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terminate called recursively -- Aborted (core dumped) #152

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0xaf1f opened this issue Dec 14, 2022 · 8 comments
Open

terminate called recursively -- Aborted (core dumped) #152

0xaf1f opened this issue Dec 14, 2022 · 8 comments

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@0xaf1f
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0xaf1f commented Dec 14, 2022

I'm trying to infer a tree using concatenated SNPs and consistently get this core dump when multithreading. I do not have this problem with the original raxmlHPC, but it does not complete within the 2 day maximum walltime of the cluster and doesn't do checkpointing either (as far as i know), so I can't restart it from where it left off.

So I'm trying raxml-ng (latest version 1.1.0):

RAxML-NG v. 1.1.0 released on 29.11.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Platinum 8260M CPU @ 2.40GHz, 96 cores, 4031 GB RAM

RAxML-NG was called at 09-Dec-2022 20:16:42 as follows:

raxml-ng --all --msa SNP.parse.raxml.rba --model GTR+G+ASC_FELS{4087123} --prefix SNP --threads 24 --bs-trees 100

Analysis options:
  run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
  start tree(s): random (10) + parsimony (10)
  bootstrap replicates: 100
  random seed: 1670635002
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (24 threads), thread pinning: OFF

WARNING: The model you specified on the command line (GTR+G+ASC_FELS{4087123}) will be ignored
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: SNP.parse.raxml.rba
[00:00:00] Alignment comprises 4832 taxa, 1 partitions and 82354 patterns

Partition 0: noname
Model: GTR+FO+G4m+ASC_FELS{4087123}
Alignment sites / patterns: 324409 / 82354
Gaps: 0.00 %
Invariant sites: 0.00 %


Parallelization scheme autoconfig: 3 worker(s) x 8 thread(s)


NOTE: Per-rate scalers were automatically enabled to prevent numerical issues on taxa-rich alignments.
NOTE: You can use --force switch to skip this check and fall back to per-site scalers.

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 10 random starting tree(s) with 4832 taxa
[00:00:01] Generating 10 parsimony starting tree(s) with 4832 taxa
[02:02:53] Data distribution: max. partitions/sites/weight per thread: 1 / 10295 / 164720
[02:02:55] Data distribution: max. searches per worker: 41

Starting ML tree search with 20 distinct starting trees

terminate called recursively
terminate called recursively
/var/spool/slurm/d/job13600690/slurm_script: line 19: 75715 Aborted                 (core dumped) raxml-ng --all --msa SNP.parse.raxml.rba --model GTR+G+ASC_FELS{$invar_sites} --prefix SNP --threads 24 --bs-trees 100

I have also tried with --threads 1 --workers 1 and it timed out at the 2 day maximum, but the log doesn't indicate that it got anywhere past

Starting ML tree search with 20 distinct starting trees

so even if it worked with 1 thread, it looks like it'd be painstakingly slow.
@amkozlov
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Could you please try to re-run with --workers 1 --log debug and also check the memory usage?

@0xaf1f
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0xaf1f commented Dec 18, 2022

Ok, it ran for a while, then there was an unrelated node failure (a few of my other unrelated jobs on other nodes also failed at the same time, so I think there was a cluster issue at the time). I restarted the run and about a day later raxml-ng fails again with the same error. Here is the second log:


RAxML-NG v. 1.1.0 released on 29.11.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: AMD EPYC 7742 64-Core Processor, 128 cores, 251 GB RAM

RAxML-NG was called at 16-Dec-2022 13:42:14 as follows:

raxml-ng --all --msa SNP.parse.raxml.rba --model GTR+G+ASC_FELS{4087123} --prefix SNP --threads 24 --workers 1 --bs-trees 100 --log debug

Analysis options:
  run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
  start tree(s): random (10) + parsimony (10)
  bootstrap replicates: 100
  random seed: 1671216134
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: PTHREADS (24 threads), thread pinning: OFF

RBA partial loading: OFF
WARNING: The model you specified on the command line (GTR+G+ASC_FELS{4087123}) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: SNP.parse.raxml.rba
[00:00:02] Alignment comprises 4832 taxa, 1 partitions and 82354 patterns

Partition 0: noname
Model: GTR+FO+G4m+ASC_FELS{4087123}
Alignment sites / patterns: 324409 / 82354
Gaps: 0.00 %
Invariant sites: 0.00 %


|noname|   |GTR+FO+G4m+ASC_FELS{4087123}|   |1-324409|

NOTE: Per-rate scalers were automatically enabled to prevent numerical issues on taxa-rich alignments.
NOTE: You can use --force switch to skip this check and fall back to per-site scalers.

Generating a random starting tree with 4832 taxa
Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:02] NOTE: Resuming execution from checkpoint (logLH: -10351404.46, ML trees: 0, bootstraps: 0)

Initial model parameters:
   Partition: noname
   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 1.000000 (ML),  weights&rates: (0.250000,0.136954) (0.250000,0.476752) (0.250000,1.000000) (0.250000,2.386294) 
   Base frequencies (ML): 0.250000 0.250000 0.250000 0.250000 
   Substitution rates (ML): 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 

[00:00:02] Data distribution: max. partitions/sites/weight per thread: 1 / 3432 / 54912

thread# part#   start   length  weight
0       0       78936   3418    54688

1       0       75504   3432    54912

2       0       72072   3432    54912

3       0       68640   3432    54912

4       0       65208   3432    54912

5       0       61776   3432    54912

6       0       58344   3432    54912

7       0       54912   3432    54912

8       0       51480   3432    54912

9       0       48048   3432    54912

10      0       44616   3432    54912

11      0       41184   3432    54912

12      0       37752   3432    54912

13      0       34320   3432    54912

14      0       30888   3432    54912

15      0       27456   3432    54912

16      0       24024   3432    54912

17      0       20592   3432    54912

18      0       17160   3432    54912

19      0       13728   3432    54912

20      0       10296   3432    54912

21      0       6864    3432    54912

22      0       3432    3432    54912

23      0       0       3432    54912

Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
[00:00:03] Data distribution: max. searches per worker: 120

BARRIER time: 0.003971 ms

Starting ML tree search with 20 distinct starting trees

[00:00:06 -10351404.457014] SPR radius for FAST iterations: 25 (autodetect)
[00:00:06 -10351404.457014] FAST spr round 6 (radius: 25)
         - after brlen: logLH = -10351387.624913
[00:20:24 -10351387.624913] FAST spr round 7 (radius: 25)
         - after brlen: logLH = -10351373.124242
[00:38:26 -10351373.124242] FAST spr round 8 (radius: 25)
         - after brlen: logLH = -10351362.911341
[00:55:22 -10351362.911341] FAST spr round 9 (radius: 25)
         - after brlen: logLH = -10351356.834441
[01:11:42 -10351356.834441] FAST spr round 10 (radius: 25)
         - after brlen: logLH = -10351351.867060
[01:27:42 -10351351.867060] FAST spr round 11 (radius: 25)
         - after brlen: logLH = -10351347.864267
[01:43:43 -10351347.864267] FAST spr round 12 (radius: 25)
         - after brlen: logLH = -10351344.716538
[01:59:22 -10351344.716538] FAST spr round 13 (radius: 25)
         - after brlen: logLH = -10351341.645818
[02:14:59 -10351341.645818] FAST spr round 14 (radius: 25)
         - after brlen: logLH = -10351338.892258
[02:30:15 -10351338.892258] FAST spr round 15 (radius: 25)
         - after brlen: logLH = -10351335.542908
[02:45:41 -10351335.542908] FAST spr round 16 (radius: 25)
         - after brlen: logLH = -10351333.301802
[03:01:20 -10351333.301802] FAST spr round 17 (radius: 25)
         - after brlen: logLH = -10351331.151827
[03:16:44 -10351331.151827] FAST spr round 18 (radius: 25)
         - after brlen: logLH = -10351329.341439
[03:32:10 -10351329.341439] FAST spr round 19 (radius: 25)
         - after brlen: logLH = -10351327.535476
[03:47:30 -10351327.535476] FAST spr round 20 (radius: 25)
         - after brlen: logLH = -10351322.997378
[04:02:53 -10351322.997378] FAST spr round 21 (radius: 25)
         - after brlen: logLH = -10351313.092002
[04:18:16 -10351313.092002] FAST spr round 22 (radius: 25)
         - after brlen: logLH = -10351311.292615
[04:33:31 -10351311.292615] FAST spr round 23 (radius: 25)
         - after brlen: logLH = -10351309.493888
[04:48:49 -10351309.493888] FAST spr round 24 (radius: 25)
         - after brlen: logLH = -10351307.726005
[05:04:22 -10351307.726005] FAST spr round 25 (radius: 25)
         - after brlen: logLH = -10351306.007903
[05:19:51 -10351306.007903] FAST spr round 26 (radius: 25)
         - after brlen: logLH = -10351304.635382
[05:35:13 -10351304.635382] FAST spr round 27 (radius: 25)
         - after brlen: logLH = -10351299.854038
[05:50:37 -10351299.854038] FAST spr round 28 (radius: 25)
         - after brlen: logLH = -10351298.535978
[06:05:53 -10351298.535978] FAST spr round 29 (radius: 25)
         - after brlen: logLH = -10351297.304712
[06:21:07 -10351297.304712] FAST spr round 30 (radius: 25)
         - after brlen: logLH = -10351296.251681
[06:36:27 -10351296.251681] FAST spr round 31 (radius: 25)
         - after brlen: logLH = -10351292.036071
[06:51:44 -10351292.036071] FAST spr round 32 (radius: 25)
         - after brlen: logLH = -10351291.153234
[07:07:18 -10351291.153234] FAST spr round 33 (radius: 25)
         - after brlen: logLH = -10351290.077628
[07:22:43 -10351290.077628] FAST spr round 34 (radius: 25)
         - after brlen: logLH = -10351289.614201
[07:37:57 -10351289.614201] FAST spr round 35 (radius: 25)
         - after brlen: logLH = -10351279.200180
[07:53:15 -10351279.200180] FAST spr round 36 (radius: 25)
         - after brlen: logLH = -10351276.008304
[08:08:31 -10351276.008304] FAST spr round 37 (radius: 25)
         - after brlen: logLH = -10351275.696520
[08:24:02 -10351275.696520] FAST spr round 38 (radius: 25)
         - after brlen: logLH = -10351275.476474
[08:39:26 -10351275.476474] FAST spr round 39 (radius: 25)
         - after brlen: logLH = -10351260.626399
[08:55:03 -10351260.626399] FAST spr round 40 (radius: 25)
         - after brlen: logLH = -10351258.278455
[09:10:30 -10351258.278455] FAST spr round 41 (radius: 25)
         - after brlen: logLH = -10351257.413502
[09:25:46 -10351257.413502] FAST spr round 42 (radius: 25)
         - after brlen: logLH = -10351257.122438
[09:41:02 -10351257.122438] FAST spr round 43 (radius: 25)
         - after brlen: logLH = -10351257.017756
[09:56:22 -10351257.017756] FAST spr round 44 (radius: 25)
         - after brlen: logLH = -10351257.017756
[10:11:41 -10351257.017756] Model parameter optimization (eps = 1.000000)
         - after rates: logLH = -10349776.244735
         - after freqs: logLH = -10349682.139791
         - after alpha: logLH = -10349574.462679
         - after p-inv: logLH = -10349574.462679
         - after freeR: logLH = -10349574.462679
         - after brlen: logLH = -10349534.314637
Iteration 1: logLH = -10349534.314637
         - after rates: logLH = -10349380.046801
         - after freqs: logLH = -10349299.910029
         - after alpha: logLH = -10349299.639095
         - after p-inv: logLH = -10349299.639095
         - after freeR: logLH = -10349299.639095
         - after brlen: logLH = -10349233.591349
Iteration 2: logLH = -10349233.591349
         - after rates: logLH = -10349220.929805
         - after freqs: logLH = -10349197.990022
         - after alpha: logLH = -10349188.612289
         - after p-inv: logLH = -10349188.612289
         - after freeR: logLH = -10349188.612289
         - after brlen: logLH = -10349157.719741
Iteration 3: logLH = -10349157.719741
         - after rates: logLH = -10349154.688967
         - after freqs: logLH = -10349152.227538
         - after alpha: logLH = -10349148.468388
         - after p-inv: logLH = -10349148.468388
         - after freeR: logLH = -10349148.468388
         - after brlen: logLH = -10349140.074094
Iteration 4: logLH = -10349140.074094
         - after rates: logLH = -10349079.391843
         - after freqs: logLH = -10349062.172494
         - after alpha: logLH = -10349062.172494
         - after p-inv: logLH = -10349062.172494
         - after freeR: logLH = -10349062.172494
         - after brlen: logLH = -10349055.367669
Iteration 5: logLH = -10349055.367669
         - after rates: logLH = -10349051.747483
         - after freqs: logLH = -10349049.803986
         - after alpha: logLH = -10349049.803986
         - after p-inv: logLH = -10349049.803986
         - after freeR: logLH = -10349049.803986
         - after brlen: logLH = -10349047.915509
Iteration 6: logLH = -10349047.915509
         - after rates: logLH = -10349001.372825
         - after freqs: logLH = -10348996.709057
         - after alpha: logLH = -10348995.707157
         - after p-inv: logLH = -10348995.707157
         - after freeR: logLH = -10348995.707157
         - after brlen: logLH = -10348993.074776
Iteration 7: logLH = -10348993.074776
         - after rates: logLH = -10348989.464290
         - after freqs: logLH = -10348988.581751
         - after alpha: logLH = -10348987.916689
         - after p-inv: logLH = -10348987.916689
         - after freeR: logLH = -10348987.916689
         - after brlen: logLH = -10348986.053077
Iteration 8: logLH = -10348986.053077
         - after rates: logLH = -10348985.145344
         - after freqs: logLH = -10348984.964685
         - after alpha: logLH = -10348984.952975
         - after p-inv: logLH = -10348984.952975
         - after freeR: logLH = -10348984.952975
         - after brlen: logLH = -10348983.522732
Iteration 9: logLH = -10348983.522732
         - after rates: logLH = -10348983.200599
         - after freqs: logLH = -10348983.157370
         - after alpha: logLH = -10348983.157370
         - after p-inv: logLH = -10348983.157370
         - after freeR: logLH = -10348983.157370
         - after brlen: logLH = -10348983.006569
Iteration 10: logLH = -10348983.006569
[10:14:26 -10348983.006569] SLOW spr round 1 (radius: 5)
         - after brlen: logLH = -10347710.411143
[10:39:31 -10347710.411143] SLOW spr round 2 (radius: 5)
         - after brlen: logLH = -10347562.616680
[11:04:07 -10347562.616680] SLOW spr round 3 (radius: 5)
         - after brlen: logLH = -10347438.191367
[11:28:24 -10347438.191367] SLOW spr round 4 (radius: 5)
         - after brlen: logLH = -10347363.209677
[11:52:23 -10347363.209677] SLOW spr round 5 (radius: 5)
         - after brlen: logLH = -10347352.031868
[12:15:43 -10347352.031868] SLOW spr round 6 (radius: 5)
         - after brlen: logLH = -10347350.366705
[12:38:54 -10347350.366705] SLOW spr round 7 (radius: 5)
         - after brlen: logLH = -10347345.307373
[13:02:06 -10347345.307373] SLOW spr round 8 (radius: 5)
         - after brlen: logLH = -10347343.897947
[13:24:47 -10347343.897947] SLOW spr round 9 (radius: 5)
         - after brlen: logLH = -10347342.808666
[13:47:44 -10347342.808666] SLOW spr round 10 (radius: 5)
         - after brlen: logLH = -10347338.980500
[14:11:03 -10347338.980500] SLOW spr round 11 (radius: 5)
         - after brlen: logLH = -10347338.980500
[14:34:15 -10347338.980500] SLOW spr round 12 (radius: 10)
         - after brlen: logLH = -10347050.078766
[14:59:52 -10347050.078766] SLOW spr round 13 (radius: 5)
         - after brlen: logLH = -10346990.991364
[15:29:43 -10346990.991364] SLOW spr round 14 (radius: 5)
         - after brlen: logLH = -10346904.424879
[15:56:10 -10346904.424879] SLOW spr round 15 (radius: 5)
         - after brlen: logLH = -10346883.152208
[16:20:15 -10346883.152208] SLOW spr round 16 (radius: 5)
         - after brlen: logLH = -10346875.243318
[16:43:17 -10346875.243318] SLOW spr round 17 (radius: 5)
         - after brlen: logLH = -10346874.840574
[17:06:05 -10346874.840574] SLOW spr round 18 (radius: 5)
         - after brlen: logLH = -10346872.440384
[17:29:03 -10346872.440384] SLOW spr round 19 (radius: 5)
         - after brlen: logLH = -10346872.440384
[17:51:37 -10346872.440384] SLOW spr round 20 (radius: 10)
         - after brlen: logLH = -10346858.054793
[18:15:44 -10346858.054793] SLOW spr round 21 (radius: 5)
         - after brlen: logLH = -10346804.247108
[18:44:54 -10346804.247108] SLOW spr round 22 (radius: 5)
         - after brlen: logLH = -10346804.247108
[19:10:39 -10346804.247108] SLOW spr round 23 (radius: 10)
         - after brlen: logLH = -10346761.657173
[19:36:35 -10346761.657173] SLOW spr round 24 (radius: 5)
         - after brlen: logLH = -10346701.226583
[20:05:56 -10346701.226583] SLOW spr round 25 (radius: 5)
         - after brlen: logLH = -10346700.950547
[20:31:23 -10346700.950547] SLOW spr round 26 (radius: 5)
         - after brlen: logLH = -10346700.950547
[20:54:48 -10346700.950547] SLOW spr round 27 (radius: 10)
         - after brlen: logLH = -10346663.314801
[21:20:00 -10346663.314801] SLOW spr round 28 (radius: 5)
         - after brlen: logLH = -10346617.223015
[21:49:52 -10346617.223015] SLOW spr round 29 (radius: 5)
         - after brlen: logLH = -10346617.223015
[22:15:01 -10346617.223015] SLOW spr round 30 (radius: 10)
         - after brlen: logLH = -10346614.904506
[22:40:49 -10346614.904506] SLOW spr round 31 (radius: 5)
         - after brlen: logLH = -10346524.197975
[23:10:32 -10346524.197975] SLOW spr round 32 (radius: 5)
         - after brlen: logLH = -10346522.361354
[23:35:44 -10346522.361354] SLOW spr round 33 (radius: 5)
         - after brlen: logLH = -10346522.361354
[23:59:23 -10346522.361354] SLOW spr round 34 (radius: 10)
         - after brlen: logLH = -10346522.361354
[24:24:20 -10346522.361354] SLOW spr round 35 (radius: 15)
         - after brlen: logLH = -10346440.916789
[25:10:31 -10346440.916789] SLOW spr round 36 (radius: 5)
         - after brlen: logLH = -10346417.940650
[25:41:11 -10346417.940650] SLOW spr round 37 (radius: 5)
         - after brlen: logLH = -10346417.940650
[26:07:39 -10346417.940650] SLOW spr round 38 (radius: 10)
         - after brlen: logLH = -10346417.940650
[26:34:23 -10346417.940650] SLOW spr round 39 (radius: 15)
         - after brlen: logLH = -10346383.511388
[27:18:57 -10346383.511388] SLOW spr round 40 (radius: 5)
         - after brlen: logLH = -10346363.066663
[27:49:52 -10346363.066663] SLOW spr round 41 (radius: 5)
         - after brlen: logLH = -10346363.066663
[28:16:19 -10346363.066663] SLOW spr round 42 (radius: 10)
         - after brlen: logLH = -10346363.066663
[28:43:06 -10346363.066663] SLOW spr round 43 (radius: 15)
         - after brlen: logLH = -10346353.271026
[29:27:54 -10346353.271026] SLOW spr round 44 (radius: 5)
         - after brlen: logLH = -10346350.970242
[29:58:42 -10346350.970242] SLOW spr round 45 (radius: 5)
         - after brlen: logLH = -10346324.073651
[30:25:39 -10346324.073651] SLOW spr round 46 (radius: 5)
         - after brlen: logLH = -10346300.343150
[30:50:35 -10346300.343150] SLOW spr round 47 (radius: 5)
         - after brlen: logLH = -10346299.867960
[31:13:45 -10346299.867960] SLOW spr round 48 (radius: 5)
         - after brlen: logLH = -10346299.867960
[31:36:29 -10346299.867960] SLOW spr round 49 (radius: 10)
         - after brlen: logLH = -10346299.867960
[32:00:48 -10346299.867960] SLOW spr round 50 (radius: 15)
         - after brlen: logLH = -10346299.867960
[32:48:09 -10346299.867960] SLOW spr round 51 (radius: 20)
         - after brlen: logLH = -10346299.867960
[34:04:05 -10346299.867960] SLOW spr round 52 (radius: 25)
         - after brlen: logLH = -10346299.867960
[35:42:37 -10346299.867960] Model parameter optimization (eps = 0.100000)
         - after rates: logLH = -10346299.698036
         - after freqs: logLH = -10346299.396250
         - after alpha: logLH = -10346299.396250
         - after p-inv: logLH = -10346299.396250
         - after freeR: logLH = -10346299.396250
         - after brlen: logLH = -10346299.331205
Iteration 1: logLH = -10346299.331205
         - after rates: logLH = -10346299.304296
         - after freqs: logLH = -10346299.290322
         - after alpha: logLH = -10346299.290322
         - after p-inv: logLH = -10346299.290322
         - after freeR: logLH = -10346299.290322
         - after brlen: logLH = -10346299.268211
Iteration 2: logLH = -10346299.268211

[35:42:51] ML tree search #1, logLikelihood: -10346299.268211

[35:42:52 -358718771.056143] Initial branch length optimization
         - after brlen: logLH = -0.000000
terminate called recursively
terminate called recursively
/var/spool/slurm/d/job13733182/slurm_script: line 29: 63733 Aborted                 (core dumped) raxml-ng --all --msa SNP.parse.raxml.rba --model GTR+G+ASC_FELS{$invar_sites} --prefix SNP --threads 24 --workers 1 --bs-trees 100 --log debug

I didn't set up a way of tracking the memory usage throughout the job, but at least in the beginning, it was using around a quarter of the available memory (~200G) on the system.

(The very first run I did had access to 1 TB of memory, but I ran out my cpu hour allocation on that system)

@0xaf1f
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0xaf1f commented Jan 6, 2023

Hi, I know this overlapped with the holiday season, but I wanted to make sure it isn't forgotten. My allocation on the cluster expired and I'll see if we can get a new one, but I did manage to get that debug output for you before that happened.

many thanks for all your help

@amkozlov
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Thank you, this debug output was very helpful.

Here are a couple of things you can try:

  1. Add --redo to ignore checkpoint and start a fresh run,
  2. Add --lh-epsilon 10 to accelerate the tree search (convergence is very slow here, which is not uncommon on datasets with thousands of taxa)
  3. Add --blopt nr_safe option (this enables additional checks which makes inference slower but more robust)

As a side note. according to the log file, your system has 128 cores and 250GB of memory. This means that: a) 200GB would be pretty close to the limit, b) you can probably use more than 24 threads (if despite the above, it turns out memory is not the constraint).

@0xaf1f
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0xaf1f commented Feb 1, 2023

sorry for the delay, but I've gotten renewed access to the cluster and just run it with these three settings. Now I've gotten a new error right before the core dump:


RAxML-NG v. 1.1.0 released on 29.11.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: AMD EPYC 7742 64-Core Processor, 128 cores, 251 GB RAM

RAxML-NG was called at 01-Feb-2023 13:05:50 as follows:

raxml-ng --redo --lh-epsilon 10 --blopt nr_safe --all --msa SNP.parse.raxml.rba --model GTR+G+ASC_FELS{4087123} --prefix SNP --threads 24 --workers 1 --bs-trees 100 --log debug

Analysis options:
  run mode: ML tree search + bootstrapping (Felsenstein Bootstrap)
  start tree(s): random (10) + parsimony (10)
  bootstrap replicates: 100
  random seed: 1675274750
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  branch lengths: proportional (ML estimate, algorithm: NR-SAFE)
  SIMD kernels: AVX2
  parallelization: PTHREADS (24 threads), thread pinning: OFF

RBA partial loading: OFF
WARNING: Running in REDO mode: existing checkpoints are ignored, and all result files will be overwritten!

WARNING: The model you specified on the command line (GTR+G+ASC_FELS{4087123}) will be ignored 
         since the binary MSA file already contains a model definition.
         If you want to change the model, please re-run RAxML-NG 
         with the original PHYLIP/FASTA alignment and --redo option.

[00:00:00] Loading binary alignment from file: SNP.parse.raxml.rba
[00:00:04] Alignment comprises 4832 taxa, 1 partitions and 82354 patterns

Partition 0: noname
Model: GTR+FO+G4m+ASC_FELS{4087123}
Alignment sites / patterns: 324409 / 82354
Gaps: 0.00 %
Invariant sites: 0.00 %


|noname|   |GTR+FO+G4m+ASC_FELS{4087123}|   |1-324409|

NOTE: Per-rate scalers were automatically enabled to prevent numerical issues on taxa-rich alignments.
NOTE: You can use --force switch to skip this check and fall back to per-site scalers.

Generating a random starting tree with 4832 taxa
Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:04] Generating 10 random starting tree(s) with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
[00:00:04] Generating 10 parsimony starting tree(s) with 4832 taxa
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 1558950843
Parsimony score of the starting tree: 940193
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 848384151
Parsimony score of the starting tree: 939019
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 1052997793
Parsimony score of the starting tree: 939156
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 400527839
Parsimony score of the starting tree: 938570
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 1112046720
Parsimony score of the starting tree: 938814
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 222282738
Parsimony score of the starting tree: 939227
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 297541634
Parsimony score of the starting tree: 940208
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 1044300830
Parsimony score of the starting tree: 938393
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 1611091263
Parsimony score of the starting tree: 939272
Generating a parsimony starting tree with 4832 taxa
Parsimony seed: 570470538
Parsimony score of the starting tree: 940064

Initial model parameters:
   Partition: noname
   Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 1.000000 (ML),  weights&rates: (0.250000,0.136954) (0.250000,0.476752) (0.250000,1.000000) (0.250000,2.386294) 
   Base frequencies (ML): 0.250000 0.250000 0.250000 0.250000 
   Substitution rates (ML): 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 

[00:47:05] Data distribution: max. partitions/sites/weight per thread: 1 / 3432 / 54912

thread# part#   start   length  weight
0       0       78936   3418    54688

1       0       75504   3432    54912

2       0       72072   3432    54912

3       0       68640   3432    54912

4       0       65208   3432    54912

5       0       61776   3432    54912

6       0       58344   3432    54912

7       0       54912   3432    54912

8       0       51480   3432    54912

9       0       48048   3432    54912

10      0       44616   3432    54912

11      0       41184   3432    54912

12      0       37752   3432    54912

13      0       34320   3432    54912

14      0       30888   3432    54912

15      0       27456   3432    54912

16      0       24024   3432    54912

17      0       20592   3432    54912

18      0       17160   3432    54912

19      0       13728   3432    54912

20      0       10296   3432    54912

21      0       6864    3432    54912

22      0       3432    3432    54912

23      0       0       3432    54912

Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
Generating a random starting tree with 4832 taxa
[00:47:05] Data distribution: max. searches per worker: 120

BARRIER time: 0.007015 ms

Starting ML tree search with 20 distinct starting trees

[00:47:09 -614172163.674568] Initial branch length optimization
         - after brlen: logLH = -0.000000

ERROR: ERROR in branch length optimization (LIBPLL-2210): Wrong likelihood derivatives

terminate called recursively
terminate called recursively
/var/spool/slurm/d/job14250675/slurm_script: line 32: 93657 Aborted                 (core dumped) raxml-ng --redo --lh-epsilon 10 --blopt nr_safe --all --msa SNP.parse.raxml.rba --model GTR+G+ASC_FELS{$invar_sites} --prefix SNP --threads 24 --workers 1 --bs-trees 100 --log debug

@amkozlov
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Sorry for the delay! Since I can't see any obvious reasons for this error, could you please send me you input file?

(Even better if you could reproduce this error on a smaller alignment)

@Dived-Jin
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Hi, I also see the same problem, Did you solve this problem?

@amkozlov
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Please send me your input files and full raxml log, and I will have a look.

@domivika domivika mentioned this issue Nov 11, 2024
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@0xaf1f @amkozlov @Dived-Jin