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]$
