PrepareJob

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Always prepare your jobs fir on your local machine and follow for each job some guidelines.
+
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: gerhard
+
* User: user01
email: gerhard@recher.de
+
* Email: max@mustermann.de
  
you may use this as a template for Beast
+
* Job files are written as a sort of "shell" commands that are common on Linux systems
simply change all occurrences of "myjobfile" to your actual project name. also change User and email to your settings.
+
* 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 "#"'''
  
example:
+
 
<source lang="bash">
+
== 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.
 +
 
 +
=== Beast ===
 +
<source lang="bash" start="1" highlight="4,7,18,19,22" enclose="div">
 
#!/bin/csh
 
#!/bin/csh
 
#
 
#
# Which account to be charged cpu time
+
## User name (Which account to be charged cpu time)
#$ -A gerhard
+
#$ -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 mail 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,LD_LIBRARY_PATH=/share/apps/beaglenew
 
#
 
#
# Send mail to these users
+
## The job is located in the current working directory.
#$ -M gerhard@recher.de
+
#$ -cwd
 +
## Filenames for output and error log files
 +
#$ -o myjobfile.out
 +
#$ -e myjobfile.err
 
#
 
#
# Mail at beginning/end/on suspension
+
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
 
#$ -m bes
 
#
 
#
# Export these environmental variables
+
## Export these environmental variables
 
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
 
#$ -v PVM_ROOT,LD_LIBRARY_PATH=/share/apps/beaglenew
 
#
 
#
# 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
+
/share/apps/beast210/bin/beast -beagle -beagle_CPU -beagle_instances $NSLOTS -overwrite ./myjobfile.xml > ./myjobfile.out
 +
</source>
  
 +
=== Mr Bayes ===
 +
<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
 +
mpirun -np $NSLOTS /share/apps/mrbayes/mb ./beispiel.nex </dev/null
 +
</source>
 +
 +
=== Raxml ===
 +
<source lang="bash" start="1" highlight="4,7,18,19,22" enclose="div">
 +
#!/bin/csh
 +
#
 +
## User name (Which account to be charged cpu time)
 +
#$ -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
 +
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
 +
#
 +
## 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 $NSLOTS /share/apps/exabayes/exabayes -f aln.phy -q aln.part -n myRun -s 57913 -c config.nex -R 2 -C 2
 +
</source>
 +
 +
=== Iq-Tree ===
 +
<source lang="bash" start="1" highlight="4,7,18,19,22" enclose="div">
 +
#!/bin/csh
 +
#
 +
## User name (Which account to be charged cpu time)
 +
#$ -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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