Segmentation fault when running HYPHYMPI ModelSelectorBranchLocal.bf

[Pleetzken]

Hi, I'm trying to run the ModelSelectorBranchLocal.bf script from the GABranchFiles on the example dataset but keep getting error "HyPhy killed by signal 15" with a seg fault error message being repeated by each thread of the mpirun. I'm running on Linux 4.15.0-52 with mpirun V 1.10.2. Full error output is at the end. I have made a folder with symlinks to all hyphy libraries to avoid #1001 because the original place is only root writable.

Thank You for your help Peter

exact call and output:

$ mpirun -np 2 HYPHYMPI ../ModelSelectorBranchLocal.bf "Universal" "../Example/lysozyme.nex" "y" "010010"
Universal

A tree was found in the data file:
(((((LANGUR_SEN_SVE,LANGUR_TOB_TFR,DOUC_LANGUR_PNE),PROBISCIS_NLA),COLOBUS_CGU_CAN),(((BABOON_PCY,MANGABEY_CAT),RHESUS_MMU),ALLEN_ANI,(TALAPOIN_MTA,(PATAS_EPA,VERVET_CAE)))),(((HUMAN,CHIMP_BONOBO_GORILLA),ORANGUTAN_PPY),GIBBON_GGO),(SQUIRREL_M,(TAMARIN_SOE,MARMOSET_CJA)))

Would you like to use it:(Y/N)?y

Nucleotide a 6-character model string specification (e.g. HKY85 = 010010):?010010
[Preliminary Step 1] A total of 33 branches. Fitting a nucleotide model to approximate branch lengths... 
[Preliminary Step 2] Nucleotide LogL = -1062.275129258495
[Preliminary Step 3] Base model has 44 parameters. Log-L = -1038.753661256471. Mean dN/dS = 0.5704177218236977

[Starting the GA with 2 rate classes.]
[Xylocalyx:86641] *** Process received signal ***
[Xylocalyx:86641] Signal: Segmentation fault (11)
[Xylocalyx:86641] Signal code: Address not mapped (1)
[Xylocalyx:86641] Failing at address: 0x68
[Xylocalyx:86641] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7fd3999ea390]
[Xylocalyx:86641] [ 1] HYPHYMPI(_ZN14_ExecutionList13ResetFormulaeEv+0xc)[0x464c2c]
[Xylocalyx:86641] [ 2] HYPHYMPI(_ZN10_Operation7ExecuteER6_StackPK18_VariableContainerP7_String+0xd2f)[0x55c8af]
[Xylocalyx:86641] [ 3] HYPHYMPI(_ZN8_Formula7ComputeElPK18_VariableContainerP5_ListP7_Stringl+0xc4)[0x4cadb4]
[Xylocalyx:86641] [ 4] HYPHYMPI(_Z14ExecuteFormulaP8_FormulaS0_llP18_VariableContainerc+0x11a)[0x56427a]
[Xylocalyx:86641] [ 5] HYPHYMPI(_ZN18_ElementaryCommand12ExecuteCase0ER14_ExecutionList+0x1c6)[0x465266]
[Xylocalyx:86641] [ 6] HYPHYMPI(_ZN18_ElementaryCommand7ExecuteER14_ExecutionList+0x9f5)[0x466c55]
[Xylocalyx:86641] [ 7] HYPHYMPI(_ZN14_ExecutionList7ExecuteEPS_b+0x232)[0x467d42]
[Xylocalyx:86641] [ 8] HYPHYMPI(_Z13mpiNormalLoopiiR7_String+0x4de)[0x6759be]
[Xylocalyx:86641] [ 9] HYPHYMPI(main+0xb15)[0x4434a5]
[Xylocalyx:86641] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fd398d8e830]
[Xylocalyx:86641] [11] HYPHYMPI(_start+0x29)[0x444349]
[Xylocalyx:86641] *** End of error message ***
--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------
Error:

Master node received an error:HyPhy killed by signal 15

Function call stack
1 :  MPIReceive(-1, fromNode, result_String);
    Standard input redirect:
        Empty Associative List
-------
2 :  fromNode=ReceiveJobs(0,0);
-------
3 :  CleanUpMPI(0);
-------
4 :  ExecuteAFile(ibfPath, /home/peter/tmp/GABranchFiles/hyphy_test/../);
-------
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 86641 on node Xylocalyx exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

[stevenweaver]

Dear Peter,

Apologies, but which version of HyPhy are you trying to run? ModelSelectorBranchLocal.bf is not in HyPhy's repository, and I'm afraid that it hasn't been since the inception of revision control on the codebase in 2008. This means it hasn't been supported in later versions of HyPhy (versions >=2).

Best, Steven

[Pleetzken]

Dear Steven, Thanks for your answer. I'm using Hyphy version 2.5.0. Thats unfortunate to hear. Would you know - by any chance - a way I could tweak the script so it is possible to run with the current version of hyphy? Best, Peter

[spond]

Dear @Pleetzken,

I'll take a look into what's going on here. Segfault 11 is never an acceptable outcome (should be an error message if anything).

In the meantime, GABranch has been generally deprecated in favor of aBSREL for most applications.

Best, Sergei

[Pleetzken]

Dear Sergei, Thank you for your help. I will take a look at aBSREL. Best, Peter

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