"illegal hardware instruction" error
Alison Ravenscraft
Hi all,
When I try to run raxml, it gives me the following error: "zsh: illegal hardware instruction ./raxml -g -s -q -m GTRGAMMA -n raxml_info_oldpartitions -p 1 -T 2" The problem might be incompatibility with arm64 architecture (I have a Mac with M2 chip) but I tried to run it in an osx64 environment. Can anyone help troubleshoot?
Below is what I did and the output I got. I created an osx-64 environment, added channels for bioconda and conda-forge, and installed raxml. Then I tried to run raxml with the call ./raxml -g tree/CONCAT_alignments RAxML Tree.newick -s tree/CONCAT_alignments.fasta -q tree/old_partitions.txt -m GTRGAMMA -n raxml_info_oldpartitions -p 1 -T 2 It started up successfully but ended with the error.
araven@BIOL ~ % conda create -n intel_env
conda activate intel_env
conda config --env --set subdir osx-64
conda install python
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.1.0
latest version: 23.5.0
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.5.0
## Package Plan ##
environment location: /opt/homebrew/Caskroom/miniforge/base/envs/intel_env
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate intel_env
#
# To deactivate an active environment, use
#
# $ conda deactivate
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.1.0
latest version: 23.5.0
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.5.0
## Package Plan ##
environment location: /opt/homebrew/Caskroom/miniforge/base/envs/intel_env
added / updated specs:
- python
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | h0d85af4_4 155 KB conda-forge
ca-certificates-2023.5.7 | h8857fd0_0 145 KB conda-forge
libexpat-2.5.0 | hf0c8a7f_1 68 KB conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB conda-forge
libsqlite-3.42.0 | h58db7d2_0 858 KB conda-forge
libzlib-1.2.13 | h8a1eda9_5 58 KB conda-forge
ncurses-6.4 | hf0c8a7f_0 809 KB conda-forge
openssl-3.1.1 | h8a1eda9_1 2.2 MB conda-forge
python-3.11.4 |h30d4d87_0_cpython 14.6 MB conda-forge
readline-8.2 | h9e318b2_1 250 KB conda-forge
tk-8.6.12 | h5dbffcc_0 3.4 MB conda-forge
xz-5.2.6 | h775f41a_0 233 KB conda-forge
------------------------------------------------------------
Total: 22.8 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
ca-certificates conda-forge/osx-64::ca-certificates-2023.5.7-h8857fd0_0
libexpat conda-forge/osx-64::libexpat-2.5.0-hf0c8a7f_1
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.42.0-h58db7d2_0
libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
ncurses conda-forge/osx-64::ncurses-6.4-hf0c8a7f_0
openssl conda-forge/osx-64::openssl-3.1.1-h8a1eda9_1
pip conda-forge/noarch::pip-23.1.2-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.11.4-h30d4d87_0_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0
tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0
wheel conda-forge/noarch::wheel-0.40.0-pyhd8ed1ab_0
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(intel_env) araven@BIOL ~ % conda activate intel_env
(intel_env) araven@BIOL ~ % conda config --env --add channels defaults
conda config --env --add channels bioconda
conda config --env --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top
(intel_env) araven@BIOL ~ % conda install raxml
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 23.1.0
latest version: 23.5.0
Please update conda by running
$ conda update -n base -c conda-forge conda
Or to minimize the number of packages updated during conda update use
conda install conda=23.5.0
## Package Plan ##
environment location: /opt/homebrew/Caskroom/miniforge/base/envs/intel_env
added / updated specs:
- raxml
The following packages will be downloaded:
package | build
---------------------------|-----------------
raxml-8.2.12 | h2413b67_6 2.6 MB bioconda
------------------------------------------------------------
Total: 2.6 MB
The following NEW packages will be INSTALLED:
raxml bioconda/osx-64::raxml-8.2.12-h2413b67_6
Proceed ([y]/n)? y
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(intel_env) araven@BIOL ~ % cd /Applications/raxmlHPC-AVX-v8
(intel_env) araven@BIOL raxmlHPC-AVX-v8 % ./raxml -g tree/CONCAT_tree.newick -s tree/CONCAT_alignments.fasta -q tree/old_partitions.txt -m GTRGAMMA -n raxml_info_oldpartitions -p 1 -T 2
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
IMPORTANT WARNING: Sequences Caballeronia_glathei_LMG_14190 and Caballeronia_glathei_DSM_50014 are exactly identical
IMPORTANT WARNING: Sequences Caballeronia_udeis_ES_FE-B12 and Caballeronia_sordidicola_ES_PA-B12 are exactly identical
IMPORTANT WARNING
Found 2 sequences that are exactly identical to other sequences in the alignment.
Normally they should be excluded from the analysis.
A mixed model file with model assignments for undetermined
columns removed has already been printed to file tree/old_partitions.txt.reduced
An alignment file with sequence duplicates removed has already
been printed to file tree/CONCAT_alignments.fasta.reduced
This is the RAxML Master Pthread
This is RAxML Worker Pthread Number: 1
This is RAxML version 8.0.0 released by Alexandros Stamatakis on Dec 13 2013.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
David Dao (KIT)
Charlie Taylor (UF)
Alignment has 4534 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 1.41%
RAxML rapid hill-climbing mode
Using 13 distinct models/data partitions with joint branch length optimization
Executing 1 inferences on the original alignment using 1 user-specifed trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 279
Name: rpoBcodon1
DataType: DNA
Substitution Matrix: GTR
Partition: 1
Alignment Patterns: 153
Name: rpoBcodon2
DataType: DNA
Substitution Matrix: GTR
Partition: 2
Alignment Patterns: 1200
Name: rpoBcodon3
DataType: DNA
Substitution Matrix: GTR
Partition: 3
Alignment Patterns: 329
Name: rpoCcodon1
DataType: DNA
Substitution Matrix: GTR
Partition: 4
Alignment Patterns: 170
Name: rpoCcodon2
DataType: DNA
Substitution Matrix: GTR
Partition: 5
Alignment Patterns: 1190
Name: rpoCcodon3
DataType: DNA
Substitution Matrix: GTR
Partition: 6
Alignment Patterns: 79
Name: rplACcodon1
DataType: DNA
Substitution Matrix: GTR
Partition: 7
Alignment Patterns: 46
Name: rplACcodon2
DataType: DNA
Substitution Matrix: GTR
Partition: 8
Alignment Patterns: 227
Name: rplACcodon3
DataType: DNA
Substitution Matrix: GTR
Partition: 9
Alignment Patterns: 126
Name: recACcodon1
DataType: DNA
Substitution Matrix: GTR
Partition: 10
Alignment Patterns: 82
Name: recACcodon2
DataType: DNA
Substitution Matrix: GTR
Partition: 11
Alignment Patterns: 340
Name: recACcodon3
DataType: DNA
Substitution Matrix: GTR
Partition: 12
Alignment Patterns: 313
Name: 16s
DataType: DNA
Substitution Matrix: GTR
RAxML was called as follows:
./raxml -g tree/CONCAT_alignments RAxML Tree.newick -s tree/CONCAT_alignments.fasta -q tree/old_partitions.txt -m GTRGAMMA -n raxml_info_oldpartitions -p 1 -T 2
Partition: 0 with name: rpoBcodon1
Base frequencies: 0.234 0.257 0.385 0.123
Partition: 1 with name: rpoBcodon2
Base frequencies: 0.329 0.208 0.163 0.300
Partition: 2 with name: rpoBcodon3
Base frequencies: 0.084 0.407 0.398 0.111
Partition: 3 with name: rpoCcodon1
Base frequencies: 0.246 0.252 0.389 0.113
Partition: 4 with name: rpoCcodon2
Base frequencies: 0.306 0.225 0.169 0.299
Partition: 5 with name: rpoCcodon3
Base frequencies: 0.077 0.372 0.437 0.114
Partition: 6 with name: rplACcodon1
Base frequencies: 0.234 0.223 0.452 0.091
Partition: 7 with name: rplACcodon2
Base frequencies: 0.276 0.276 0.156 0.291
Partition: 8 with name: rplACcodon3
Base frequencies: 0.097 0.356 0.386 0.160
Partition: 9 with name: recACcodon1
Base frequencies: 0.263 0.203 0.431 0.102
Partition: 10 with name: recACcodon2
Base frequencies: 0.299 0.220 0.183 0.297
Partition: 11 with name: recACcodon3
Base frequencies: 0.100 0.415 0.393 0.091
Partition: 12 with name: 16s
Base frequencies: 0.249 0.234 0.322 0.196
zsh: illegal hardware instruction ./raxml -g -s -q -m GTRGAMMA -n raxml_info_oldpartitions -p 1 -T 2
Alexandros Stamatakis
Please see this prior conversation here:
https://groups.google.com/g/raxml/c/1cRSPXcZa1o/m/TR57KjI0BgAJ
for a possible solution.
Alexis
On 13.07.23 01:21, Alison Ravenscraft wrote:
> Hi all,
>
> I tried to run it in an osx64 environment. Can anyone help troubleshoot?
>
> Below is what I did and the output I got. I created an osx-64
> environment, added channels for bioconda and conda-forge, and installed
> -q tree/old_partitions.txt -m GTRGAMMA -n raxml_info_oldpartitions -p 1
>
>
> /araven@BIOL ~ % conda create -n intel_env/
>
> /conda activate intel_env/
>
> /conda config --env --set subdir osx-64/
>
> /conda install python/
> libexpat conda-forge/osx-64::libexpat-2.5.0-hf0c8a7f_1
>
> libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
>
> libsqliteconda-forge/osx-64::libsqlite-3.42.0-h58db7d2_0
>
> libzlibconda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
>
> ncursesconda-forge/osx-64::ncurses-6.4-hf0c8a7f_0
>
> opensslconda-forge/osx-64::openssl-3.1.1-h8a1eda9_1
>
> python conda-forge/osx-64::python-3.11.4-h30d4d87_0_cpython
>
> readline conda-forge/osx-64::readline-8.2-h9e318b2_1
>
> setuptools conda-forge/noarch::setuptools-68.0.0-pyhd8ed1ab_0
>
> tk conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
>
> tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0
>
> xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
>
>
> Proceed ([y]/n)? y
>
>
> Downloading and Extracting Packages
>
> Preparing transaction: done
>
> Verifying transaction: done
>
> Executing transaction: done
>
>
> /(intel_env) araven@BIOL ~ % conda config --env --add channels defaults/
>
> /conda config --env --add channels bioconda/
>
> /conda config --env --add channels conda-forge/
>
> /
> /
> Warning: 'conda-forge' already in 'channels' list, moving to the top
>
>
> Collecting package metadata (current_repodata.json): done
>
> Solving environment: done
>
>
> ==> WARNING: A newer version of conda exists. <==
>
> current version: 23.1.0
>
> latest version: 23.5.0
>
>
> Please update conda by running
>
> $ conda update -n base -c conda-forge conda
>
> Or to minimize the number of packages updated during conda update use
>
> conda install conda=23.5.0
>
>
> ## Package Plan ##
>
> environment location: /opt/homebrew/Caskroom/miniforge/base/envs/intel_env
>
> added / updated specs:
>
> - raxml
>
>
> The following packages will be downloaded:
>
> package|build
>
> ---------------------------|-----------------
>
> raxml-8.2.12 | h2413b67_6 2.6 MBbioconda
>
> ------------------------------------------------------------
>
> Total: 2.6 MB
>
>
> The following NEW packages will be INSTALLED:
>
>
> Proceed ([y]/n)? y
>
>
> Downloading and Extracting Packages
>
> Preparing transaction: done
>
> Verifying transaction: done
>
> Executing transaction: done
>
>
>
> /(intel_env) araven@BIOL raxmlHPC-AVX-v8 % ./raxml -g
> tree/CONCAT_tree.newick -s tree/CONCAT_alignments.fasta -q
> tree/old_partitions.txt -m GTRGAMMA -n raxml_info_oldpartitions -p 1 -T 2/
>
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/raxml/5c294e62-38f5-4248-83a0-787f8ec9700dn%40googlegroups.com <https://groups.google.com/d/msgid/raxml/5c294e62-38f5-4248-83a0-787f8ec9700dn%40googlegroups.com?utm_medium=email&utm_source=footer>.
--
Alexandros (Alexis) Stamatakis
ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)