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A question about MPI and HYPHY GARD (Read 6462 times)
Zhuofei
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A question about MPI and HYPHY GARD
Nov 12th, 2013 at 12:36pm
 
Hi All,

I have a question and need your help! I hope to use GARD on multiple data sets of DNA alignments.

I have installed openmpi-1.6.5.tar.gz and HYPHYMPI (hyphy-2.2.tar.gz) in my local computer (Fedora system). Both installation look normal and both can work separately.

[root@Fedora software]# mpirun -V
mpirun (Open MPI) 1.6.5

I have tested mpirun using an example

[root@Fedora examples]# mpirun -np 4 hello_c
Hello, world, I am 3 of 4
Hello, world, I am 1 of 4
Hello, world, I am 2 of 4
Hello, world, I am 0 of 4


For running HYPHYMPI
[root@Fedora GARD]# HYPHYMPI


       /HYPHY 2.220131112beta(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

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

But when I run the following command

[root@Fedora GARD]# mpirun -np 4 HYPHYMPI GARD.bf
[ERROR] This analysis requires an MPI environment to run


[ERROR] This analysis requires an MPI environment to run
[ERROR] This analysis requires an MPI environment to run


[ERROR] This analysis requires an MPI environment to run


And if I run the command without GARD.bf
mpirun -np 4 HYPHYMPI
It will display the same interface as the above command (HYPHYMPI) but the interface is serial and can't stop automatically.


I also tested a test script MPItest.bf provided by Sergei  in the forum.
[root@Fedora examples]# mpirun -np 4 HYPHYMPI MPItest.bf
Running a HYPHY-MPI test

Program launched in a single process environment
Running a HYPHY-MPI test

Program launched in a single process environment


Running a HYPHY-MPI test

Program launched in a single process environment
Running a HYPHY-MPI test

Program launched in a single process environment



Would you like to give me advices to solve this problem and let HYPHYMPI run normally?

Thanks a lot in advance!

Best regards,
Zhuofei
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« Last Edit: Nov 13th, 2013 at 2:32am by Zhuofei »  
 
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Zhuofei
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Curious HyPhy user

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Re: A question about MPI and HYPHY GARD
Reply #1 - Nov 13th, 2013 at 6:48am
 
Hi All,

I have re-installed low version of Hyphy 2.1. HYPHYMPI can work with mpirun normally now!

I don't know why Hyphy 2.2 can't work. But at least, I can start to learn how to use GARD deal with multiple data sets.

Cheers,
Zhuofei
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