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

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

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

cluster.options.txt535 bytes
list_of_pdbs.txt66.41 KB
test.sh_.txt827 bytes
Post Situation: 
Fri, 2014-11-14 09:32

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.

Tue, 2014-11-18 10:30

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

Thu, 2014-11-20 02:15