PrepareJob

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To run your job on the cluster, prepare it on your local machine, then copy it to the cluster. Beside the datafiles you will need a jobfile containing all you setting.
+
To run a job on the cluster, prepare the data files on your local machine, then [[File Transfers|copy it to the cluster]]. Beside the data files, you will need a job file with the settings as outlined below.
  
Name your job file and your data files in a consistent way:
+
Name your job and data files in a consistent way:
 
* Job file: myjobfile.sh
 
* Job file: myjobfile.sh
* User: Mustermann
+
* User: user01
 
* Email: max@mustermann.de
 
* Email: max@mustermann.de
  
These jobfiles are written in a sort of "shell" command syntax of Linux systems.
+
* Job files are written as a sort of "shell" commands that are common on Linux systems
 +
* Lines starting with "##" or "# " are comment lines to document some stuff for better reading afterwards
 +
* Lines starting with "#$" are commands for the job scheduler "qsub"
 +
* Lines starting not with "#" are commands executed
 +
* '''Make sure that the skript does not contain empty lines! Delete them or comment them out using "#"'''
  
Lines starting with "##" or "# " are comment lines to document some stuff for better reading afterwards.
 
  
Lines starting with "#$" are commands for the job scheduler "qsub".
+
== Examples ==
 +
You may use one of the following examples as a template for you job. Lines that need to be modified are highlighted. Make sure to change username, email adress, filenames, and, if necessary, program options. The last line of each script calls the program you want to run, including all parameters. The number of CPUs is stored in $NSLOTS and is set later when starting the job.
  
Lines starting not with "#" are commands to execute programs in this job.
+
=== Beast ===
 +
<source lang="bash" start="1" highlight="4,7,18,19,22" enclose="div">
 +
#!/bin/csh
 +
#
 +
## User name (Which account to be charged cpu time)
 +
#$ -A user01
 +
#
 +
## Send email to users
 +
#$ -M max@mustermann.de
 +
#
 +
## Send mail at beginning/end/on suspension
 +
#$ -m bes
 +
#
 +
## Export these environmental variables
 +
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
 +
#
 +
## The job is located in the current working directory.
 +
#$ -cwd
 +
## Filenames for output and error log files
 +
#$ -o myjobfile.out
 +
#$ -e myjobfile.err
 +
#
 +
env >./xenv
 +
/share/apps/beast/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out
 +
</source>
  
 +
=== Beast2 ===
 +
<source lang="bash" start="1" highlight="4,7,18,19,22" enclose="div">
 +
#!/bin/csh
 +
#
 +
## User name (Which account to be charged cpu time)
 +
#$ -A user01
 +
#
 +
## Send email to users
 +
#$ -M max@mustermann.de
 +
#
 +
## Send email at beginning/end/on suspension
 +
#$ -m bes
 +
#
 +
## Export these environmental variables
 +
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
 +
#
 +
## The job is located in the current working directory.
 +
#$ -cwd
 +
## Filenames for output and error log files
 +
#$ -o myjobfile.out
 +
#$ -e myjobfile.err
 +
#
 +
env >./xenv
 +
/share/apps/beast210/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out
 +
</source>
  
== Example (Beast) ==
+
=== Mr Bayes ===
you may use this as a template for Beast
+
<source lang="bash" start="1" highlight="4,7,18,19,22" enclose="div">
simply change all occurrences of "myjobfile" to your actual project name. also change User and email to your settings.
+
#!/bin/csh
 +
#
 +
## User name (Which account to be charged cpu time)
 +
#$ -A user01
 +
#
 +
## Send email to users
 +
#$ -M max@mustermann.de
 +
#
 +
## Send email at beginning/end/on suspension
 +
#$ -m bes
 +
#
 +
## Export these environmental variables
 +
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
 +
#
 +
## The job is located in the current working directory
 +
#$ -cwd
 +
## Filenames for output and error log files
 +
#$ -o myjobfile.out
 +
#$ -e myjobfile.err
 +
#
 +
env >./xenv
 +
mpirun -np $NSLOTS /share/apps/mrbayes/mb ./beispiel.nex </dev/null
 +
</source>
  
<source lang="bash" line start="1" highlight="4,13,24,25,28" enclose="div">
+
=== Raxml ===
 +
<source lang="bash" start="1" highlight="4,7,18,19,22" enclose="div">
 
#!/bin/csh
 
#!/bin/csh
 
#
 
#
# Username (Which account to be charged cpu time)
+
## User name (Which account to be charged cpu time)
#$ -A Mustermann
+
#$ -A user01
 
#
 
#
 +
## Send email to users
 +
#$ -M max@mustermann.de
 
#
 
#
# If you want to make it queue now, get rid of the -a option by adding ## before $
+
## Send email at beginning/end/on suspension
# If you want to make it queue later, use this format [[CC]yy]MMDDhhmm[.SS]
+
#$ -m bes
##$ -a 201407300600
+
 
#
 
#
 +
## Export these environmental variables
 +
#$ -v PVM_ROOT
 
#
 
#
# Send mail to these users
+
## The job is located in the current working directory.
 +
#$ -cwd
 +
## Filenames for output and error log files
 +
#$ -o myjobfile.out
 +
#$ -e myjobfile.err
 +
#
 +
env >./xenv
 +
mpirun -np $NSLOTS /share/apps/raxml/raxmlHPC-MPI-SSE3.icc -s sequencefile.phy -n outputfile.phy -m PROTGAMMAWAG
 +
</source>
 +
 
 +
=== Exabayes ===
 +
<source lang="bash" start="1" highlight="4,7,18,19,22" enclose="div">
 +
#!/bin/csh
 +
#
 +
## User name (Which account to be charged cpu time)
 +
#$ -A user01
 +
#
 +
## Send email to users
 
#$ -M max@mustermann.de
 
#$ -M max@mustermann.de
 
#
 
#
# Mail at beginning/end/on suspension
+
## Send email at beginning/end/on suspension
 
#$ -m bes
 
#$ -m bes
 
#
 
#
# Export these environmental variables
+
## Export these environmental variables
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
+
#$ -v PVM_ROOT
 
#
 
#
# The job is located in the current
+
## The job is located in the current working directory.
# working directory.
+
 
#$ -cwd
 
#$ -cwd
 +
## Filenames for output and error log files
 
#$ -o myjobfile.out
 
#$ -o myjobfile.out
 
#$ -e myjobfile.err
 
#$ -e myjobfile.err
 
#
 
#
 
env >./xenv
 
env >./xenv
/share/apps/beast180/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out
+
mpirun -np $NSLOTS /share/apps/exabayes/exabayes -f aln.phy -q aln.part -n myRun -s 57913 -c config.nex -R 2 -C 2
 +
</source>
  
 +
=== Iq-Tree ===
 +
<source lang="bash" start="1" highlight="4,7,18,19,22" enclose="div">
 +
#!/bin/csh
 +
#
 +
## User name (Which account to be charged cpu time)
 +
#$ -A user01
 +
#
 +
## Send email to users
 +
#$ -M max@mustermann.de
 +
#
 +
## Send email at beginning/end/on suspension
 +
#$ -m bes
 +
#
 +
## Export these environmental variables
 +
#$ -v PVM_ROOT
 +
#
 +
## The job is located in the current working directory.
 +
#$ -cwd
 +
## Filenames for output and error log files
 +
#$ -o myjobfile.out
 +
#$ -e myjobfile.err
 +
#
 +
env >./xenv
 +
/share/apps/iqtree/iqtree-omp -omp $NSLOTS -s example.phy -m TEST
 
</source>
 
</source>

Latest revision as of 15:37, 24 May 2017

To run a job on the cluster, prepare the data files on your local machine, then copy it to the cluster. Beside the data files, you will need a job file with the settings as outlined below.

Name your job and data files in a consistent way:

  • Job file: myjobfile.sh
  • User: user01
  • Email: max@mustermann.de
  • Job files are written as a sort of "shell" commands that are common on Linux systems
  • Lines starting with "##" or "# " are comment lines to document some stuff for better reading afterwards
  • Lines starting with "#$" are commands for the job scheduler "qsub"
  • Lines starting not with "#" are commands executed
  • Make sure that the skript does not contain empty lines! Delete them or comment them out using "#"


Contents

[edit] Examples

You may use one of the following examples as a template for you job. Lines that need to be modified are highlighted. Make sure to change username, email adress, filenames, and, if necessary, program options. The last line of each script calls the program you want to run, including all parameters. The number of CPUs is stored in $NSLOTS and is set later when starting the job.

[edit] Beast

#!/bin/csh
#
## User name (Which account to be charged cpu time)
#$ -A user01
#
## Send email to users
#$ -M max@mustermann.de
#
## Send mail at beginning/end/on suspension
#$ -m bes
#
## Export these environmental variables
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
#
## The job is located in the current working directory.
#$ -cwd
## Filenames for output and error log files
#$ -o myjobfile.out
#$ -e myjobfile.err
#
env >./xenv
/share/apps/beast/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out

[edit] Beast2

#!/bin/csh
#
## User name (Which account to be charged cpu time)
#$ -A user01
#
## Send email to users
#$ -M max@mustermann.de
#
## Send email at beginning/end/on suspension
#$ -m bes
#
## Export these environmental variables
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
#
## The job is located in the current working directory.
#$ -cwd
## Filenames for output and error log files
#$ -o myjobfile.out
#$ -e myjobfile.err
#
env >./xenv
/share/apps/beast210/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out

[edit] Mr Bayes

#!/bin/csh
#
## User name (Which account to be charged cpu time)
#$ -A user01
#
## Send email to users
#$ -M max@mustermann.de
#
## Send email at beginning/end/on suspension
#$ -m bes
#
## Export these environmental variables
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
#
## The job is located in the current working directory
#$ -cwd
## Filenames for output and error log files
#$ -o myjobfile.out
#$ -e myjobfile.err
#
env >./xenv
mpirun -np $NSLOTS /share/apps/mrbayes/mb ./beispiel.nex </dev/null

[edit] Raxml

#!/bin/csh
#
## User name (Which account to be charged cpu time)
#$ -A user01
#
## Send email to users
#$ -M max@mustermann.de
#
## Send email at beginning/end/on suspension
#$ -m bes
#
## Export these environmental variables
#$ -v PVM_ROOT
#
## The job is located in the current working directory.
#$ -cwd
## Filenames for output and error log files
#$ -o myjobfile.out
#$ -e myjobfile.err
#
env >./xenv
mpirun -np $NSLOTS /share/apps/raxml/raxmlHPC-MPI-SSE3.icc -s sequencefile.phy -n outputfile.phy -m PROTGAMMAWAG

[edit] Exabayes

#!/bin/csh
#
## User name (Which account to be charged cpu time)
#$ -A user01
#
## Send email to users
#$ -M max@mustermann.de
#
## Send email at beginning/end/on suspension
#$ -m bes
#
## Export these environmental variables
#$ -v PVM_ROOT
#
## The job is located in the current working directory.
#$ -cwd
## Filenames for output and error log files
#$ -o myjobfile.out
#$ -e myjobfile.err
#
env >./xenv
mpirun -np $NSLOTS /share/apps/exabayes/exabayes -f aln.phy -q aln.part -n myRun -s 57913 -c config.nex -R 2 -C 2

[edit] Iq-Tree

#!/bin/csh
#
## User name (Which account to be charged cpu time)
#$ -A user01
#
## Send email to users
#$ -M max@mustermann.de
#
## Send email at beginning/end/on suspension
#$ -m bes
#
## Export these environmental variables
#$ -v PVM_ROOT
#
## The job is located in the current working directory.
#$ -cwd
## Filenames for output and error log files
#$ -o myjobfile.out
#$ -e myjobfile.err
#
env >./xenv
/share/apps/iqtree/iqtree-omp -omp $NSLOTS -s example.phy -m TEST
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