I am running two benchmarks in the command line by the following a script for Mi-bench, kindly confirm whether I am using the right script or not- I am separating two applications through semicolon; please help.
./build/X86/gem5.opt -d ./Mi-combination ./configs/example/se.py -c "/media/shukla/Windows/gem5_old/benchmar/MiBench/X86/network/dijkstra/dijkstra_small;/media/shukla/Windows/gem5_old/benchmar/MiBench/X86/network/patricia/patricia" -o "/media/shukla/Windows/gem5_old/benchmar/MiBench/X86/network/dijkstra/input.dat;/media/shukla/Windows/gem5_old/benchmar/MiBench/X86/network/patricia/small.udp" --cpu-type=MinorCPU --cpu-clock=1GHz --num-cpu=2 --caches --l2cache --l1d_size=32kB --l1i_size=32kB --l2_size=512kB --l1d_assoc=2 --l1i_assoc=2 --l2_assoc=2
Thanks in advance
Related
I'm trying to use the --immediate-submit on a PBSPro cluster. I tried using an in-place modification of the dependencies string to adapt it to PBSPro, similar to what is done here.
snakemake --cluster "qsub -l wd -l mem={cluster.mem}GB -l ncpus={threads} -e {cluster.stderr} -q {cluster.queue} -l walltime={cluster.walltime} -o {cluster.stdout} -S /bin/bash -W $(echo '{dependencies}' | sed 's/^/depend=afterok:/g' | sed 's/ /:/g')"
This last part gets converted into, for example:
-W depend=afterok: /g/data1a/va1/dk0741/analysis/2018-03-25_marmo_test/.snakemake/tmp.cyrhf51c/snakejob.trimmomatic_pe.7.sh
There are two problems here:
How can I get the dependencies string to output job ID instead of the script path? The qsub command normally outputs the job ID to stdout, so I'm not sure why it's not doing so here.
How do I get rid of the space after afterok:? I've tried everything!
As an aside, it would be helpful if there were some option to debug the submission or not to delete the tmp.cyrhf51c directory in .snakemake -- is there some way to do this?
Thanks,
David
I suggest to use a profile for this, instead of trying to find an ad-hoc solution. This will also help with debugging. E.g., there is already a pbs-torque profile available (https://github.com/Snakemake-Profiles/pbs-torque), probably there is not much to change towards pbspro?
My problem is that I have a cluster-server with Torque PBS and want to use it to run a sequence-comparison with the program rapsearch.
The normal RapSearch command is:
./rapsearch -q protein.fasta -d database -o output -e 0.001 -v 10 -x t -z 32
Now I want to run it with 2 nodes on the cluster-server.
I've tried with: echo "./rapsearch -q protein.fasta -d database -o output -e 0.001 -v 10 -x t -z 32" | qsub -l nodes=2 but nothing happened.
Do you have any suggestions? Where I'm wrong? Help please.
Standard output (and error output) files are placed in your home directory by default; take a look. You are looking for a file named STDIN.e[numbers], it will contain the error message.
However, I see that you're using ./rapsearch but are not really being explicit about what directory you're in. Your problem is therefore probably a matter of changing directory into the directory that you submitted from. When your terminal is in the directory of the rapsearch executable, try echo "cd \$PBS_O_WORKDIR && ./rapsearch [arguments]" | qsub [arguments] to submit your job to the cluster.
Other tips:
You could add rapsearch to your path if you use it often. Then you can use it like a regular command anywhere. It's a matter of adding the line export PATH=/full/path/to/rapsearch/bin:$PATH to your .bashrc file.
Create a submission script for use with qsub. Here is a good example.
I have Synology with ipkg installed, and mkvmerge working.
When I use
/opt/bin/mkvmerge -o /path_to_file/filename.added_subs.mkv
--default-track 0 --language 0:eng /path_to_file/filename.srt
/path_to_file/filename.mkv
This works perfectly, and the file gets remuxed with the subtitles added.
But because I have many (many) files I want to do this with, I;d like to run a batch for this.
I've found this line to explain what I want to do:
FOR %A IN (/path_to_files/*.mkv) DO /opt/bin/mkvmerge -o /path_to_files/%~nA.added_subs.mkv --default-track 0 --language 0:eng /path_to_files/%~nA.srt /path_to_files/%~nA.mkv
But the Synology won't accept the FOR ... IN command.
Anyone have an idea how to accomplish this?
Found it:
FILES=/path/*.mkv
for f in $FILES
do /opt/bin/mkvmerge -o ${f%.*}.EN.mkv --default-track 0 --language 0:en ${f%.*}.srt ${f%.*}.mkv
done
I'm using a library that generates a whole ton of output to stderr (and there is really no way to suppress the output directly in the code; it is ROOT's Minuit2 minimizer which is known for not having a way to suppress the output). I'm running batch jobs through the LSF system, and the error output files are so big that they exceed my disk quota. Erk.
When I run locally on a shell, I do:
python main.py 2> >( grep -v Minuit2 2>&1 )
to suppress the output, as is done here.
This works great, but unfortunately I can't seem to get that or any variation of it to work when running on LSF. I think this is due to LSF not spawning the necessary subshell, but it's not clear.
I run on batch by passing LSF a submit script. The relevant line is:
python main.py $INPUT_FILE
which works great, aside from the aforementioned problem of gigantic error files.
When I try changing that line to
python main.py $INPUT_FILE 2> >( grep -v Minuit2 2>&1 )
I end up with
./singleSubmit.sh: line 16: syntax error near unexpected token `>'
./singleSubmit.sh: line 16: `python $MAIN $1 2> >( grep -v Minuit2 2>&1 )'
in the error log file.
Any idea how I could accomplish what I want, or why this is not working?
Thanks a ton!
The syntax you're using works in bash, not in csh/tcsh. Try changing the first line of your submission script to
#!/bin/bash
I am learning the shell language. I have creating a shell script whose function is to login into the DB and run a .sql file. Following are the contents of the script -
#!/bin/bash
set -x
echo "Login to postgres user for autoqa_rpt_production"
$DB_PATH -U $POSTGRESS_USER $Auto_rpt_production$TARGET_DB -p $TARGET_PORT
echo "Running SQL Dump - auto_qa_db_sync"
\\i auto_qa_db_sync.sql
After running the above script, I get the following error
./autoqa_script.sh: 39: ./autoqa_script.sh: /i: not found
Following one article, I tried reversing the slash but it didn't worked.
I don't understand why this is happening. Because when I try manually running the sql file, it works properly. Can anyone help?
#!/bin/bash
set -x
echo "Login to postgres user for autoqa_rpt_production and run script"
$DB_PATH -U $POSTGRESS_USER $Auto_rpt_production$TARGET_DB -p $TARGET_PORT -f auto_qa_db_sync.sql
The lines you put in a shell script are (moreless, let's say so for now) equivalent to what you would put right to the Bash prompt (the one ending with '$' or '#' if you're a root). When you execute a script (a list of commands), one command will be run after the previous terminates.
What you wanted to do is to run the client and issue a "\i ./autoqa_script.sh" comand in it.
What you did was to run the client, and after the client terminated, issue that command in Bash.
You should read about Bash pipelines - these are the way to run programs and input text inside them. Following your original idea to solving the problem, you'd write something like:
echo '\i auto_qa_db_sync.sql' | $DB_PATH -U $POSTGRESS_USER $Auto_rpt_production$TARGET_DB -p $TARGET_PORT
Hope that helps to understand.