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segmentation fault #279

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dlema82 opened this issue Mar 21, 2023 · 0 comments
Open

segmentation fault #279

dlema82 opened this issue Mar 21, 2023 · 0 comments
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need more info Need more info from issuer

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@dlema82
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dlema82 commented Mar 21, 2023

Hello,
I have tried running mrbayes-v3.2.6 on my university cluster with a text block in my nexus file, as below:
begin mrbayes;
set autoclose=yes nowarn=yes;
CHARSET mtgenome = 1-16701;
partition favored = 1: mtgenome;

set partition = favored;
unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all) tratio=(all);
prset applyto=(all) ratepr=variable;
lset applyto=(1) nst=2 rates=invgamma;
mcmc nruns=2 ngen=10000000 samplefreq=1000
printfreq=1000 nchains=4 savebrlens=yes;
mcmc;
sump burnin=2500;
sumt burnin=2500;
END;

I call the operation using a .sh script here:
#!/bin/bash
#PBS -V
#PBS -N mrbayes_mito
#PBS -q batch
#PBS -S /bin/bash
#PBS -l select=1:ncpus=16
#PBS -l walltime=720:00:00
cd $PBS_O_WORKDIR
module load beagle-2.1.2 mrbayes-3.2.6

mb /nas1/dlema/pardus_africa_outgroup_mt_alignment.nexus

The operation aborts with this error log:
var/spool/pbs/mom_priv/jobs/1065581.huxley-head.SC: line 11: 18480 Segmentation fault mb ./pardus_africa_outgroup_mt_alignment.nexus

And the output log says this (after successfully running several dozen "Average standard deviation of split frequencies"):
Average standard deviation of split frequencies: 0.227872
46000 -- (-42285.050) [-42185.491] (-42276.483) (-42301.598) * (-42279.110) (-42208.973) (-42276.280) [-42212.730] (...0 remote chains...) -- 640:24:45
47000 -- (-42280.792) [-42176.176] (-42271.630) (-42289.592) * (-42299.672) (-42210.341) (-42284.872) [-42206.358] (...0 remote chains...) -- 640:21:17
48000 -- (-42293.219) [-42189.734] (-42261.749) (-42283.816) * (-42299.638) (-42191.706) (-42284.769) [-42202.821] (...0 remote chains...) -- 640:17:56
49000 -- (-42293.278) [-42195.849] (-42280.603) (-42272.094) * (-42293.363) (-42205.396) (-42294.548) [-42209.644] (...0 remote chains...) -- 640:31:41
50000 -- (-42285.433) [-42176.144] (-42282.690) (-42276.438) * (-42287.526) (-42208.512) (-42289.159) [-42200.776] (...0 remote chains...) -- 640:11:33

  Could not remove partition 87 in RemoveTreeFromPartitionCounters

.........***.............................................[huxley-n0001:18480] *** Process received signal ***
[huxley-n0001:18480] Signal: Segmentation fault (11)
[huxley-n0001:18480] Signal code: Address not mapped (1)
[huxley-n0001:18480] Failing at address: 0x3f15a000
[huxley-n0001:18480] [ 0] /lib64/libpthread.so.0(+0xf6d0)[0x2b923ee576d0]
[huxley-n0001:18480] [ 1] /lib64/libc.so.6(_IO_vfprintf+0x4a79)[0x2b923f0b0f19]
[huxley-n0001:18480] [ 2] mb[0x554541]
[huxley-n0001:18480] [ 3] mb[0x4d26b8]
[huxley-n0001:18480] [ 4] mb[0x4a3a1b]
[huxley-n0001:18480] [ 5] mb[0x42ce4f]
[huxley-n0001:18480] [ 6] mb[0x40d80b]
[huxley-n0001:18480] [ 7] mb[0x42ce4f]
[huxley-n0001:18480] [ 8] mb[0x402bdb]
[huxley-n0001:18480] [ 9] mb[0x402883]
[huxley-n0001:18480] [10] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b923f086445]
[huxley-n0001:18480] [11] mb[0x4026a9]
[huxley-n0001:18480] *** End of error message ***

Forgive me, but I don't know what this means, or what the workaround might be. I am fairly inexperienced. Please help!

Regards

@nylander nylander added the need more info Need more info from issuer label Feb 2, 2024
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