Syntax for python-based (.py) command line on cluster

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    • November 14, 2014 at 5:32 pm #2067
      Anonymous

        Dear friends,
        Can I ask the syntax for running clustering.py on cluster?

        When using it on Ubuntu, the command line is something like the below and works fine:

        python /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/clustering.py –pdb_list /home/lanselibai/Cheng/20141106_Homology/7_HC_score_RMSD/7.3_cluster/input/list_of_pdbs.txt –rosetta /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/cluster.linuxgccrelease –database /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database –options /mnt/hgfs/Mutagenesis_Rosetta/4KMT/5.0_floppy_tail/outputs/20141017/cluster/cluster.options /mnt/hgfs/Mutagenesis_Rosetta/4KMT/5.0_floppy_tail/outputs/20141017/cluster/cluster_summary.txt /mnt/hgfs/Mutagenesis_Rosetta/4KMT/5.0_floppy_tail/outputs/20141017/cluster/cluster_histogram.txt >& /mnt/hgfs/Mutagenesis_Rosetta/4KMT/5.0_floppy_tail/outputs/20141017/cluster/cluster.log &

        Based on my understanding, I changed it into the below so as to run it on our cluster:

        python clustering.py –pdb_list /home/ucbechz/Scratch/20141114_cluster_HC/input/list_of_pdbs.txt –rosetta cluster.linuxgccrelease –options /home/ucbechz/Scratch/20141114_cluster_HC/input/cluster.options cluster_summary.txt cluster_histogram.txt > cluster.log

        However, when I submit the job, the job disappeared after a few seconds of “qw” status. And no output has been generated.

        The “test.sh”, options file and PDB list file are attached. Could you please help me identify the problem?

        Thank you very much! Have a good weekends!

        Yours sincerely
        Cheng

      • November 18, 2014 at 6:30 pm #10599
        Anonymous

          Is there anything printed to your cluster.log file, or to the captured stdout and stderr files which are saved by your cluster job management software.

          I think the issue here is with the missing –database parameter on for the clustering.py script. While Rosetta programs themselves can autodetect the database location, the cluster.py script isn’t so robust, and will halt with an error if you don’t provide it.

        • November 20, 2014 at 10:15 am #10613
          Anonymous

            Hi R Moretti,
            Thank you for your help. I should have take a look at the error file.

            It is said:
            python: can’t open file ‘clustering.py’: [Errno 2] No such file or directory

            So I put a full path to the “clustering.py” and specified the database.

            Then, it is said
            ImportError: No module named rosettautil.rosetta

            I think I know how to solve this like I did on Ubuntu:
            lanselibai@ubuntu:~/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools$ python setup.py build
            lanselibai@ubuntu:~/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools$ sudo python setup.py install

            I will ask you again if I still have problem. :)

            Yours sincerely
            Cheng

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