Answers.Body: <p>It is not trivial getting MB to run in parallel because from my experience it required granting privileges to regular users. I used this via MPI (MPICH) on a Slurm/SGE cluster.</p>
  <p>Essentially, this is coarse grain parallel processing.</p>
  <p>It is certainly worth parallelizing MB because each chain can be run on a different nodes and avoids RAM bottlenecks on complex models and big data sets. For example, 8 to 10+ chains can be run, ensuring convergence quickly by running chains across nodes.</p>
  <hr />
  <p><strong>Update</strong> I later found it was much easier to run via EasyBuild with OpenMPI using the command <code>runmpi</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-17T15:05:16.633Z
Answers.Text: Interesting, so this might be an MPI permissions issue then. I will run this by the university IT folks and see if they can help me figure this out. I'll report back.
Answers.UserDisplayName: Pascal
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-17T18:42:52.647Z
Answers.Text: This seems to most likely have been an issue with mpi on my system, rather than with MrBayes, and this now works for me, although I'm not sure what changed.
Answers.UserDisplayName: Pascal
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-14T13:34:45.963Z
Answers.LastActivityDate: 2023-10-28T01:03:07.463Z
Answers.LastEditDate: 2023-10-28T01:03:07.463Z
Answers.UserDisplayName: M__
Body: <p>I compiled MrBayes v3.2.7 from github, with the configuration options <code>./configure --without-beagle --enable-mpi</code>. The program is called mb.</p>
  
  <p>I tried one of the included example files "sceloporus.nex". I find that if I run <code>mb sceloporus.nex</code>, then it appears to make progress, and writes files to disk. </p>
  
  <p>I used MPI with 1 core, and it behaves as before, making progress, writing files to disk.</p>
  
  <p>But if I run with more than 1 core, using MPI, with <code>mpirun -np 2 mb sceloporus.nex</code>, then it only makes it through some of the analysis setup, doesn't write any files to disk, and just hangs. If I look at <code>top</code>, I see activity on the number of cores I specified. I finally had to manually terminate the program.</p>
  
  <p>Is there something I should be doing differently to have MrBayes properly run in parallel?</p>
  
  <p>Here is a copy of my terminal from these 3 attempts:</p>
  
  <pre><code>[ptitle@iu mbTest]<span class="math-container">$ ls
  sceloporus.nex
  [ptitle@iu mbTest]$</span> ~/MrBayes/src/mb sceloporus.nex 
  
  
                              MrBayes pre-3.2.7 x86_64
  
                        (Bayesian Analysis of Phylogeny)
  
                               (Parallel version)
                           (1 processors available)
  
                Distributed under the GNU General Public License
  
  
                 Type "help" or "help &lt;command&gt;" for information
                       on the commands that are available.
  
                     Type "about" for authorship and general
                         information about the program.
  
  
  
     Executing file "sceloporus.nex"
     DOS line termination
     Longest line length = 1632
     Parsing file
     Expecting NEXUS formatted file
     Reading data block
        Allocated taxon set
        Allocated matrix
        Defining new matrix with 123 taxa and 1606 characters
        Data is Dna
        Missing data coded as ?
        Gaps coded as -
        Taxon   1 -&gt; AZYuJAS289
        Taxon   2 -&gt; AZYuJAS290
        Taxon   3 -&gt; AZlaJAS294
        Taxon   4 -&gt; AZcoTBP271
        Taxon   5 -&gt; AZcoGM1054
        Taxon   6 -&gt; AZcoDGM994
        Taxon   7 -&gt; AZgiP26438
        Taxon   8 -&gt; AZgrGM1012
        Taxon   9 -&gt; AZgrGM1013
        Taxon  10 -&gt; AZgrGM1024
        Taxon  11 -&gt; AZlaDGM856
        Taxon  12 -&gt; AZmaDGM984
        Taxon  13 -&gt; AZmaDGM992
        Taxon  14 -&gt; AZmaRM4401
        Taxon  15 -&gt; AZmaRM4402
        Taxon  16 -&gt; AZmaRM4403
        Taxon  17 -&gt; AZmoGM1045
        Taxon  18 -&gt; AZmoDGM492
        Taxon  19 -&gt; AZmoDGM699
        Taxon  20 -&gt; AZmoDGM704
        Taxon  21 -&gt; AZmoRM4394
        Taxon  22 -&gt; AZpiKWS238
        Taxon  23 -&gt; AZyuDGM826
        Taxon  24 -&gt; AZyuDGM838
        Taxon  25 -&gt; AZyuDGM852
        Taxon  26 -&gt; AZyuDGM858
        Taxon  27 -&gt; AZyuDGM865
        Taxon  28 -&gt; CAfrP25750
        Taxon  29 -&gt; CAimDGM534
        Taxon  30 -&gt; CAimDGM558
        Taxon  31 -&gt; CAimDGM694
        Taxon  32 -&gt; CAimKWS170
        Taxon  33 -&gt; CAinCRF530
        Taxon  34 -&gt; CAinoDGM74
        Taxon  35 -&gt; CAinCRF529
        Taxon  36 -&gt; CAkeDS2SP7
        Taxon  37 -&gt; CAkeP26556
        Taxon  38 -&gt; CAla78323
        Taxon  39 -&gt; CAlaDAW220
        Taxon  40 -&gt; CAlaM14610
        Taxon  41 -&gt; CAlaM23289
        Taxon  42 -&gt; CAmoJQR132
        Taxon  43 -&gt; CArvJOS138
        Taxon  44 -&gt; CArvESA441
        Taxon  45 -&gt; CAsaBUR167
        Taxon  46 -&gt; CAsaMCFMAG
        Taxon  47 -&gt; CAsarnMCC
        Taxon  48 -&gt; CAsa150079
        Taxon  49 -&gt; CAsa150088
        Taxon  50 -&gt; CAsa179886
        Taxon  51 -&gt; CAsaM19838
        Taxon  52 -&gt; CAsdDGM691
        Taxon  53 -&gt; CAsdDGM748
        Taxon  54 -&gt; CAsdSWT701
        Taxon  55 -&gt; MXBCDGM474
        Taxon  56 -&gt; MXBCDGM475
        Taxon  57 -&gt; MXBCDGM486
        Taxon  58 -&gt; MXchRM4860
        Taxon  59 -&gt; MXduA83134
        Taxon  60 -&gt; MXsoM14488
        Taxon  61 -&gt; MXsoP26449
        Taxon  62 -&gt; MXso210345
        Taxon  63 -&gt; NMdoTWR230
        Taxon  64 -&gt; NMedDGM938
        Taxon  65 -&gt; NMhiU48819
        Taxon  66 -&gt; NMluGM947
        Taxon  67 -&gt; NMluDGM948
        Taxon  68 -&gt; NMsiDGM891
        Taxon  69 -&gt; NMsoDGM900
        Taxon  70 -&gt; NMsoDGM904
        Taxon  71 -&gt; NMsoDGM905
        Taxon  72 -&gt; NMvaDGM924
        Taxon  73 -&gt; NVchDGM612
        Taxon  74 -&gt; NVch162077
        Taxon  75 -&gt; NVclDGM296
        Taxon  76 -&gt; NVclDGM678
        Taxon  77 -&gt; NVesDGM210
        Taxon  78 -&gt; NVlyDGM610
        Taxon  79 -&gt; NVwaDGM608
        Taxon  80 -&gt; UTemGM1058
        Taxon  81 -&gt; UTgrDGM156
        Taxon  82 -&gt; UTgrDGM169
        Taxon  83 -&gt; UTgrDGM175
        Taxon  84 -&gt; UTkaGM1034
        Taxon  85 -&gt; UTsnDM142
        Taxon  86 -&gt; UTsnDG043
        Taxon  87 -&gt; UTsnnDGM645
        Taxon  88 -&gt; UTwsGM261
        Taxon  89 -&gt; UTwsGM263
        Taxon  90 -&gt; UTwsnDGM751
        Taxon  91 -&gt; UTwsJRM4437
        Taxon  92 -&gt; hunsiM376
        Taxon  93 -&gt; hunsiM377
        Taxon  94 -&gt; hunsiRWM619
        Taxon  95 -&gt; lickGM378
        Taxon  96 -&gt; lineatulus
        Taxon  97 -&gt; orcuOM14377
        Taxon  98 -&gt; orcuOM14453
        Taxon  99 -&gt; orcuOM14673
        Taxon 100 -&gt; orcuRWM798
        Taxon 101 -&gt; orcuS201108
        Taxon 102 -&gt; orcuS201124
        Taxon 103 -&gt; zostZ16290
        Taxon 104 -&gt; zosV161292
        Taxon 105 -&gt; zosV161293
        Taxon 106 -&gt; zosV161311
        Taxon 107 -&gt; zosWM1890
        Taxon 108 -&gt; zosGM364
        Taxon 109 -&gt; zosGM365
        Taxon 110 -&gt; zosGM387
        Taxon 111 -&gt; zosGM393
        Taxon 112 -&gt; zosRO332
        Taxon 113 -&gt; zosOM37006
        Taxon 114 -&gt; zosWM1601
        Taxon 115 -&gt; clarkii
        Taxon 116 -&gt; edwardti80
        Taxon 117 -&gt; smaragdnus
        Taxon 118 -&gt; graciosus
        Taxon 119 -&gt; grammicus
        Taxon 120 -&gt; maculosus
        Taxon 121 -&gt; bicanthlis
        Taxon 122 -&gt; torquatus
        Taxon 123 -&gt; variabilis
        Successfully read matrix
        Setting default partition (does not divide up characters)
        Setting model defaults
        Seed (for generating default start values) = 1544128156
        Setting output file names to "sceloporus.nex.run&lt;i&gt;.&lt;p|t&gt;"
     Exiting data block
     Reading mrbayes block
        Excluding character(s)
        Setting Nst to 6
        Setting Rates to Gamma
        Successfully set likelihood model parameters
        Setting Brlenspr to Unconstrained:GammaDir(1.00,1.0000,0.70,0.50)
        Successfully set prior model parameters
        Setting number of generations to 5000000
        Running Markov chain
        MCMC stamp = 9284864458
        Seed = 753696747
        Swapseed = 1544128156
        Model settings:
  
           Data not partitioned --
              Datatype  = DNA
              Nucmodel  = 4by4
              Nst       = 6
                          Substitution rates, expressed as proportions
                          of the rate sum, have a Dirichlet prior
                          (1.00,1.00,1.00,1.00,1.00,1.00)
              Covarion  = No
              # States  = 4
                          State frequencies have a Dirichlet prior
                          (1.00,1.00,1.00,1.00)
              Rates     = Gamma
                          The distribution is approximated using 4 categories.
                          Shape parameter is exponentially
                          distributed with parameter (1.00).
  
        Active parameters: 
  
           Parameters
           ---------------------
           Revmat              1
           Statefreq           2
           Shape               3
           Ratemultiplier      4
           Topology            5
           Brlens              6
           ---------------------
  
           1 --  Parameter  = Revmat
                 Type       = Rates of reversible rate matrix
                 Prior      = Dirichlet(1.00,1.00,1.00,1.00,1.00,1.00)
  
           2 --  Parameter  = Pi
                 Type       = Stationary state frequencies
                 Prior      = Dirichlet
  
           3 --  Parameter  = Alpha
                 Type       = Shape of scaled gamma distribution of site rates
                 Prior      = Exponential(1.00)
  
           4 --  Parameter  = Ratemultiplier
                 Type       = Partition-specific rate multiplier
                 Prior      = Fixed(1.0)
  
           5 --  Parameter  = Tau
                 Type       = Topology
                 Prior      = All topologies equally probable a priori
                 Subparam.  = V
  
           6 --  Parameter  = V
                 Type       = Branch lengths
                 Prior      = Unconstrained:GammaDir(1.0,1.0000,0.7,0.5)
  
  
        Number of chains per MPI processor = 8
  
        The MCMC sampler will use the following moves:
           With prob.  Chain will use move
              0.94 %   Dirichlet(Revmat)
              0.94 %   Slider(Revmat)
              0.94 %   Dirichlet(Pi)
              0.94 %   Slider(Pi)
              1.89 %   Multiplier(Alpha)
              9.43 %   ExtSPR(Tau,V)
              9.43 %   ExtTBR(Tau,V)
              9.43 %   NNI(Tau,V)
              9.43 %   ParsSPR(Tau,V)
             37.74 %   Multiplier(V)
             13.21 %   Nodeslider(V)
              5.66 %   TLMultiplier(V)
  
        Division 1 has 624 unique site patterns
        Initializing conditional likelihoods
        Using standard FMA likelihood calculator for division 1 (single-precision)
  
        Initial log likelihoods and log prior probs for run 1:
           Chain 1 -- -38239.042144 -- 53.554896
           Chain 2 -- -37743.352685 -- 53.554896
           Chain 3 -- -38049.750737 -- 53.554896
           Chain 4 -- -38759.582835 -- 53.554896
  
        Initial log likelihoods and log prior probs for run 2:
           Chain 1 -- -38348.591921 -- 53.554896
           Chain 2 -- -39602.594468 -- 53.554896
           Chain 3 -- -38874.065643 -- 53.554896
           Chain 4 -- -39227.723762 -- 53.554896
  
  
        Using a relative burnin of 25.0 % for diagnostics
  
        Chain results (5000000 generations requested):
  
           0 -- [-38239.042] (-37743.353) (-38049.751) (-38759.583) * [-38348.592] (-39602.594) (-38874.066) (-39227.724) (...0 remote chains...) 
  ^C
  [ptitle@iu mbTest]<span class="math-container">$ ls
  sceloporus.nex  sceloporus.nex.mcmc  sceloporus.nex.run1.p  sceloporus.nex.run1.t  sceloporus.nex.run2.p  sceloporus.nex.run2.t
  [ptitle@iu mbTest]$</span> mpirun -np 1 ~/MrBayes/src/mb sceloporus.nex 
  
  
                              MrBayes pre-3.2.7 x86_64
  
                        (Bayesian Analysis of Phylogeny)
  
                               (Parallel version)
                           (1 processors available)
  
                Distributed under the GNU General Public License
  
  
                 Type "help" or "help &lt;command&gt;" for information
                       on the commands that are available.
  
                     Type "about" for authorship and general
                         information about the program.
  
  
  
     Executing file "sceloporus.nex"
     DOS line termination
     Longest line length = 1632
     Parsing file
     Expecting NEXUS formatted file
     Reading data block
        Allocated taxon set
        Allocated matrix
        Defining new matrix with 123 taxa and 1606 characters
        Data is Dna
        Missing data coded as ?
        Gaps coded as -
        Taxon   1 -&gt; AZYuJAS289
        Taxon   2 -&gt; AZYuJAS290
        Taxon   3 -&gt; AZlaJAS294
        Taxon   4 -&gt; AZcoTBP271
        Taxon   5 -&gt; AZcoGM1054
        Taxon   6 -&gt; AZcoDGM994
        Taxon   7 -&gt; AZgiP26438
        Taxon   8 -&gt; AZgrGM1012
        Taxon   9 -&gt; AZgrGM1013
        Taxon  10 -&gt; AZgrGM1024
        Taxon  11 -&gt; AZlaDGM856
        Taxon  12 -&gt; AZmaDGM984
        Taxon  13 -&gt; AZmaDGM992
        Taxon  14 -&gt; AZmaRM4401
        Taxon  15 -&gt; AZmaRM4402
        Taxon  16 -&gt; AZmaRM4403
        Taxon  17 -&gt; AZmoGM1045
        Taxon  18 -&gt; AZmoDGM492
        Taxon  19 -&gt; AZmoDGM699
        Taxon  20 -&gt; AZmoDGM704
        Taxon  21 -&gt; AZmoRM4394
        Taxon  22 -&gt; AZpiKWS238
        Taxon  23 -&gt; AZyuDGM826
        Taxon  24 -&gt; AZyuDGM838
        Taxon  25 -&gt; AZyuDGM852
        Taxon  26 -&gt; AZyuDGM858
        Taxon  27 -&gt; AZyuDGM865
        Taxon  28 -&gt; CAfrP25750
        Taxon  29 -&gt; CAimDGM534
        Taxon  30 -&gt; CAimDGM558
        Taxon  31 -&gt; CAimDGM694
        Taxon  32 -&gt; CAimKWS170
        Taxon  33 -&gt; CAinCRF530
        Taxon  34 -&gt; CAinoDGM74
        Taxon  35 -&gt; CAinCRF529
        Taxon  36 -&gt; CAkeDS2SP7
        Taxon  37 -&gt; CAkeP26556
        Taxon  38 -&gt; CAla78323
        Taxon  39 -&gt; CAlaDAW220
        Taxon  40 -&gt; CAlaM14610
        Taxon  41 -&gt; CAlaM23289
        Taxon  42 -&gt; CAmoJQR132
        Taxon  43 -&gt; CArvJOS138
        Taxon  44 -&gt; CArvESA441
        Taxon  45 -&gt; CAsaBUR167
        Taxon  46 -&gt; CAsaMCFMAG
        Taxon  47 -&gt; CAsarnMCC
        Taxon  48 -&gt; CAsa150079
        Taxon  49 -&gt; CAsa150088
        Taxon  50 -&gt; CAsa179886
        Taxon  51 -&gt; CAsaM19838
        Taxon  52 -&gt; CAsdDGM691
        Taxon  53 -&gt; CAsdDGM748
        Taxon  54 -&gt; CAsdSWT701
        Taxon  55 -&gt; MXBCDGM474
        Taxon  56 -&gt; MXBCDGM475
        Taxon  57 -&gt; MXBCDGM486
        Taxon  58 -&gt; MXchRM4860
        Taxon  59 -&gt; MXduA83134
        Taxon  60 -&gt; MXsoM14488
        Taxon  61 -&gt; MXsoP26449
        Taxon  62 -&gt; MXso210345
        Taxon  63 -&gt; NMdoTWR230
        Taxon  64 -&gt; NMedDGM938
        Taxon  65 -&gt; NMhiU48819
        Taxon  66 -&gt; NMluGM947
        Taxon  67 -&gt; NMluDGM948
        Taxon  68 -&gt; NMsiDGM891
        Taxon  69 -&gt; NMsoDGM900
        Taxon  70 -&gt; NMsoDGM904
        Taxon  71 -&gt; NMsoDGM905
        Taxon  72 -&gt; NMvaDGM924
        Taxon  73 -&gt; NVchDGM612
        Taxon  74 -&gt; NVch162077
        Taxon  75 -&gt; NVclDGM296
        Taxon  76 -&gt; NVclDGM678
        Taxon  77 -&gt; NVesDGM210
        Taxon  78 -&gt; NVlyDGM610
        Taxon  79 -&gt; NVwaDGM608
        Taxon  80 -&gt; UTemGM1058
        Taxon  81 -&gt; UTgrDGM156
        Taxon  82 -&gt; UTgrDGM169
        Taxon  83 -&gt; UTgrDGM175
        Taxon  84 -&gt; UTkaGM1034
        Taxon  85 -&gt; UTsnDM142
        Taxon  86 -&gt; UTsnDG043
        Taxon  87 -&gt; UTsnnDGM645
        Taxon  88 -&gt; UTwsGM261
        Taxon  89 -&gt; UTwsGM263
        Taxon  90 -&gt; UTwsnDGM751
        Taxon  91 -&gt; UTwsJRM4437
        Taxon  92 -&gt; hunsiM376
        Taxon  93 -&gt; hunsiM377
        Taxon  94 -&gt; hunsiRWM619
        Taxon  95 -&gt; lickGM378
        Taxon  96 -&gt; lineatulus
        Taxon  97 -&gt; orcuOM14377
        Taxon  98 -&gt; orcuOM14453
        Taxon  99 -&gt; orcuOM14673
        Taxon 100 -&gt; orcuRWM798
        Taxon 101 -&gt; orcuS201108
        Taxon 102 -&gt; orcuS201124
        Taxon 103 -&gt; zostZ16290
        Taxon 104 -&gt; zosV161292
        Taxon 105 -&gt; zosV161293
        Taxon 106 -&gt; zosV161311
        Taxon 107 -&gt; zosWM1890
        Taxon 108 -&gt; zosGM364
        Taxon 109 -&gt; zosGM365
        Taxon 110 -&gt; zosGM387
        Taxon 111 -&gt; zosGM393
        Taxon 112 -&gt; zosRO332
        Taxon 113 -&gt; zosOM37006
        Taxon 114 -&gt; zosWM1601
        Taxon 115 -&gt; clarkii
        Taxon 116 -&gt; edwardti80
        Taxon 117 -&gt; smaragdnus
        Taxon 118 -&gt; graciosus
        Taxon 119 -&gt; grammicus
        Taxon 120 -&gt; maculosus
        Taxon 121 -&gt; bicanthlis
        Taxon 122 -&gt; torquatus
        Taxon 123 -&gt; variabilis
        Successfully read matrix
        Setting default partition (does not divide up characters)
        Setting model defaults
        Seed (for generating default start values) = 1544128192
        Setting output file names to "sceloporus.nex.run&lt;i&gt;.&lt;p|t&gt;"
     Exiting data block
     Reading mrbayes block
        Excluding character(s)
        Setting Nst to 6
        Setting Rates to Gamma
        Successfully set likelihood model parameters
        Setting Brlenspr to Unconstrained:GammaDir(1.00,1.0000,0.70,0.50)
        Successfully set prior model parameters
        Setting number of generations to 5000000
        Running Markov chain
        MCMC stamp = 9909051894
        Seed = 1261289135
        Swapseed = 1544128192
        Model settings:
  
           Data not partitioned --
              Datatype  = DNA
              Nucmodel  = 4by4
              Nst       = 6
                          Substitution rates, expressed as proportions
                          of the rate sum, have a Dirichlet prior
                          (1.00,1.00,1.00,1.00,1.00,1.00)
              Covarion  = No
              # States  = 4
                          State frequencies have a Dirichlet prior
                          (1.00,1.00,1.00,1.00)
              Rates     = Gamma
                          The distribution is approximated using 4 categories.
                          Shape parameter is exponentially
                          distributed with parameter (1.00).
  
        Active parameters: 
  
           Parameters
           ---------------------
           Revmat              1
           Statefreq           2
           Shape               3
           Ratemultiplier      4
           Topology            5
           Brlens              6
           ---------------------
  
           1 --  Parameter  = Revmat
                 Type       = Rates of reversible rate matrix
                 Prior      = Dirichlet(1.00,1.00,1.00,1.00,1.00,1.00)
  
           2 --  Parameter  = Pi
                 Type       = Stationary state frequencies
                 Prior      = Dirichlet
  
           3 --  Parameter  = Alpha
                 Type       = Shape of scaled gamma distribution of site rates
                 Prior      = Exponential(1.00)
  
           4 --  Parameter  = Ratemultiplier
                 Type       = Partition-specific rate multiplier
                 Prior      = Fixed(1.0)
  
           5 --  Parameter  = Tau
                 Type       = Topology
                 Prior      = All topologies equally probable a priori
                 Subparam.  = V
  
           6 --  Parameter  = V
                 Type       = Branch lengths
                 Prior      = Unconstrained:GammaDir(1.0,1.0000,0.7,0.5)
  
  
        Number of chains per MPI processor = 8
  
        The MCMC sampler will use the following moves:
           With prob.  Chain will use move
              0.94 %   Dirichlet(Revmat)
              0.94 %   Slider(Revmat)
              0.94 %   Dirichlet(Pi)
              0.94 %   Slider(Pi)
              1.89 %   Multiplier(Alpha)
              9.43 %   ExtSPR(Tau,V)
              9.43 %   ExtTBR(Tau,V)
              9.43 %   NNI(Tau,V)
              9.43 %   ParsSPR(Tau,V)
             37.74 %   Multiplier(V)
             13.21 %   Nodeslider(V)
              5.66 %   TLMultiplier(V)
  
        Division 1 has 624 unique site patterns
        Initializing conditional likelihoods
        Using standard FMA likelihood calculator for division 1 (single-precision)
  
        Initial log likelihoods and log prior probs for run 1:
           Chain 1 -- -39098.978535 -- 53.554896
           Chain 2 -- -38054.044640 -- 53.554896
           Chain 3 -- -39425.015629 -- 53.554896
           Chain 4 -- -40157.756230 -- 53.554896
  
        Initial log likelihoods and log prior probs for run 2:
           Chain 1 -- -40084.553712 -- 53.554896
           Chain 2 -- -39002.725314 -- 53.554896
           Chain 3 -- -38719.752582 -- 53.554896
           Chain 4 -- -39156.129424 -- 53.554896
  
  
        Using a relative burnin of 25.0 % for diagnostics
  
        Chain results (5000000 generations requested):
  
           0 -- [-39098.979] (-38054.045) (-39425.016) (-40157.756) * [-40084.554] (-39002.725) (-38719.753) (-39156.129) (...0 remote chains...) 
  ^C[ptitle@iu mbTest]$ mpirun -np 2 ~/MrBayes/src/mb sceloporus.nex 
  
  
                              MrBayes pre-3.2.7 x86_64
  
                        (Bayesian Analysis of Phylogeny)
  
                               (Parallel version)
                           (2 processors available)
  
                Distributed under the GNU General Public License
  
  
                 Type "help" or "help &lt;command&gt;" for information
                       on the commands that are available.
  
                     Type "about" for authorship and general
                         information about the program.
  
  
  
     Executing file "sceloporus.nex"
     DOS line termination
     Longest line length = 1632
     Parsing file
     Expecting NEXUS formatted file
     Reading data block
        Allocated taxon set
        Allocated matrix
        Defining new matrix with 123 taxa and 1606 characters
        Data is Dna
        Missing data coded as ?
        Gaps coded as -
        Taxon   1 -&gt; AZYuJAS289
        Taxon   2 -&gt; AZYuJAS290
        Taxon   3 -&gt; AZlaJAS294
        Taxon   4 -&gt; AZcoTBP271
        Taxon   5 -&gt; AZcoGM1054
        Taxon   6 -&gt; AZcoDGM994
        Taxon   7 -&gt; AZgiP26438
        Taxon   8 -&gt; AZgrGM1012
        Taxon   9 -&gt; AZgrGM1013
        Taxon  10 -&gt; AZgrGM1024
  ^C[ptitle@iu mbTest]$ 
  </code></pre>
  
Tags: <phylogenetics><phylogeny><molecular-genetics><mrbayes>
Title: MrBayes runs as single-core, but hangs when multi-core
ThreadText: # MrBayes runs as single-core, but hangs when multi-core
  
  (Asked by: username_0 on 2018-12-06)
  
  I compiled MrBayes v3.2.7 from github, with the configuration options `./configure --without-beagle --enable-mpi`. The program is called mb.
  
  I tried one of the included example files "sceloporus.nex". I find that if I run `mb sceloporus.nex`, then it appears to make progress, and writes files to disk.
  
  I used MPI with 1 core, and it behaves as before, making progress, writing files to disk.
  
  But if I run with more than 1 core, using MPI, with `mpirun -np 2 mb sceloporus.nex`, then it only makes it through some of the analysis setup, doesn't write any files to disk, and just hangs. If I look at `top`, I see activity on the number of cores I specified. I finally had to manually terminate the program.
  
  Is there something I should be doing differently to have MrBayes properly run in parallel?
  
  Here is a copy of my terminal from these 3 attempts:
  
  ```
  [ptitle@iu mbTest]$ ls
  sceloporus.nex
  [ptitle@iu mbTest]$ ~/MrBayes/src/mb sceloporus.nex 
  
                              MrBayes pre-3.2.7 x86_64
  
                        (Bayesian Analysis of Phylogeny)
  
                               (Parallel version)
                           (1 processors available)
  
                Distributed under the GNU General Public License
  
                 Type "help" or "help <command>" for information
                       on the commands that are available.
  
                     Type "about" for authorship and general
                         information about the program.
  
     Executing file "sceloporus.nex"
     DOS line termination
     Longest line length = 1632
     Parsing file
     Expecting NEXUS formatted file
     Reading data block
        Allocated taxon set
        Allocated matrix
        Defining new matrix with 123 taxa and 1606 characters
        Data is Dna
        Missing data coded as ?
        Gaps coded as -
        Taxon   1 -> AZYuJAS289
        Taxon   2 -> AZYuJAS290
        Taxon   3 -> AZlaJAS294
        Taxon   4 -> AZcoTBP271
        Taxon   5 -> AZcoGM1054
        Taxon   6 -> AZcoDGM994
        Taxon   7 -> AZgiP26438
        Taxon   8 -> AZgrGM1012
        Taxon   9 -> AZgrGM1013
        Taxon  10 -> AZgrGM1024
        Taxon  11 -> AZlaDGM856
        Taxon  12 -> AZmaDGM984
        Taxon  13 -> AZmaDGM992
        Taxon  14 -> AZmaRM4401
        Taxon  15 -> AZmaRM4402
        Taxon  16 -> AZmaRM4403
        Taxon  17 -> AZmoGM1045
        Taxon  18 -> AZmoDGM492
        Taxon  19 -> AZmoDGM699
        Taxon  20 -> AZmoDGM704
        Taxon  21 -> AZmoRM4394
        Taxon  22 -> AZpiKWS238
        Taxon  23 -> AZyuDGM826
        Taxon  24 -> AZyuDGM838
        Taxon  25 -> AZyuDGM852
        Taxon  26 -> AZyuDGM858
        Taxon  27 -> AZyuDGM865
        Taxon  28 -> CAfrP25750
        Taxon  29 -> CAimDGM534
        Taxon  30 -> CAimDGM558
        Taxon  31 -> CAimDGM694
        Taxon  32 -> CAimKWS170
        Taxon  33 -> CAinCRF530
        Taxon  34 -> CAinoDGM74
        Taxon  35 -> CAinCRF529
        Taxon  36 -> CAkeDS2SP7
        Taxon  37 -> CAkeP26556
        Taxon  38 -> CAla78323
        Taxon  39 -> CAlaDAW220
        Taxon  40 -> CAlaM14610
        Taxon  41 -> CAlaM23289
        Taxon  42 -> CAmoJQR132
        Taxon  43 -> CArvJOS138
        Taxon  44 -> CArvESA441
        Taxon  45 -> CAsaBUR167
        Taxon  46 -> CAsaMCFMAG
        Taxon  47 -> CAsarnMCC
        Taxon  48 -> CAsa150079
        Taxon  49 -> CAsa150088
        Taxon  50 -> CAsa179886
        Taxon  51 -> CAsaM19838
        Taxon  52 -> CAsdDGM691
        Taxon  53 -> CAsdDGM748
        Taxon  54 -> CAsdSWT701
        Taxon  55 -> MXBCDGM474
        Taxon  56 -> MXBCDGM475
        Taxon  57 -> MXBCDGM486
        Taxon  58 -> MXchRM4860
        Taxon  59 -> MXduA83134
        Taxon  60 -> MXsoM14488
        Taxon  61 -> MXsoP26449
        Taxon  62 -> MXso210345
        Taxon  63 -> NMdoTWR230
        Taxon  64 -> NMedDGM938
        Taxon  65 -> NMhiU48819
        Taxon  66 -> NMluGM947
        Taxon  67 -> NMluDGM948
        Taxon  68 -> NMsiDGM891
        Taxon  69 -> NMsoDGM900
        Taxon  70 -> NMsoDGM904
        Taxon  71 -> NMsoDGM905
        Taxon  72 -> NMvaDGM924
        Taxon  73 -> NVchDGM612
        Taxon  74 -> NVch162077
        Taxon  75 -> NVclDGM296
        Taxon  76 -> NVclDGM678
        Taxon  77 -> NVesDGM210
        Taxon  78 -> NVlyDGM610
        Taxon  79 -> NVwaDGM608
        Taxon  80 -> UTemGM1058
        Taxon  81 -> UTgrDGM156
        Taxon  82 -> UTgrDGM169
        Taxon  83 -> UTgrDGM175
        Taxon  84 -> UTkaGM1034
        Taxon  85 -> UTsnDM142
        Taxon  86 -> UTsnDG043
        Taxon  87 -> UTsnnDGM645
        Taxon  88 -> UTwsGM261
        Taxon  89 -> UTwsGM263
        Taxon  90 -> UTwsnDGM751
        Taxon  91 -> UTwsJRM4437
        Taxon  92 -> hunsiM376
        Taxon  93 -> hunsiM377
        Taxon  94 -> hunsiRWM619
        Taxon  95 -> lickGM378
        Taxon  96 -> lineatulus
        Taxon  97 -> orcuOM14377
        Taxon  98 -> orcuOM14453
        Taxon  99 -> orcuOM14673
        Taxon 100 -> orcuRWM798
        Taxon 101 -> orcuS201108
        Taxon 102 -> orcuS201124
        Taxon 103 -> zostZ16290
        Taxon 104 -> zosV161292
        Taxon 105 -> zosV161293
        Taxon 106 -> zosV161311
        Taxon 107 -> zosWM1890
        Taxon 108 -> zosGM364
        Taxon 109 -> zosGM365
        Taxon 110 -> zosGM387
        Taxon 111 -> zosGM393
        Taxon 112 -> zosRO332
        Taxon 113 -> zosOM37006
        Taxon 114 -> zosWM1601
        Taxon 115 -> clarkii
        Taxon 116 -> edwardti80
        Taxon 117 -> smaragdnus
        Taxon 118 -> graciosus
        Taxon 119 -> grammicus
        Taxon 120 -> maculosus
        Taxon 121 -> bicanthlis
        Taxon 122 -> torquatus
        Taxon 123 -> variabilis
        Successfully read matrix
        Setting default partition (does not divide up characters)
        Setting model defaults
        Seed (for generating default start values) = 1544128156
        Setting output file names to "sceloporus.nex.run<i>.<p|t>"
     Exiting data block
     Reading mrbayes block
        Excluding character(s)
        Setting Nst to 6
        Setting Rates to Gamma
        Successfully set likelihood model parameters
        Setting Brlenspr to Unconstrained:GammaDir(1.00,1.0000,0.70,0.50)
        Successfully set prior model parameters
        Setting number of generations to 5000000
        Running Markov chain
        MCMC stamp = 9284864458
        Seed = 753696747
        Swapseed = 1544128156
        Model settings:
  
           Data not partitioned --
              Datatype  = DNA
              Nucmodel  = 4by4
              Nst       = 6
                          Substitution rates, expressed as proportions
                          of the rate sum, have a Dirichlet prior
                          (1.00,1.00,1.00,1.00,1.00,1.00)
              Covarion  = No
              # States  = 4
                          State frequencies have a Dirichlet prior
                          (1.00,1.00,1.00,1.00)
              Rates     = Gamma
                          The distribution is approximated using 4 categories.
                          Shape parameter is exponentially
                          distributed with parameter (1.00).
  
        Active parameters: 
  
           Parameters
           ---------------------
           Revmat              1
           Statefreq           2
           Shape               3
           Ratemultiplier      4
           Topology            5
           Brlens              6
           ---------------------
  
           1 --  Parameter  = Revmat
                 Type       = Rates of reversible rate matrix
                 Prior      = Dirichlet(1.00,1.00,1.00,1.00,1.00,1.00)
  
           2 --  Parameter  = Pi
                 Type       = Stationary state frequencies
                 Prior      = Dirichlet
  
           3 --  Parameter  = Alpha
                 Type       = Shape of scaled gamma distribution of site rates
                 Prior      = Exponential(1.00)
  
           4 --  Parameter  = Ratemultiplier
                 Type       = Partition-specific rate multiplier
                 Prior      = Fixed(1.0)
  
           5 --  Parameter  = Tau
                 Type       = Topology
                 Prior      = All topologies equally probable a priori
                 Subparam.  = V
  
           6 --  Parameter  = V
                 Type       = Branch lengths
                 Prior      = Unconstrained:GammaDir(1.0,1.0000,0.7,0.5)
  
        Number of chains per MPI processor = 8
  
        The MCMC sampler will use the following moves:
           With prob.  Chain will use move
              0.94 %   Dirichlet(Revmat)
              0.94 %   Slider(Revmat)
              0.94 %   Dirichlet(Pi)
              0.94 %   Slider(Pi)
              1.89 %   Multiplier(Alpha)
              9.43 %   ExtSPR(Tau,V)
              9.43 %   ExtTBR(Tau,V)
              9.43 %   NNI(Tau,V)
              9.43 %   ParsSPR(Tau,V)
             37.74 %   Multiplier(V)
             13.21 %   Nodeslider(V)
              5.66 %   TLMultiplier(V)
  
        Division 1 has 624 unique site patterns
        Initializing conditional likelihoods
        Using standard FMA likelihood calculator for division 1 (single-precision)
  
        Initial log likelihoods and log prior probs for run 1:
           Chain 1 -- -38239.042144 -- 53.554896
           Chain 2 -- -37743.352685 -- 53.554896
           Chain 3 -- -38049.750737 -- 53.554896
           Chain 4 -- -38759.582835 -- 53.554896
  
        Initial log likelihoods and log prior probs for run 2:
           Chain 1 -- -38348.591921 -- 53.554896
           Chain 2 -- -39602.594468 -- 53.554896
           Chain 3 -- -38874.065643 -- 53.554896
           Chain 4 -- -39227.723762 -- 53.554896
  
        Using a relative burnin of 25.0 % for diagnostics
  
        Chain results (5000000 generations requested):
  
           0 -- [-38239.042] (-37743.353) (-38049.751) (-38759.583) * [-38348.592] (-39602.594) (-38874.066) (-39227.724) (...0 remote chains...) 
  ^C
  [ptitle@iu mbTest]$ ls
  sceloporus.nex  sceloporus.nex.mcmc  sceloporus.nex.run1.p  sceloporus.nex.run1.t  sceloporus.nex.run2.p  sceloporus.nex.run2.t
  [ptitle@iu mbTest]$ mpirun -np 1 ~/MrBayes/src/mb sceloporus.nex 
  
                              MrBayes pre-3.2.7 x86_64
  
                        (Bayesian Analysis of Phylogeny)
  
                               (Parallel version)
                           (1 processors available)
  
                Distributed under the GNU General Public License
  
                 Type "help" or "help <command>" for information
                       on the commands that are available.
  
                     Type "about" for authorship and general
                         information about the program.
  
     Executing file "sceloporus.nex"
     DOS line termination
     Longest line length = 1632
     Parsing file
     Expecting NEXUS formatted file
     Reading data block
        Allocated taxon set
        Allocated matrix
        Defining new matrix with 123 taxa and 1606 characters
        Data is Dna
        Missing data coded as ?
        Gaps coded as -
        Taxon   1 -> AZYuJAS289
        Taxon   2 -> AZYuJAS290
        Taxon   3 -> AZlaJAS294
        Taxon   4 -> AZcoTBP271
        Taxon   5 -> AZcoGM1054
        Taxon   6 -> AZcoDGM994
        Taxon   7 -> AZgiP26438
        Taxon   8 -> AZgrGM1012
        Taxon   9 -> AZgrGM1013
        Taxon  10 -> AZgrGM1024
        Taxon  11 -> AZlaDGM856
        Taxon  12 -> AZmaDGM984
        Taxon  13 -> AZmaDGM992
        Taxon  14 -> AZmaRM4401
        Taxon  15 -> AZmaRM4402
        Taxon  16 -> AZmaRM4403
        Taxon  17 -> AZmoGM1045
        Taxon  18 -> AZmoDGM492
        Taxon  19 -> AZmoDGM699
        Taxon  20 -> AZmoDGM704
        Taxon  21 -> AZmoRM4394
        Taxon  22 -> AZpiKWS238
        Taxon  23 -> AZyuDGM826
        Taxon  24 -> AZyuDGM838
        Taxon  25 -> AZyuDGM852
        Taxon  26 -> AZyuDGM858
        Taxon  27 -> AZyuDGM865
        Taxon  28 -> CAfrP25750
        Taxon  29 -> CAimDGM534
        Taxon  30 -> CAimDGM558
        Taxon  31 -> CAimDGM694
        Taxon  32 -> CAimKWS170
        Taxon  33 -> CAinCRF530
        Taxon  34 -> CAinoDGM74
        Taxon  35 -> CAinCRF529
        Taxon  36 -> CAkeDS2SP7
        Taxon  37 -> CAkeP26556
        Taxon  38 -> CAla78323
        Taxon  39 -> CAlaDAW220
        Taxon  40 -> CAlaM14610
        Taxon  41 -> CAlaM23289
        Taxon  42 -> CAmoJQR132
        Taxon  43 -> CArvJOS138
        Taxon  44 -> CArvESA441
        Taxon  45 -> CAsaBUR167
        Taxon  46 -> CAsaMCFMAG
        Taxon  47 -> CAsarnMCC
        Taxon  48 -> CAsa150079
        Taxon  49 -> CAsa150088
        Taxon  50 -> CAsa179886
        Taxon  51 -> CAsaM19838
        Taxon  52 -> CAsdDGM691
        Taxon  53 -> CAsdDGM748
        Taxon  54 -> CAsdSWT701
        Taxon  55 -> MXBCDGM474
        Taxon  56 -> MXBCDGM475
        Taxon  57 -> MXBCDGM486
        Taxon  58 -> MXchRM4860
        Taxon  59 -> MXduA83134
        Taxon  60 -> MXsoM14488
        Taxon  61 -> MXsoP26449
        Taxon  62 -> MXso210345
        Taxon  63 -> NMdoTWR230
        Taxon  64 -> NMedDGM938
        Taxon  65 -> NMhiU48819
        Taxon  66 -> NMluGM947
        Taxon  67 -> NMluDGM948
        Taxon  68 -> NMsiDGM891
        Taxon  69 -> NMsoDGM900
        Taxon  70 -> NMsoDGM904
        Taxon  71 -> NMsoDGM905
        Taxon  72 -> NMvaDGM924
        Taxon  73 -> NVchDGM612
        Taxon  74 -> NVch162077
        Taxon  75 -> NVclDGM296
        Taxon  76 -> NVclDGM678
        Taxon  77 -> NVesDGM210
        Taxon  78 -> NVlyDGM610
        Taxon  79 -> NVwaDGM608
        Taxon  80 -> UTemGM1058
        Taxon  81 -> UTgrDGM156
        Taxon  82 -> UTgrDGM169
        Taxon  83 -> UTgrDGM175
        Taxon  84 -> UTkaGM1034
        Taxon  85 -> UTsnDM142
        Taxon  86 -> UTsnDG043
        Taxon  87 -> UTsnnDGM645
        Taxon  88 -> UTwsGM261
        Taxon  89 -> UTwsGM263
        Taxon  90 -> UTwsnDGM751
        Taxon  91 -> UTwsJRM4437
        Taxon  92 -> hunsiM376
        Taxon  93 -> hunsiM377
        Taxon  94 -> hunsiRWM619
        Taxon  95 -> lickGM378
        Taxon  96 -> lineatulus
        Taxon  97 -> orcuOM14377
        Taxon  98 -> orcuOM14453
        Taxon  99 -> orcuOM14673
        Taxon 100 -> orcuRWM798
        Taxon 101 -> orcuS201108
        Taxon 102 -> orcuS201124
        Taxon 103 -> zostZ16290
        Taxon 104 -> zosV161292
        Taxon 105 -> zosV161293
        Taxon 106 -> zosV161311
        Taxon 107 -> zosWM1890
        Taxon 108 -> zosGM364
        Taxon 109 -> zosGM365
        Taxon 110 -> zosGM387
        Taxon 111 -> zosGM393
        Taxon 112 -> zosRO332
        Taxon 113 -> zosOM37006
        Taxon 114 -> zosWM1601
        Taxon 115 -> clarkii
        Taxon 116 -> edwardti80
        Taxon 117 -> smaragdnus
        Taxon 118 -> graciosus
        Taxon 119 -> grammicus
        Taxon 120 -> maculosus
        Taxon 121 -> bicanthlis
        Taxon 122 -> torquatus
        Taxon 123 -> variabilis
        Successfully read matrix
        Setting default partition (does not divide up characters)
        Setting model defaults
        Seed (for generating default start values) = 1544128192
        Setting output file names to "sceloporus.nex.run<i>.<p|t>"
     Exiting data block
     Reading mrbayes block
        Excluding character(s)
        Setting Nst to 6
        Setting Rates to Gamma
        Successfully set likelihood model parameters
        Setting Brlenspr to Unconstrained:GammaDir(1.00,1.0000,0.70,0.50)
        Successfully set prior model parameters
        Setting number of generations to 5000000
        Running Markov chain
        MCMC stamp = 9909051894
        Seed = 1261289135
        Swapseed = 1544128192
        Model settings:
  
           Data not partitioned --
              Datatype  = DNA
              Nucmodel  = 4by4
              Nst       = 6
                          Substitution rates, expressed as proportions
                          of the rate sum, have a Dirichlet prior
                          (1.00,1.00,1.00,1.00,1.00,1.00)
              Covarion  = No
              # States  = 4
                          State frequencies have a Dirichlet prior
                          (1.00,1.00,1.00,1.00)
              Rates     = Gamma
                          The distribution is approximated using 4 categories.
                          Shape parameter is exponentially
                          distributed with parameter (1.00).
  
        Active parameters: 
  
           Parameters
           ---------------------
           Revmat              1
           Statefreq           2
           Shape               3
           Ratemultiplier      4
           Topology            5
           Brlens              6
           ---------------------
  
           1 --  Parameter  = Revmat
                 Type       = Rates of reversible rate matrix
                 Prior      = Dirichlet(1.00,1.00,1.00,1.00,1.00,1.00)
  
           2 --  Parameter  = Pi
                 Type       = Stationary state frequencies
                 Prior      = Dirichlet
  
           3 --  Parameter  = Alpha
                 Type       = Shape of scaled gamma distribution of site rates
                 Prior      = Exponential(1.00)
  
           4 --  Parameter  = Ratemultiplier
                 Type       = Partition-specific rate multiplier
                 Prior      = Fixed(1.0)
  
           5 --  Parameter  = Tau
                 Type       = Topology
                 Prior      = All topologies equally probable a priori
                 Subparam.  = V
  
           6 --  Parameter  = V
                 Type       = Branch lengths
                 Prior      = Unconstrained:GammaDir(1.0,1.0000,0.7,0.5)
  
        Number of chains per MPI processor = 8
  
        The MCMC sampler will use the following moves:
           With prob.  Chain will use move
              0.94 %   Dirichlet(Revmat)
              0.94 %   Slider(Revmat)
              0.94 %   Dirichlet(Pi)
              0.94 %   Slider(Pi)
              1.89 %   Multiplier(Alpha)
              9.43 %   ExtSPR(Tau,V)
              9.43 %   ExtTBR(Tau,V)
              9.43 %   NNI(Tau,V)
              9.43 %   ParsSPR(Tau,V)
             37.74 %   Multiplier(V)
             13.21 %   Nodeslider(V)
              5.66 %   TLMultiplier(V)
  
        Division 1 has 624 unique site patterns
        Initializing conditional likelihoods
        Using standard FMA likelihood calculator for division 1 (single-precision)
  
        Initial log likelihoods and log prior probs for run 1:
           Chain 1 -- -39098.978535 -- 53.554896
           Chain 2 -- -38054.044640 -- 53.554896
           Chain 3 -- -39425.015629 -- 53.554896
           Chain 4 -- -40157.756230 -- 53.554896
  
        Initial log likelihoods and log prior probs for run 2:
           Chain 1 -- -40084.553712 -- 53.554896
           Chain 2 -- -39002.725314 -- 53.554896
           Chain 3 -- -38719.752582 -- 53.554896
           Chain 4 -- -39156.129424 -- 53.554896
  
        Using a relative burnin of 25.0 % for diagnostics
  
        Chain results (5000000 generations requested):
  
           0 -- [-39098.979] (-38054.045) (-39425.016) (-40157.756) * [-40084.554] (-39002.725) (-38719.753) (-39156.129) (...0 remote chains...) 
  ^C[ptitle@iu mbTest]$ mpirun -np 2 ~/MrBayes/src/mb sceloporus.nex 
  
                              MrBayes pre-3.2.7 x86_64
  
                        (Bayesian Analysis of Phylogeny)
  
                               (Parallel version)
                           (2 processors available)
  
                Distributed under the GNU General Public License
  
                 Type "help" or "help <command>" for information
                       on the commands that are available.
  
                     Type "about" for authorship and general
                         information about the program.
  
     Executing file "sceloporus.nex"
     DOS line termination
     Longest line length = 1632
     Parsing file
     Expecting NEXUS formatted file
     Reading data block
        Allocated taxon set
        Allocated matrix
        Defining new matrix with 123 taxa and 1606 characters
        Data is Dna
        Missing data coded as ?
        Gaps coded as -
        Taxon   1 -> AZYuJAS289
        Taxon   2 -> AZYuJAS290
        Taxon   3 -> AZlaJAS294
        Taxon   4 -> AZcoTBP271
        Taxon   5 -> AZcoGM1054
        Taxon   6 -> AZcoDGM994
        Taxon   7 -> AZgiP26438
        Taxon   8 -> AZgrGM1012
        Taxon   9 -> AZgrGM1013
        Taxon  10 -> AZgrGM1024
  ^C[ptitle@iu mbTest]$ 
  
  ```
  
  **Tags:** phylogenetics, phylogeny, molecular-genetics, mrbayes
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-12-14. Score: 1
  
  It is not trivial getting MB to run in parallel because from my experience it required granting privileges to regular users. I used this via MPI (MPICH) on a Slurm/SGE cluster.
  
  Essentially, this is coarse grain parallel processing.
  
  It is certainly worth parallelizing MB because each chain can be run on a different nodes and avoids RAM bottlenecks on complex models and big data sets. For example, 8 to 10+ chains can be run, ensuring convergence quickly by running chains across nodes.
  
  ---
  
  **Update** I later found it was much easier to run via EasyBuild with OpenMPI using the command `runmpi`.
  
  > **Comments:**
  > **username_0**: Interesting, so this might be an MPI permissions issue then. I will run this by the university IT folks and see if they can help me figure this out. I'll report back.  
  > **username_0**: This seems to most likely have been an issue with mpi on my system, rather than with MrBayes, and this now works for me, although I'm not sure what changed.  
  
  ---
  
  