936_2FIF61,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2936__PZplz,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2936_ImcuR2,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2936_Jm3zxC,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3175.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2936_qkgfR7" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2935_5Ozbvu,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2935_H_7TWw,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2935_Rp42fp,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2935_ycng_Q,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3174.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2935_gbk6Im" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2934_wM1GtU,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2934_pUrJqr,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2934__8Jvh6,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2934_n_AZt2,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3173.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2934_ovKSAZ" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:41,890 (1829) submitting file /mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/galaxy_1829.sh galaxy.jobs.runners.drmaa INFO 2016-04-04 11:22:41,900 (1829) queued as 9507 galaxy.jobs DEBUG 2016-04-04 11:22:41,950 (1829) Persisting job destination (destination id: sge_default) galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:42,159 (1829/9507) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:44,286 (1829/9507) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:47:59,005 (1829/9507) state change: job finished normally galaxy.jobs DEBUG 2016-04-04 11:47:59,500 setting dataset state to ERROR galaxy.jobs DEBUG 2016-04-04 11:47:59,527 setting dataset state to ERROR galaxy.jobs DEBUG 2016-04-04 11:47:59,559 setting dataset state to ERROR galaxy.jobs DEBUG 2016-04-04 11:47:59,602 setting dataset state to ERROR galaxy.jobs INFO 2016-04-04 11:47:59,779 Collecting job metrics for <galaxy.model.Job object at 0x7f3f346d89d0> galaxy.jobs DEBUG 2016-04-04 11:47:59,798 job 1829 ended (finish() executed in (595.557 ms))
On Mon, Apr 4, 2016 at 6:52 AM, Jager, Victor de <V.deJager@nioo.knaw.nl> wrote:
Dear Galaxy Team,
I'm trying to install the repeatexplorer tool https://bitbucket.org/repeatexplorer/
I get the following message that I cannot solve. it does not seem to be releated to the repeatexplorer tool itself since it is not using MPI as far as I can tell although it does not seem to happen with other tools at the galaxy instance.
ERROR: ld.so: object '/usr/lib/openmpi/lib/libmpi.so' from LD_PRELOAD cannot be preloaded (wrong ELF class: ELFCLASS64): ignored.
note: /usr/lib/openmpi/lib/libmpi.so exists and is a 64 bits lib
Hi Victor, It'd appear that one of RepeatExplorer's dependencies must have been compiled 32 bit, which is why runtime linking of libmpi.so failed.
I've tried unsetting the LD_PRELOAD library for the galaxy user but that did not help,. According to the logs it looks like this error occurs *after* the job finishes.
This seems like a good solution, but if you are doing this on the Galaxy server it will not take effect on your SGE jobs. You will need to cause this to happen in the execution environment, which you can do with the <env> tag in your SGE <destination>(s). This may work: <env id="LD_PRELOAD"></env> If not, you can create a script that unsets LD_PRELOAD and have Galaxy source it with: <env file="/path/to/unsource_ld_preload.sh" /> --nate
I would appreciate any clues on how to debug this and to find out where this message comes from.
below the snippet from the logfiles:
galaxy.jobs DEBUG 2016-04-04 11:22:40,544 (1829) Working directory for job is: /mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829 galaxy.jobs.handler DEBUG 2016-04-04 11:22:40,556 (1829) Dispatching to drmaa runner galaxy.jobs DEBUG 2016-04-04 11:22:40,760 (1829) Persisting job destination (destination id: sge_default) galaxy.jobs.runners DEBUG 2016-04-04 11:22:40,765 Job [1829] queued (207.994 ms) galaxy.jobs.handler INFO 2016-04-04 11:22:40,808 (1829) Job dispatched galaxy.jobs.runners DEBUG 2016-04-04 11:22:41,841 (1829) command is: bash /mnt/data/home/NIOO/galaxy/galaxy-dist/tools/umbr_programs/seqclust/seqclust-main.sh -s /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3137.dat -m 0.01 -o 40 -d Viridiplantae -v /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3173.dat -w /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3174.dat -y /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3175.dat -z RMSKtable -r /mnt/data/home/NIOO/galaxy/galaxy-dist -t /mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3176.dat -u '/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/dataset_3176_files' -p false -f 0 -a True -l 55 -x " " -K 10; return_code=$?; python "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/set_metadata_VcdaXP.py" "/tmp/tmpOOJhc4" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/galaxy.json" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2937_ivd_QV,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2937__9U8lt,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2937_zmXF2T,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2937_XHZd2p,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3176.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2937_0_rQHI" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2936_2FIF61,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2936__PZplz,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2936_ImcuR2,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2936_Jm3zxC,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3175.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2936_qkgfR7" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2935_5Ozbvu,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2935_H_7TWw,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2935_Rp42fp,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2935_ycng_Q,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3174.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2935_gbk6Im" "/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_in_HistoryDatasetAssociation_2934_wM1GtU,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_kwds_HistoryDatasetAssociation_2934_pUrJqr,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_out_HistoryDatasetAssociation_2934__8Jvh6,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_results_HistoryDatasetAssociation_2934_n_AZt2,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/files/003/dataset_3173.dat,/mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/metadata_override_HistoryDatasetAssociation_2934_ovKSAZ" 5242880; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:41,890 (1829) submitting file /mnt/data/home/NIOO/galaxy/galaxy-dist/database/job_working_directory/001/1829/galaxy_1829.sh galaxy.jobs.runners.drmaa INFO 2016-04-04 11:22:41,900 (1829) queued as 9507 galaxy.jobs DEBUG 2016-04-04 11:22:41,950 (1829) Persisting job destination (destination id: sge_default) galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:42,159 (1829/9507) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:22:44,286 (1829/9507) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2016-04-04 11:47:59,005 (1829/9507) state change: job finished normally galaxy.jobs DEBUG 2016-04-04 11:47:59,500 setting dataset state to ERROR galaxy.jobs DEBUG 2016-04-04 11:47:59,527 setting dataset state to ERROR galaxy.jobs DEBUG 2016-04-04 11:47:59,559 setting dataset state to ERROR galaxy.jobs DEBUG 2016-04-04 11:47:59,602 setting dataset state to ERROR galaxy.jobs INFO 2016-04-04 11:47:59,779 Collecting job metrics for <galaxy.model.Job object at 0x7f3f346d89d0> galaxy.jobs DEBUG 2016-04-04 11:47:59,798 job 1829 ended (finish() executed in (595.557 ms))
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participants (2)
-
Jager, Victor de -
Nate Coraor