James: Text replacement - "[pP][bB][sS]" to "SLURM"

2022-10-27T19:33:01Z

Text replacement - "[pP][bB][sS]" to "SLURM"

← Older revision		Revision as of 19:33, 27 October 2022
Line 46:		Line 46:
	</pre>		</pre>

	A ~~PBS~~ Pro batch script must be created to run your job. The first script below shows a MPI parallel run		A SLURM Pro batch script must be created to run your job. The first script below shows a MPI parallel run
	of the above '.nex' input file. This script selects 4 processors (cores) and allows ~~PBS~~ to put them on any		of the above '.nex' input file. This script selects 4 processors (cores) and allows SLURM to put them on any
	compute node. Note, that when running any parallel program one must be cognizant of the scaling		compute node. Note, that when running any parallel program one must be cognizant of the scaling
	properties of its parallel algorithm; in other words, how much does a given job's running time drop		properties of its parallel algorithm; in other words, how much does a given job's running time drop
Line 91:		Line 91:
	This test case should take no more than a couple of minutes to run and will produce SLURM output and		This test case should take no more than a couple of minutes to run and will produce SLURM output and
	error files beginning with the job name 'MRBAYES_mpi'. Other MrBayes specific outputs will also be		error files beginning with the job name 'MRBAYES_mpi'. Other MrBayes specific outputs will also be
	produced. Details on the meaning of the ~~PBS~~ script are covered above in this Wiki's SLURM section. The		produced. Details on the meaning of the SLURM script are covered above in this Wiki's SLURM section. The
	most important lines are '#SBATCH --nodes=4 ntasks=1 mem=1920'. The		most important lines are '#SBATCH --nodes=4 ntasks=1 mem=1920'. The
	first instructs SLURM to select 4 resource 'chunks' each with 1 processor (core) and 1,920 MBs of memory		first instructs SLURM to select 4 resource 'chunks' each with 1 processor (core) and 1,920 MBs of memory

James: Created page with "MrBayes is installed on ANDY and PENZIAS (GPU enabled version). In order to set-up the environment required to run MrBayes corresponding module needs to be loaded first. This is done with

 module load mrbayes

Running MrBayes is a two-step process that first requires the creation of the NEXUS-formatted MrBayes input file and then the SLURM Pro script to run it. MrBayes can be run in serial, MPI-parallel, or GPU-accelerated mode (on PENZIAS only). Here is..."

2022-10-20T20:10:41Z

Created page with "MrBayes is installed on ANDY and PENZIAS (GPU enabled version). In order to set-up the environment required to run MrBayes corresponding module needs to be loaded first. This is done with <pre> module load mrbayes </pre> Running MrBayes is a two-step process that first requires the creation of the NEXUS-formatted MrBayes input file and then the SLURM Pro script to run it. MrBayes can be run in serial, MPI-parallel, or GPU-accelerated mode (on PENZIAS only). Here is..."

New page

MrBayes is installed on ANDY and PENZIAS (GPU enabled version). In order to
set-up the environment required to run MrBayes corresponding module needs to be loaded first. This is done with

<pre>
module load mrbayes
</pre>

Running MrBayes is a two-step process that first requires the creation of the
NEXUS-formatted MrBayes input file and then the SLURM Pro script to run it. MrBayes can be
run in serial, MPI-parallel, or GPU-accelerated mode (on PENZIAS only).

Here is NEXUS input file ('''primates.nex''') which includes both a DATA block and a MRBAYES block.
The MRBAYES block simply contains the MrBayes runtime commands terminated with a semi-colon.
The example below shows 12 mitochondrial DNA sequences of primates and yields at least 1,000
samples from the posterior probability distribution. If you need more detail on generating
the NEXUS file or on MrBayes in general, please check the MrBayes Wiki here [http://mrbayes.sourceforge.net]
and the online manual here [http://mrbayes.scs.fsu.edu/wiki/index.php/Main_Page on-line manual].

<pre>
#NEXUS

begin data;
dimensions ntax=12 nchar=898;
format datatype=dna interleave=no gap=-;
matrix
Tarsius_syrichta AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT
Lemur_catta AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT
Homo_sapiens AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT
Pan AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT
Gorilla AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT
Pongo AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT
Hylobates AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT
Macaca_fuscata AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT
M_mulatta AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT
M_fascicularis AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT
M_sylvanus AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT
Saimiri_sciureus AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT
;
end;

begin mrbayes;
set autoclose=yes nowarn=yes;
lset nst=6 rates=gamma;
mcmc nruns=1 ngen=10000 samplefreq=10;
end;
</pre>

A PBS Pro batch script must be created to run your job. The first script below shows a MPI parallel run
of the above '.nex' input file. This script selects 4 processors (cores) and allows PBS to put them on any
compute node. Note, that when running any parallel program one must be cognizant of the scaling
properties of its parallel algorithm; in other words, how much does a given job's running time drop
as one doubles the number of processors used. All parallel programs arrive at point of diminishing returns
that depend on the algorithm, size of the problem being solved, and the performance features of the
system that it is being run on. We might have chosen to run this job on 8, 16, or 32 processors (cores),
but would only do so if the improvement in performance scales. Improvements of less than 25% after a
doubling are an indication of a reasonable maximum number of processors under those particular set
of circumstances

Here is the 4 processor MPI parallel SLURM batch script:

<pre>
#!/bin/bash
#SBATCH --partition production
#SBATCH --job-name MRBAYES_mpi
#SBATCH --nodes=4
#SBATCH --ntasks=1
#SBATCH --mem=1920

# Find out name of master execution host (compute node)
echo -n ">>>> SBATCH Master compute node is: "
hostname

# You must explicitly change to the working directory in SLURM
cd $SLURM_SUBMIT_DIR

# Use 'mpirun' and point to the MPI parallel executable to run
echo ">>>> Begin MRBAYES MPI Run ..."
echo ""
mpirun -np 4 /share/apps/mrbayes/default/bin/mb ./primates.nex > primates.out 2>&1
echo ""
echo ">>>> End MRBAYES MPI Run ..."
</pre>

This script can be dropped into a file (say 'mrbayes_mpi.job) on ANDY and
run with:

<pre>
qsub mrbayes_mpi.job
</pre>

This test case should take no more than a couple of minutes to run and will produce SLURM output and
error files beginning with the job name 'MRBAYES_mpi'. Other MrBayes specific outputs will also be
produced. Details on the meaning of the PBS script are covered above in this Wiki's SLURM section. The
most important lines are '#SBATCH --nodes=4 ntasks=1 mem=1920'. The
first instructs SLURM to select 4 resource 'chunks' each with 1 processor (core) and 1,920 MBs of memory
in it for the job (on ANDY as much as 2,880 MBs might have been selected, on PENZIAS this number is 3860mb).
The second line instructs SLURM to place this job wherever the least used resources are found (i.e. freely).
The master compute node that it finally selects to run your job will be printed in the SLURM output file by the 'hostname' command.
As this is a parallel job, other compute nodes may also be called into service to complete this job.

The CUNY HPC Center also provides a serial version of MrBayes. A SLURM batch script for running the
serial version is easy to prepare from the above by making a few changes. Here is a listing of the
differences between the above MPI script and the serial script:

<pre>
3,4c3,4
< #SBATCH --job-name MRBAYES_mpi
< #SBATCH --nodes=4
#SBATCH --ntasks=1
#SBATCH --mem=2880
---
> #SBATCH --job-name MRBAYES_serial
> #SBATCH --nodes=1
#SBATCH --ntasks=1
16c16
< echo ">>>> Begin MRBAYES MPI Run ..."
---
> echo ">>>> Begin MRBAYES Serial Run ..."
18c18
< mpirun -np 4 /share/apps/mrbayes/default/bin/mb ./primates.nex
---
> /share/apps/mrbayes/default/bin/mb-serial ./primates.nex
20c20
< echo ">>>> End MRBAYES MPI Run ..."
---
> echo ">>>> End MRBAYES Serial Run ..."
</pre>

Finally, it is possible to run MrBayes in GPU-accelerated mode on PENZIAS (only). This is an experimental
version of the code and users are cautioned to check their results and note their performance to
be sure they are getting accurate answers in shorter time periods. Nothing is worse in HPC than
going in the wrong direction, more slowly (this principle applies to NYC Taxi rides as well). Here
is yet another script that will run the GPU-accelerated version of MrBayes (again, on PENZIAS only).

<pre>
#!/bin/bash
#SBATCH --partition production
#SBATCH --job-name MRBAYES_gpu
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --gres=gpu:1
#SBATCH --accel=kepler

# Find out name of master execution host (compute node)
echo -n ">>>> SLURM Master compute node is: "
hostname

# You must explicitly change to the working directory in SLURM
cd $SLURM_SUBMIT_DIR

# Point to the GPU parallel executable to run
echo ">>>> Begin MRBAYES GPU Run ..."
echo ""
/share/apps/mrbayes/default/bin/mb-gpu ./primates.nex
echo ""
echo ">>>> End MRBAYES GPU Run ..."
</pre>

There are several differences worth pointing out. First, he resource request line '-l select' request more that just
a processor and some memory, but also a GPU (ntasks=1) and a particular flavor of GPU (accel=kepler).
Second the the name of the executable, is now 'mb-gpu', which selects the GPU-accelerated
version of the code.

MRBAYES - Revision history

James: Text replacement - "[pP][bB][sS]" to "SLURM"