Dear All,
I am running hyphy in linux with MPI environment, to do GARD data analysis. The MPI is running, however, when I load the file and try to run GARD.bf, I got error message. I could not figure out what is wrong... could anyone help me? Thanks!
Sadiexiaoyu
And the MPI running seems ok, like this:
mpirun -np 24 /usr/local/bin/HYPHYMPI
/HYPHY 2.220160120beta(MPI) for Linux on x86_64\ ***** TYPES OF STANDARD ANALYSES *****
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 (http://sray.med.som.jhmi.edu/SCRoftware/simplot/)
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
/downloads/seq.fas
/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
1 more process has sent help message help-mpi-api.txt / mpi-abort
Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
HYPHYMPI terminated.
Error:
HyPhy killed by signal 15
2 more processes have sent help message help-mpi-api.txt / mpi-abort
Dear All, I am running hyphy in linux with MPI environment, to do GARD data analysis. The MPI is running, however, when I load the file and try to run GARD.bf, I got error message. I could not figure out what is wrong... could anyone help me? Thanks!
Sadiexiaoyu
And the MPI running seems ok, like this: mpirun -np 24 /usr/local/bin/HYPHYMPI /HYPHY 2.220160120beta(MPI) for Linux on x86_64\
***** TYPES OF STANDARD ANALYSES *****
11 Please select type of analyses you want to list (or press ENTER to process custom batch file):
***** FILES IN 'Recombination' *****
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 /downloads/seq.fas /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
1 more process has sent help message help-mpi-api.txt / mpi-abort Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages HYPHYMPI terminated. Error: HyPhy killed by signal 15
HYPHYMPI terminated. Error: HyPhy killed by signal 15
HYPHYMPI terminated. Error: HyPhy killed by signal 15
2 more processes have sent help message help-mpi-api.txt / mpi-abort