Hello,

We trying to use HyPhy for detect recombinants.

We install HYPHY in a cluster with open MPI.
We call HYPHY

$mpirun -np 4  /usr/local/bin/HYPHYMPI

and then display the next message

/HYPHY 2.1020120130beta(MPI) for Linux on x86_64\      
***************** TYPES OF STANDARD ANALYSES *****************

We choose 11 and after that, We choose 1 for Screen an alignment using GARD.

We choose an alignment (we can not download the example file) in fasta or phy.
and then we choose the Batch File:

SingleBreakpointRecomb.bf

And the next  error message is:
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
/usr/local/lib/hyphy/TemplateBatchFiles/Nucleotide file to screen::Error:

Master node received an error:The format of the sequence file has not been recognized and may be invalid

Function call stack
1 : Read Data Set ds from file PROMPT_FOR_FILE
-------
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 23329 on
node biosistemas1.ira.cinvestav.mx exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------

Do you have any idea about What we are doing wrong?
Thankyou for your help.

Cheers,

Ricardo I.

Sergei,

Yeah, sorry I mean GARD.bf...
The error message is the same:

Thank you.

Ricardo
$ mpirun -np 4  /usr/local/bin/HYPHYMPI


      /HYPHY 2.1020120130beta(MPI) for Linux on x86_64\      
***************** TYPES OF STANDARD ANALYSES *****************


     (1) Basic Analyses
     (2) Codon Selection Analyses
     (3) Compartmentalization
     (4) Data File Tools
     (5) Miscellaneous
     (6) Model Comparison
     (7) Kernel Analysis Tools
     (8) Molecular Clock
     (9) Phylogeny Reconstruction
     (10) Positive Selection
     (11) Recombination
     (12) Selection/Recombination
     (13) Relative Rate
     (14) Relative Ratio
     (15) Substitution Rates

11
Please select type of analyses you want to list (or press ENTER to process custom batch file):

***************** FILES IN 'Recombination' *****************


     (1) Screen an alignment using GARD (requires an MPI environment).
     (2) Process GARD results.
     (3) A Likelihood Ratio Test to detect conflicting phylogenetic signal Huelsenbeck and Bull, 1996. [Contributed by Olivier Fedrigo].
     (4) Search an alignment for a single breakpoint.
     (5) Plot genetic distances (similarity) of one sequence against all others in an alignment, using a sliding window. Optionally, determine NJ-based clustering and bootstrap support in every window. This is a HyPhy adaptation of the excellent (but Windows only tool) SimPlot (and/or VarPlot) written by Stuart Ray (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login)

1
Please select the file you want to use (or press ENTER to return to the list of analysis types):Initialized GARD on 4 MPI nodes.
Population size is 6 models

seqs.fasta 
/usr/local/lib/hyphy/TemplateBatchFiles/Nucleotide file to screen::
GARD.bf
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
/usr/local/lib/hyphy/TemplateBatchFiles/Nucleotide file to screen::Error:

Master node received an error:The format of the sequence file has not been recognized and may be invalid

Function call stack
1 : Read Data Set ds from file PROMPT_FOR_FILE
-------
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 3182 on
node biosistemas1.ira.cinvestav.mx exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------

Dear Sergei,

Thanks for your help, we knew that we were doing something wrong, but we never thought about the path.

Sorry for the inconveniences,
Kind regards!

Ricardo I.