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

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    • #2067

        Dear friends,
        Can I ask the syntax for running 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/ –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 –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 “”, 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

      • #10599

          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 script. While Rosetta programs themselves can autodetect the database location, the script isn’t so robust, and will halt with an error if you don’t provide it.

        • #10613

            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 ‘’: [Errno 2] No such file or directory

            So I put a full path to the “” 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 build
            lanselibai@ubuntu:~/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools$ sudo python install

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

            Yours sincerely

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