search

davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
704 stars 188 forks source link

STRIDE ERROR #566

Open lisiruiyu opened 3 years ago

lisiruiyu commented 3 years ago

Hello, after I downloaded orthofinder with conda, the following code appeared For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default. To enable it, please set the environmental variable OMPI_MCA_opal_cuda_support=true before launching your MPI processes. Equivalently, you can set the MCA parameter in the command line: mpiexec --mca opal_cuda_support 1 ... Appeared during operation stdout b'' stderr Cause the kernel to crash

davidemms commented 3 years ago

Hi

Unfortunately I don't know what this about, OrthoFinder doesn't use Open MPI or CUDA, I think this is probably from something else.

Best wishes David

davidemms commented 3 years ago

Hi

I'd like to dig into this a bit more, do you have the full output produced by orthofinder? Or if not, do you know at what stage of the algorithm this occurred?

Many thanks David

rrrongon commented 10 months ago

I have the same issue

SilentGene commented 7 months ago

fyi, I got a similar message after installation by Conda, although the program didn't crash:

$ conda install bioconda::orthofinder
Channels:
 - bioconda
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/lin92/miniconda3/envs/orthofinder

  added / updated specs:
    - bioconda::orthofinder

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    aria2-1.36.0               |       h1e4e653_3         1.8 MB  conda-forge
    curl-8.6.0                 |       hca28451_0          91 KB  conda-forge
    diamond-2.1.9              |       h43eeafb_0         3.5 MB  bioconda
    entrez-direct-21.6         |       he881be0_0        14.0 MB  bioconda
    fastme-2.1.6.1             |       h031d066_3         147 KB  bioconda
    fasttree-2.1.11            |       h031d066_3         262 KB  bioconda
    gmp-6.3.0                  |       h59595ed_1         556 KB  conda-forge
    iqtree-2.3.0               |       h21ec9f0_0         7.5 MB  bioconda
    mafft-7.525                |       h031d066_1         3.3 MB  bioconda
    mmseqs2-15.6f452           | pl5321h6a68c12_1         4.2 MB  bioconda
    mpi-1.0                    |          openmpi           4 KB  conda-forge
    muscle-3.8.1551            |       h7d875b9_6         262 KB  bioconda
    ncbi-vdb-3.1.0             |       hdbdd923_0        10.6 MB  bioconda
    openmpi-4.1.6              |     hc5af2df_101         3.9 MB  conda-forge
    orthofinder-2.5.5          |       hdfd78af_2         132 KB  bioconda
    raxml-ng-1.2.1             |       h6d1f11b_0         1.8 MB  bioconda
    wget-1.21.4                |       hda4d442_0         752 KB  conda-forge
    wheel-0.43.0               |     pyhd8ed1ab_0          57 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        52.8 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
  aria2              conda-forge/linux-64::aria2-1.36.0-h1e4e653_3
  blast              bioconda/linux-64::blast-2.15.0-pl5321h6f7f691_1
  bzip2              conda-forge/linux-64::bzip2-1.0.8-hd590300_5
  c-ares             conda-forge/linux-64::c-ares-1.27.0-hd590300_0
  ca-certificates    conda-forge/linux-64::ca-certificates-2024.2.2-hbcca054_0
  curl               conda-forge/linux-64::curl-8.6.0-hca28451_0
  diamond            bioconda/linux-64::diamond-2.1.9-h43eeafb_0
  entrez-direct      bioconda/linux-64::entrez-direct-21.6-he881be0_0
  fastme             bioconda/linux-64::fastme-2.1.6.1-h031d066_3
  fasttree           bioconda/linux-64::fasttree-2.1.11-h031d066_3
  gawk               conda-forge/linux-64::gawk-5.3.0-ha916aea_0
  gettext            conda-forge/linux-64::gettext-0.21.1-h27087fc_0
  gmp                conda-forge/linux-64::gmp-6.3.0-h59595ed_1
  icu                conda-forge/linux-64::icu-70.1-h27087fc_0
  iqtree             bioconda/linux-64::iqtree-2.3.0-h21ec9f0_0
  keyutils           conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
  krb5               conda-forge/linux-64::krb5-1.21.2-h659d440_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
  libblas            conda-forge/linux-64::libblas-3.9.0-21_linux64_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-21_linux64_openblas
  libcurl            conda-forge/linux-64::libcurl-8.6.0-hca28451_0
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-hd590300_2
  libexpat           conda-forge/linux-64::libexpat-2.6.2-h59595ed_0
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5
  libgcc-ng          conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_5
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_5
  libgfortran5       conda-forge/linux-64::libgfortran5-13.2.0-ha4646dd_5
  libgomp            conda-forge/linux-64::libgomp-13.2.0-h807b86a_5
  libiconv           conda-forge/linux-64::libiconv-1.17-hd590300_2
  libidn2            conda-forge/linux-64::libidn2-2.3.7-hd590300_0
  liblapack          conda-forge/linux-64::liblapack-3.9.0-21_linux64_openblas
  libnghttp2         conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_1
  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0
  libopenblas        conda-forge/linux-64::libopenblas-0.3.26-pthreads_h413a1c8_0
  libsqlite          conda-forge/linux-64::libsqlite-3.45.2-h2797004_0
  libssh2            conda-forge/linux-64::libssh2-1.11.0-h0841786_0
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_5
  libunistring       conda-forge/linux-64::libunistring-0.9.10-h7f98852_0
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
  libxml2            conda-forge/linux-64::libxml2-2.9.14-h22db469_4
  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5
  mafft              bioconda/linux-64::mafft-7.525-h031d066_1
  mcl                bioconda/linux-64::mcl-22.282-pl5321h031d066_1
  mmseqs2            bioconda/linux-64::mmseqs2-15.6f452-pl5321h6a68c12_1
  mpfr               conda-forge/linux-64::mpfr-4.2.1-h9458935_0
  mpi                conda-forge/linux-64::mpi-1.0-openmpi
  muscle             bioconda/linux-64::muscle-3.8.1551-h7d875b9_6
  ncbi-vdb           bioconda/linux-64::ncbi-vdb-3.1.0-hdbdd923_0
  ncurses            conda-forge/linux-64::ncurses-6.4.20240210-h59595ed_0
  numpy              conda-forge/linux-64::numpy-1.26.4-py312heda63a1_0
  openmpi            conda-forge/linux-64::openmpi-4.1.6-hc5af2df_101
  openssl            conda-forge/linux-64::openssl-3.2.1-hd590300_1
  orthofinder        bioconda/noarch::orthofinder-2.5.5-hdfd78af_2
  ossuuid            conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000
  pcre               conda-forge/linux-64::pcre-8.45-h9c3ff4c_0
  perl               conda-forge/linux-64::perl-5.32.1-7_hd590300_perl5
  perl-alien-build   bioconda/linux-64::perl-alien-build-2.48-pl5321hec16e2b_0
  perl-alien-libxml2 bioconda/linux-64::perl-alien-libxml2-0.17-pl5321hec16e2b_0
  perl-archive-tar   bioconda/noarch::perl-archive-tar-2.40-pl5321hdfd78af_0
  perl-business-isbn bioconda/noarch::perl-business-isbn-3.007-pl5321hdfd78af_0
  perl-business-isb~ bioconda/noarch::perl-business-isbn-data-20210112.006-pl5321hdfd78af_0
  perl-capture-tiny  bioconda/noarch::perl-capture-tiny-0.48-pl5321hdfd78af_2
  perl-carp          bioconda/noarch::perl-carp-1.38-pl5321hdfd78af_4
  perl-common-sense  bioconda/noarch::perl-common-sense-3.75-pl5321hdfd78af_0
  perl-compress-raw~ bioconda/linux-64::perl-compress-raw-bzip2-2.201-pl5321h87f3376_1
  perl-compress-raw~ bioconda/linux-64::perl-compress-raw-zlib-2.105-pl5321h87f3376_0
  perl-constant      bioconda/noarch::perl-constant-1.33-pl5321hdfd78af_2
  perl-data-dumper   bioconda/linux-64::perl-data-dumper-2.183-pl5321hec16e2b_1
  perl-encode        bioconda/linux-64::perl-encode-3.19-pl5321hec16e2b_1
  perl-exporter      bioconda/noarch::perl-exporter-5.72-pl5321hdfd78af_2
  perl-exporter-tiny bioconda/noarch::perl-exporter-tiny-1.002002-pl5321hdfd78af_0
  perl-extutils-mak~ conda-forge/noarch::perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0
  perl-ffi-checklib  bioconda/noarch::perl-ffi-checklib-0.28-pl5321hdfd78af_0
  perl-file-chdir    bioconda/noarch::perl-file-chdir-0.1010-pl5321hdfd78af_3
  perl-file-path     conda-forge/noarch::perl-file-path-2.18-pl5321hd8ed1ab_0
  perl-file-temp     conda-forge/noarch::perl-file-temp-0.2304-pl5321hd8ed1ab_0
  perl-file-which    conda-forge/noarch::perl-file-which-1.24-pl5321hd8ed1ab_0
  perl-importer      bioconda/noarch::perl-importer-0.026-pl5321hdfd78af_0
  perl-io-compress   bioconda/linux-64::perl-io-compress-2.201-pl5321hdbdd923_2
  perl-io-zlib       bioconda/noarch::perl-io-zlib-1.14-pl5321hdfd78af_0
  perl-json          bioconda/noarch::perl-json-4.10-pl5321hdfd78af_0
  perl-json-xs       bioconda/linux-64::perl-json-xs-2.34-pl5321h4ac6f70_6
  perl-list-moreuti~ bioconda/noarch::perl-list-moreutils-0.430-pl5321hdfd78af_0
  perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-xs-0.430-pl5321h031d066_2
  perl-mime-base64   bioconda/linux-64::perl-mime-base64-3.16-pl5321hec16e2b_2
  perl-parent        bioconda/noarch::perl-parent-0.236-pl5321hdfd78af_2
  perl-path-tiny     bioconda/noarch::perl-path-tiny-0.122-pl5321hdfd78af_0
  perl-pathtools     bioconda/linux-64::perl-pathtools-3.75-pl5321hec16e2b_3
  perl-scalar-list-~ bioconda/linux-64::perl-scalar-list-utils-1.62-pl5321hec16e2b_1
  perl-scope-guard   bioconda/noarch::perl-scope-guard-0.21-pl5321hdfd78af_3
  perl-sub-info      bioconda/noarch::perl-sub-info-0.002-pl5321hdfd78af_1
  perl-term-table    bioconda/noarch::perl-term-table-0.016-pl5321hdfd78af_0
  perl-test2-suite   bioconda/noarch::perl-test2-suite-0.000145-pl5321hdfd78af_0
  perl-types-serial~ bioconda/noarch::perl-types-serialiser-1.01-pl5321hdfd78af_0
  perl-uri           bioconda/noarch::perl-uri-5.12-pl5321hdfd78af_0
  perl-xml-libxml    bioconda/linux-64::perl-xml-libxml-2.0207-pl5321h661654b_0
  perl-xml-namespac~ bioconda/noarch::perl-xml-namespacesupport-1.12-pl5321hdfd78af_1
  perl-xml-sax       bioconda/noarch::perl-xml-sax-1.02-pl5321hdfd78af_1
  perl-xml-sax-base  bioconda/noarch::perl-xml-sax-base-1.09-pl5321hdfd78af_1
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
  python             conda-forge/linux-64::python-3.12.2-hab00c5b_0_cpython
  python_abi         conda-forge/linux-64::python_abi-3.12-4_cp312
  raxml              bioconda/linux-64::raxml-8.2.13-h031d066_0
  raxml-ng           bioconda/linux-64::raxml-ng-1.2.1-h6d1f11b_0
  readline           conda-forge/linux-64::readline-8.2-h8228510_1
  scipy              conda-forge/linux-64::scipy-1.12.0-py312heda63a1_2
  setuptools         conda-forge/noarch::setuptools-69.2.0-pyhd8ed1ab_0
  tk                 conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0
  wget               conda-forge/linux-64::wget-1.21.4-hda4d442_0
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_0
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0
  zlib               conda-forge/linux-64::zlib-1.2.13-hd590300_5
  zstd               conda-forge/linux-64::zstd-1.5.5-hfc55251_0

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: \
For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
mpiexec --mca opal_cuda_support 1 ...

In addition, the UCX support is also built but disabled by default.
To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
Equivalently, you can set the MCA parameters in the command line:
mpiexec --mca pml ucx --mca osc ucx ...
Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
Please consult UCX's documentation for detail.

                                                                      done