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proteomicsunitcrg / qcloud2-pipeline

QCloud2 pipeline
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Pipeline migration to new cluster (Slurm) #83

Open rolivella opened 2 months ago

rolivella commented 2 months ago
rolivella commented 1 week ago

proteomics@proteomics-qc:~/mygit$ module load OpenSSL

The following have been reloaded with a version change: 1) OpenSSL/1.1 => OpenSSL/3

proteomics@proteomics-qc:~/mygit$ git clone git@github.com:proteomicsunitcrg/qcloud2-pipeline.git

rolivella commented 1 week ago

[request.crg.es #203900] ncurses Library Compatibility Issue with Nextflow on proteomics-qc VM

This is because I'm running NF from a login node. NF should run inside a new slurm queue.

rolivella commented 1 week ago 
proteomics@proteomics-qc:~/mygit/qcloud2-pipeline$ squeue -j 1613506
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
proteomics@proteomics-qc:~/mygit/qcloud2-pipeline$
proteomics@proteomics-qc:~/mygit/qcloud2-pipeline$
proteomics@proteomics-qc:~/mygit/qcloud2-pipeline$
proteomics@proteomics-qc:~/mygit/qcloud2-pipeline$ squeue -j 1613506
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
proteomics@proteomics-qc:~/mygit/qcloud2-pipeline$ sacct -j 1613506
JobID           JobName  Partition    Account  AllocCPUS      State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
1613506      submit_nf+    genoa64 crg_prote+          1     FAILED      1:0
1613506.bat+      batch            crg_prote+          1     FAILED      1:0
1613506.ext+     extern            crg_prote+          1  COMPLETED      0:0
rolivella commented 1 week ago 
proteomics@proteomics-qc:~/mygit/qcloud2-pipeline$ cat slurm-1613506.out
Waiting for 2525648
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: symbol lookup error: tput: undefined symbol: _nc_reset_tparm, version NCURSES6_TINFO_6.2.20211010
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: symbol lookup error: tput: undefined symbol: _nc_reset_tparm, version NCURSES6_TINFO_6.2.20211010
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: symbol lookup error: tput: undefined symbol: _nc_reset_tparm, version NCURSES6_TINFO_6.2.20211010
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
tput: /usr/lib64/libncursesw.so.6: no version information available (required by tput)
ERROR: Cannot find Java or it's a wrong version -- please make sure that Java 8 or later (up to 18) is installed
NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:
 JAVA_CMD: /software/sit/EasyBuild/software/Java/21.0.2/bin/java
 JAVA_HOME: /software/sit/EasyBuild/software/Java/21.0.2
rolivella commented 9 hours ago

Emyr: incrontab at login node -> trigger script -> sbatch -> nf pipeline