Migrate error: *** glibc detected *** migrate-n-mpi: corrupted double-linked list: 0x0000000001754e80 ***

[lpl...@umces.edu]

Compiled MigrateN (make mpis) on Ubuntu 12.04 without any errors ( I have 64 GB ram 24 cpu).  However, when I run 

mpirun -np 25 migrate-n-mpi 

I get the following error:  

Migrate error:  *** glibc detected *** migrate-n-mpi: corrupted double-linked list: 0x0000000001754e80 ***

Migrate appears to run, but then stalls somewhere before or after the burnin, and never completes (left for hours) on a small, 2 locus toy SNP dataset. 

Like I said, compiled with mpi with out error....but something must be up wiht the parallel compile. 
attached below is the full output from the run:

Any ideas? 

Thanks,

LP

-----------------------------------------------------------------------------------------

Reading parmfile "parmfile"....

  =============================================

  MIGRATION RATE AND POPULATION SIZE ESTIMATION

  using Markov Chain Monte Carlo simulation

  =============================================

  Compiled for a PARALLEL COMPUTER ARCHITECTURE

  One master and 24 compute nodes are available.

  PDF output enabled [Letter-size]

  Version 3.6.6 

  Program started at   Tue Feb 24 16:35:35 2015

  Settings for this run:

  D       Data type currently set to: SNP model                     

  I       Input/Output formats

  P       Parameters  [start, migration model]

  S       Search strategy

  W       Write a parmfile

  Q       Quit the program

  To change the settings type the letter for the menu to change

  Start the program with typing Yes or Y

===> y

Master random number seed: 1363131055

Reading (0) pop_1 ...

Bj138     |C

Bj138   |T

Bj142     |C

Bj142     |C

Bj143     |C

Bj143     |T

Reading (1) pop_2 ...

Mel42     |G

Mel42     |G

Mel45     |A

Mel45     |G

Mel49     |G

Mel49     |A

Mel51     |A

Mel51     |A

WARNING: Reading geofile: adjusting dist[0][1]=0.000000 to 0.000001

WARNING: Reading geofile: adjusting dist[1][0]=0.000000 to 0.000001

Options in use:

---------------

Analysis strategy is MAXIMUM LIKELIHOOD

Datatype: Single nucleotide polymorphism data

Inheritance scalers in use for Thetas (specified scalars=1)

1.00 1.00 

[Each Theta uses the (true) ineritance scalar of the first locus as a reference]

Pseudo-random number generator: Mersenne-Twister                                

Random number seed (with internal timer)           1363131055

Start parameters:

   First genealogy was started using a random tree

   Theta values were generated  from an FST-calculation

   M values were generated from the FST-calculation

Migration model:

   Migration matrix model with variable Theta  

   Geographic distance matrix between locations

      pop_1             -    0.000 

      pop_2           0.000    -   

      

Mutation rate among loci is varying with

   Rates per locus: 1.000, 1.000

[Estimated from the data using the Watterson estimator (ignoring migration)]

Markov chain settings:

   Short chains (short-chains):                           20

      Trees sampled (short-inc*samples):              100000

      Trees recorded (short-sample):                    1000

   Long chains (long-chains):                              3

      Trees sampled (long-inc*samples):              1000000

      Trees recorded (long-sample):                    10000

   Averaging over long chains

   Adaptive_Standard heating scheme

      5 chains with start temperatures

       1.00, 1.50, 3.00,100.00,1000000.00

      No swapping

   Burn-in per chain:                             1000000

Print options:

   Data file:                                         infile

   Output file (ASCII text):                         outfile

   Output file (PDF):                            outfile.pdf

   Print data:                                           Yes

   Print genealogies:                                     No

   Plot data: Yes, to outfile and mathfile                  

              Parameter: {Theta, M}, Scale: Log10, Intervals: 36

              Ranges: X-    M: 0.000100 - 100.000000

*** glibc detected *** migrate-n-mpi: corrupted double-linked list: 0x0000000001c08e80 ***

              Ranges: Y-Theta: 0.000100 - 100.000000

   Frequency histogram of events       Yes: Migration events

*** glibc detected *** migrate-n-mpi: corrupted double-linked list: 0x0000000001754e80 ***

   Time of events are saved in file              mighistfile

   Histogram of the parameter values through time        Yes

   Parameters through time are saved in file     skylinefile

   Profile likelihood: Yes, tables and summary             

             Percentile method

             with df=1 and for Theta and M=m/mu

Summary of data:

Title:                                          stacksoutput

Data file:                                            infile

Datatype:                                           SNP data

Number of loci:                                            2

Population                   Locus   Gene copies    

----------------------------------------------------

  1 pop_1                        1         3

  1                              2         3

  2 pop_2                        1         4

  2                              2         4

    Total of all populations     1         7

                                 2         7

Relative mutation rate among loci estimated from the data 

==========================================================

Locus       Relative        Watterson's Theta  Segregating

            mutation rate   (per site)         sites      

--------    -------------   -----------------  -----------

    1           1.00000         0.40816327           1

    2           1.00000         0.40816327           1

  All           1.00000         0.40816328         1.0

^Cmpirun: killing job...

--------------------------------------------------------------------------

mpirun noticed that process rank 0 with PID 7126 on node lplough-ubuntu exited on signal 0 (Unknown signal 0).

--------------------------------------------------------------------------

25 total processes killed (some possibly by mpirun during cleanup)

[Himanshu Midha]

Hi, Did you find the solution to this problem ? Please reply

[Peter Beerli]

Could you download a newer version and recompile and test again?

We had just our datacenter flooded (Hurricane Hermine), so you need to go to http://peterbeerli.com/migrate/

to get the source  for 3.7, 

thanks

Peter

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