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Error occurred when use ' conda create -y -v --clone ' to clone pytorch, but tensorflow not.

mpi_new_user
New Contributor II
‎05-10-2021 07:50 PM
3,413 Views

Hi，

I run the image which is built by singularity and based on Intel AI Toolkit.

When I run the command  `conda env list`:

root@head:/home/hpcadmin# conda env list
# conda environments:
#
                         /home/hpcadmin/fy/test_ai/tensorflow2
base                  *  /opt/intel/oneapi/intelpython/latest
2021.2.0                 /opt/intel/oneapi/intelpython/latest/envs/2021.2.0
pytorch                  /opt/intel/oneapi/intelpython/latest/envs/pytorch
pytorch-1.7.0            /opt/intel/oneapi/intelpython/latest/envs/pytorch-1.7.0
tensorflow               /opt/intel/oneapi/intelpython/latest/envs/tensorflow
tensorflow-2.3.0         /opt/intel/oneapi/intelpython/latest/envs/tensorflow-2.3.0
                         /tmp/hpcadmin/oneapi/pytorch/latest

 And  the error will happen after I run the clone command:

 

root@head:/home/hpcadmin/fy/test_ai# conda create -y -v --clone pytorch -p /home/hpcadmin/fy/test_ai/pytorch
Source:      /opt/intel/oneapi/intelpython/latest/envs/pytorch-1.7.0
Destination: /home/hpcadmin/fy/test_ai/pytorch
The following packages cannot be cloned out of the root environment:
 - defaults/linux-64::conda-4.10.1-py37h06a4308_1
Packages: 145
Files: 203

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/opt/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/opt/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/opt/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
        return getattr(module, func_name)(args, parser)
      File "/opt/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/conda/cli/main_create.py", line 41, in execute
        install(args, parser, 'create')
      File "/opt/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/conda/cli/install.py", line 222, in install
        clone(args.clone, prefix, json=context.json, quiet=context.quiet, index_args=index_args)
      File "/opt/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/conda/cli/install.py", line 74, in clone
        index_args=index_args)
      File "/opt/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/conda/misc.py", line 290, in clone_env
        force_extract=False, index_args=index_args)
      File "/opt/intel/oneapi/intelpython/latest/lib/python3.7/site-packages/conda/misc.py", line 90, in explicit
        assert not any(spec_pcrec[1] is None for spec_pcrec in specs_pcrecs)
    AssertionError

`$ /opt/intel/oneapi/intelpython/latest/bin/conda create -y -v --clone pytorch-1.7.0 -p /home/hpcadmin/fy/test_ai/pytorch`

  environment variables:
    ACL_BOARD_VENDOR_PATH=/opt/Intel/OpenCLFPGA/oneAPI/Boards
                 CIO_TEST=<not set>
                CLASSPATH=/opt/intel/oneapi/mpi/2021.2.0//lib/mpi.jar:/opt/intel/oneapi/dal/2021
                          .2.0/lib/onedal.jar
        CMAKE_PREFIX_PATH=/opt/intel/oneapi/vpl:/opt/intel/oneapi/tbb/2021.2.0/env/..:/opt/intel
                          /oneapi/dal/2021.2.0
                CONDA_EXE=/opt/intel/oneapi/intelpython/latest/bin/conda
         CONDA_PYTHON_EXE=/opt/intel/oneapi/intelpython/latest/bin/python
               CONDA_ROOT=/opt/intel/oneapi/intelpython/latest
              CONDA_SHLVL=0
                    CPATH=/opt/intel/oneapi/vpl/2021.2.2/include:/opt/intel/oneapi/tbb/2021.2.0/
                          env/../include:/opt/intel/oneapi/mpi/2021.2.0//include:/opt/intel/onea
                          pi/mkl/latest/include:/opt/intel/oneapi/ippcp/2021.2.0/include:/opt/in
                          tel/oneapi/ipp/2021.2.0/include:/opt/intel/oneapi/dpl/2021.2.0/linux/i
                          nclude:/opt/intel/oneapi/dnnl/2021.2.0/cpu_dpcpp_gpu_dpcpp/lib:/opt/in
                          tel/oneapi/dev-utilities/2021.2.0/include:/opt/intel/oneapi/dal/2021.2
                          .0/include:/opt/intel/oneapi/compiler/2021.2.0/linux/include:/opt/inte
                          l/oneapi/ccl/2021.2.0/include/cpu_gpu_dpcpp
           CURL_CA_BUNDLE=<not set>
         FI_PROVIDER_PATH=/opt/intel/oneapi/mpi/2021.2.0/libfabric/lib/prov:/usr/lib64/libfabric
                 INFOPATH=/opt/intel/oneapi/debugger/10.1.1/documentation/info/
          LD_LIBRARY_PATH=/opt/ohpc/pub/mpi/libfabric/1.10.1/lib:/opt/ohpc/pub/mpi/ucx-ohpc/1.8.
                          0/lib:/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/lib:/opt/ohpc/pub/compiler
                          /gcc/9.3.0/lib64:/.singularity.d/libs
             LIBRARY_PATH=/opt/intel/oneapi/vpl/2021.2.2/lib:/opt/intel/oneapi/tbb/2021.2.0/env/
                          ../lib/intel64/gcc4.8:/opt/intel/oneapi/mpi/2021.2.0//libfabric/lib:/o
                          pt/intel/oneapi/mpi/2021.2.0//lib/release:/opt/intel/oneapi/mpi/2021.2
                          .0//lib:/opt/intel/oneapi/mkl/latest/lib/intel64:/opt/intel/oneapi/ipp
                          cp/2021.2.0/lib/intel64:/opt/intel/oneapi/ipp/2021.2.0/lib/intel64:/op
                          t/intel/oneapi/dnnl/2021.2.0/cpu_dpcpp_gpu_dpcpp/lib:/opt/intel/oneapi
                          /dal/2021.2.0/lib/intel64:/opt/intel/oneapi/compiler/2021.2.0/linux/co
                          mpiler/lib/intel64_lin:/opt/intel/oneapi/compiler/2021.2.0/linux/lib:/
                          opt/intel/oneapi/ccl/2021.2.0/lib/cpu_gpu_dpcpp
                  MANPATH=/opt/xcat/share/man:/opt/ohpc/pub/libs/singularity/3.4.2/share/man:/op
                          t/ohpc/pub/mpi/libfabric/1.10.1/share/man:/opt/ohpc/pub/mpi/openmpi4-g
                          nu9/4.0.4/share/man:/opt/ohpc/pub/compiler/gcc/9.3.0/share/man:/usr/lo
                          cal/share/man:/usr/share/man/overrides:/usr/share/man/en:/usr/share/ma
                          n:/opt/confluent/share/man::
               MODULEPATH=/opt/ohpc/pub/moduledeps/gnu9-openmpi4:/opt/ohpc/pub/moduledeps/gnu9:/
                          opt/ohpc/admin/modulefiles:/opt/ohpc/pub/modulefiles:/opt/intel/oneapi
                          /modulefiles
                  NLSPATH=/opt/intel/oneapi/mkl/latest/lib/intel64/locale/%l_%t/%N
                     PATH=/opt/intel/oneapi/intelpython/latest/bin:/opt/intel/oneapi/intelpython
                          /latest/bin:/opt/intel/oneapi/vtune/2021.2.0/bin64:/opt/intel/oneapi/v
                          pl/2021.2.2/bin:/opt/intel/oneapi/mpi/2021.2.0/libfabric/bin:/opt/inte
                          l/oneapi/mpi/2021.2.0/bin:/opt/intel/oneapi/mkl/latest/bin/intel64:/op
                          t/intel/oneapi/intelpython/latest/bin:/opt/intel/oneapi/intelpython/la
                          test/condabin:/opt/intel/oneapi/dev-utilities/2021.2.0/bin:/opt/intel/
                          oneapi/debugger/10.1.1/gdb/intel64/bin:/opt/intel/oneapi/compiler/2021
                          .2.0/linux/lib/oclfpga/llvm/aocl-bin:/opt/intel/oneapi/compiler/2021.2
                          .0/linux/lib/oclfpga/bin:/opt/intel/oneapi/compiler/2021.2.0/linux/bin
                          /intel64:/opt/intel/oneapi/compiler/2021.2.0/linux/bin:/opt/intel/onea
                          pi/compiler/2021.2.0/linux/ioc/bin:/opt/intel/oneapi/advisor/2021.2.0/
                          bin64:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
          PKG_CONFIG_PATH=/opt/ohpc/pub/mpi/libfabric/1.10.1/lib/pkgconfig:/opt/ohpc/pub/mpi/ucx
                          -ohpc/1.8.0/lib/pkgconfig:/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/lib/pk
                          gconfig
               PYTHONPATH=/opt/intel/oneapi/advisor/2021.2.0/pythonapi
       REQUESTS_CA_BUNDLE=<not set>
        SETVARS_VARS_PATH=/opt/intel/oneapi/vtune/latest/env/vars.sh
            SSL_CERT_FILE=<not set>
                USER_PATH=/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/share/xcat/tools:/opt/ohpc/pub/
                          libs/singularity/3.4.2/bin:/opt/ohpc/pub/mpi/libfabric/1.10.1/bin:/opt
                          /ohpc/pub/mpi/ucx-ohpc/1.8.0/bin:/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4
                          /bin:/opt/ohpc/pub/compiler/gcc/9.3.0/bin:/opt/ohpc/pub/utils/prun/2.0
                          :/opt/ohpc/pub/bin:/opt/confluent/bin:/usr/local/sbin:/usr/local/bin:/
                          usr/sbin:/usr/bin:/root/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/b
                          in:/usr/local/sbin
__LMOD_REF_COUNT_LD_LIBRARY_PATH=/opt/ohpc/pub/mpi/libfabric/1.10.1/lib:1;/opt/ohpc/pub/mpi/ucx-ohpc/1.
                          8.0/lib:1;/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/lib:1;/opt/ohpc/pub/co
                          mpiler/gcc/9.3.0/lib64:1
 __LMOD_REF_COUNT_MANPATH=/opt/ohpc/pub/libs/singularity/3.4.2/share/man:1;/opt/ohpc/pub/mpi/lib
                          fabric/1.10.1/share/man:1;/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/share/
                          man:1;/opt/ohpc/pub/compiler/gcc/9.3.0/share/man:1;/usr/local/share/ma
                          n:1;/usr/share/man/overrides:1;/usr/share/man/en:1;/usr/share/man:1;/o
                          pt/confluent/share/man:1
__LMOD_REF_COUNT_MODULEPATH=/opt/ohpc/pub/moduledeps/gnu9-openmpi4:1;/opt/ohpc/pub/moduledeps/gnu9
                          :1;/opt/ohpc/admin/modulefiles:1;/opt/ohpc/pub/modulefiles:1;/opt/inte
                          l/oneapi/modulefiles:1
    __LMOD_REF_COUNT_PATH=/opt/ohpc/pub/libs/singularity/3.4.2/bin:1;/opt/ohpc/pub/mpi/libfabric
                          /1.10.1/bin:1;/opt/ohpc/pub/mpi/ucx-ohpc/1.8.0/bin:1;/opt/ohpc/pub/mpi
                          /openmpi4-gnu9/4.0.4/bin:1;/opt/ohpc/pub/compiler/gcc/9.3.0/bin:1;/opt
                          /ohpc/pub/utils/prun/2.0:1;/opt/ohpc/pub/bin:1;/opt/confluent/bin:1;/u
                          sr/local/sbin:1;/usr/local/bin:1;/usr/sbin:1;/usr/bin:1
__LMOD_REF_COUNT_PKG_CONFIG_PATH=/opt/ohpc/pub/mpi/libfabric/1.10.1/lib/pkgconfig:1;/opt/ohpc/pub/mpi/u
                          cx-ohpc/1.8.0/lib/pkgconfig:1;/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/li
                          b/pkgconfig:1

     active environment : None
            shell level : 0
       user config file : /root/.condarc
 populated config files : /opt/intel/oneapi/intelpython/latest/.condarc
          conda version : 4.9.2
    conda-build version : not installed
         python version : 3.7.9.final.0
       virtual packages : __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /opt/intel/oneapi/intelpython/latest  (read only)
           channel URLs : file:///opt/intel/oneapi/conda_channel/linux-64
                          file:///opt/intel/oneapi/conda_channel/noarch
                          https://conda.anaconda.org/intel/linux-64
                          https://conda.anaconda.org/intel/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/intel/oneapi/intelpython/latest/pkgs
                          /root/.conda/pkgs
       envs directories : /root/.conda/envs
                          /opt/intel/oneapi/intelpython/latest/envs
               platform : linux-64
             user-agent : conda/4.9.2 requests/2.25.1 CPython/3.7.9 Linux/4.18.0-193.el8.x86_64 ubuntu/18.04.5 glibc/2.27
                UID:GID : 0:0
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

Upload successful.

 

 

But,it is successful when I clone the tensorflow environment.

 

initializing UnlinkLinkTransaction with
  target_prefix: /home/hpcadmin/fy/test_ai/tensorflow
  unlink_precs:

  link_precs:
    defaults/linux-64::ca-certificates-2021.4.13-h06a4308_1
    file:///opt/intel/oneapi/conda_channel/linux-64::common_cmplr_lib_rt-2021.2.0-intel_610
    file:///opt/intel/oneapi/conda_channel/linux-64::common_cmplr_lic_rt-2021.2.0-intel_610
    file:///opt/intel/oneapi/conda_channel/linux-64::impi_rt-2021.2.0-intel_215
    file:///opt/intel/oneapi/conda_channel/linux-64::intel-openmp-2021.2.0-intel_610
    file:///opt/intel/oneapi/conda_channel/linux-64::intelpython-2021.1.1-1
    file:///opt/intel/oneapi/conda_channel/linux-64::libgcc-ng-9.3.0-hdf63c60_101
    file:///opt/intel/oneapi/conda_channel/linux-64::libstdcxx-ng-9.3.0-hdf63c60_101
    defaults/linux-64::pandoc-2.12-h06a4308_0
    file:///opt/intel/oneapi/conda_channel/linux-64::tbb-2021.2.0-intel_357
    file:///opt/intel/oneapi/conda_channel/linux-64::tcl-8.6.10-0
    file:///opt/intel/oneapi/conda_channel/linux-64::tensorflow-base-2.3.0-0
    file:///opt/intel/oneapi/conda_channel/linux-64::bzip2-1.0.8-hb9a14ef_6
    file:///opt/intel/oneapi/conda_channel/linux-64::c-ares-1.17.1-h14c3975_0
    defaults/linux-64::expat-2.3.0-h2531618_2
    file:///opt/intel/oneapi/conda_channel/linux-64::fortran_rt-2021.2.0-intel_610
    defaults/linux-64::icu-58.2-he6710b0_3
    defaults/linux-64::jpeg-9b-h024ee3a_2
    file:///opt/intel/oneapi/conda_channel/linux-64::libffi-3.3-13
    defaults/linux-64::libsodium-1.0.18-h7b6447c_0
    defaults/linux-64::libuuid-1.0.3-h1bed415_2
    defaults/linux-64::libxcb-1.14-h7b6447c_0
    file:///opt/intel/oneapi/conda_channel/linux-64::lz4-c-1.9.2-h5c78bee_3
    file:///opt/intel/oneapi/conda_channel/linux-64::lzo-2.10-hb9a14ef_6
    file:///opt/intel/oneapi/conda_channel/linux-64::mkl-2021.2.0-intel_296
    file:///opt/intel/oneapi/conda_channel/linux-64::opencl_rt-2021.2.0-intel_610
    defaults/linux-64::openssl-1.1.1k-h27cfd23_0
    defaults/linux-64::pcre-8.44-he6710b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::sqlite-3.34.0-h2132df7_0
    file:///opt/intel/oneapi/conda_channel/linux-64::xz-5.2.5-h85f8e93_2
    file:///opt/intel/oneapi/conda_channel/linux-64::yaml-0.1.7-7
    file:///opt/intel/oneapi/conda_channel/linux-64::zlib-1.2.11.1-h047b5d8_3
    defaults/linux-64::glib-2.68.1-h36276a3_0
    file:///opt/intel/oneapi/conda_channel/linux-64::hdf5-1.10.2-3
    defaults/linux-64::libpng-1.6.37-hbc83047_0
    file:///opt/intel/oneapi/conda_channel/linux-64::libprotobuf-3.14.0-hdfd0036_0
    file:///opt/intel/oneapi/conda_channel/linux-64::libxml2-2.9.10-h58efa85_4
    file:///opt/intel/oneapi/conda_channel/linux-64::tk-8.6.10-h8e2d9d6_2
    defaults/linux-64::zeromq-4.3.4-h2531618_0
    file:///opt/intel/oneapi/conda_channel/linux-64::zstd-1.4.5-ha6fa1a4_0
    defaults/linux-64::dbus-1.13.18-hb2f20db_0
    defaults/linux-64::freetype-2.10.4-h5ab3b9f_0
    defaults/linux-64::gstreamer-1.14.0-h28cd5cc_2
    file:///opt/intel/oneapi/conda_channel/linux-64::libarchive-3.4.2-hae7a978_7
    file:///opt/intel/oneapi/conda_channel/linux-64::python-3.7.9-h86c8c07_7
    file:///opt/intel/oneapi/conda_channel/linux-64::asn1crypto-1.4.0-py37_2
    file:///opt/intel/oneapi/conda_channel/linux-64::async-timeout-3.0.1-py37h06a4308_0
    defaults/linux-64::async_generator-1.10-py37h28b3542_0
    file:///opt/intel/oneapi/conda_channel/linux-64::attrs-20.3.0-pyhd3eb1b0_0
    defaults/noarch::backcall-0.2.0-pyhd3eb1b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::blinker-1.4-py37_0
    file:///opt/intel/oneapi/conda_channel/linux-64::cachetools-4.2.1-pyhd3eb1b0_0
    defaults/linux-64::certifi-2020.12.5-py37h06a4308_0
    file:///opt/intel/oneapi/conda_channel/linux-64::chardet-4.0.0-py37_0
    file:///opt/intel/oneapi/conda_channel/linux-64::click-7.1.2-py_0
    defaults/noarch::decorator-5.0.6-pyhd3eb1b0_0
    defaults/noarch::defusedxml-0.7.1-pyhd3eb1b0_0
    defaults/linux-64::entrypoints-0.3-py37_0
    defaults/linux-64::fontconfig-2.13.1-h6c09931_0
    file:///opt/intel/oneapi/conda_channel/linux-64::gast-0.3.3-py_0
    defaults/linux-64::gst-plugins-base-1.14.0-h8213a91_2
    file:///opt/intel/oneapi/conda_channel/linux-64::idna-3.1-py37_0
    defaults/noarch::ipython_genutils-0.2.0-pyhd3eb1b0_1
    defaults/noarch::jupyterlab_widgets-1.0.0-pyhd3eb1b0_1
    defaults/linux-64::markupsafe-1.1.1-py37h14c3975_1
    defaults/linux-64::mistune-0.8.4-py37h14c3975_1001
    file:///opt/intel/oneapi/conda_channel/linux-64::multidict-4.7.6-py37h7b6447c_1
    defaults/noarch::nest-asyncio-1.5.1-pyhd3eb1b0_0
    defaults/linux-64::pandocfilters-1.4.3-py37h06a4308_1
    defaults/noarch::parso-0.8.2-pyhd3eb1b0_0
    defaults/noarch::pickleshare-0.7.5-pyhd3eb1b0_1003
    defaults/noarch::prometheus_client-0.10.1-pyhd3eb1b0_0
    defaults/noarch::ptyprocess-0.7.0-pyhd3eb1b0_2
    file:///opt/intel/oneapi/conda_channel/linux-64::pyasn1-0.4.8-py_0
    file:///opt/intel/oneapi/conda_channel/linux-64::pycosat-0.6.3-py37_6
    file:///opt/intel/oneapi/conda_channel/linux-64::pycparser-2.20-py37_2
    defaults/noarch::pyparsing-2.4.7-pyhd3eb1b0_0
    defaults/linux-64::pyrsistent-0.17.3-py37h7b6447c_0
    file:///opt/intel/oneapi/conda_channel/linux-64::pysocks-1.7.0-py37_2
    file:///opt/intel/oneapi/conda_channel/linux-64::python-libarchive-c-2.8-py37_14
    defaults/linux-64::pyzmq-20.0.0-py37h2531618_1
    defaults/noarch::qtpy-1.9.0-py_0
    file:///opt/intel/oneapi/conda_channel/linux-64::ruamel_yaml-0.15.99-py37h725dc98_6
    defaults/noarch::send2trash-1.5.0-pyhd3eb1b0_1
    defaults/linux-64::sip-4.19.8-py37hf484d3e_0
    file:///opt/intel/oneapi/conda_channel/linux-64::six-1.15.0-py37_1
    file:///opt/intel/oneapi/conda_channel/linux-64::tbb4py-2021.2.0-py37_intel_357
    file:///opt/intel/oneapi/conda_channel/linux-64::tensorflow-estimator-2.3.0-pyheb71bc4_0
    file:///opt/intel/oneapi/conda_channel/linux-64::termcolor-1.1.0-py37_1
    defaults/noarch::testpath-0.4.4-pyhd3eb1b0_0
    defaults/linux-64::tornado-6.1-py37h27cfd23_0
    file:///opt/intel/oneapi/conda_channel/linux-64::tqdm-4.56.2-py37_0
    defaults/noarch::wcwidth-0.2.5-py_0
    defaults/linux-64::webencodings-0.5.1-py37_1
    file:///opt/intel/oneapi/conda_channel/linux-64::werkzeug-1.0.1-py_0
    file:///opt/intel/oneapi/conda_channel/linux-64::wrapt-1.12.1-py37h7b6447c_1
    file:///opt/intel/oneapi/conda_channel/linux-64::zipp-3.4.0-pyhd3eb1b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::absl-py-0.11.0-pyhd3eb1b0_1
    file:///opt/intel/oneapi/conda_channel/linux-64::astunparse-1.6.3-py_0
    file:///opt/intel/oneapi/conda_channel/linux-64::cffi-1.14.4-py37h14c3975_0
    file:///opt/intel/oneapi/conda_channel/linux-64::conda-package-handling-1.4.1-py37_4
    file:///opt/intel/oneapi/conda_channel/linux-64::google-pasta-0.2.0-py_0
    file:///opt/intel/oneapi/conda_channel/linux-64::importlib-metadata-2.0.0-py_1
    defaults/linux-64::jedi-0.17.0-py37_0
    file:///opt/intel/oneapi/conda_channel/linux-64::mkl-service-2.3.0-py37hb9838c7_10
    defaults/noarch::packaging-20.9-pyhd3eb1b0_0
    defaults/noarch::pexpect-4.8.0-pyhd3eb1b0_3
    defaults/noarch::prompt-toolkit-3.0.17-pyh06a4308_0
    file:///opt/intel/oneapi/conda_channel/linux-64::pyasn1-modules-0.2.8-py_0
    defaults/noarch::python-dateutil-2.8.1-pyhd3eb1b0_0
    defaults/linux-64::qt-5.9.7-h5867ecd_1
    file:///opt/intel/oneapi/conda_channel/linux-64::rsa-4.7-pyhd3eb1b0_1
    file:///opt/intel/oneapi/conda_channel/linux-64::setuptools-51.1.2-py37_0
    defaults/linux-64::terminado-0.9.4-py37h06a4308_0
    defaults/noarch::traitlets-5.0.5-pyhd3eb1b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::yarl-1.6.3-py37h27cfd23_0
    file:///opt/intel/oneapi/conda_channel/linux-64::aiohttp-3.6.3-py37h7b6447c_0
    defaults/linux-64::argon2-cffi-20.1.0-py37h27cfd23_1
    defaults/noarch::bleach-3.3.0-pyhd3eb1b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::cryptography-3.3.2-py37_0
    file:///opt/intel/oneapi/conda_channel/linux-64::grpcio-1.31.0-py37hf8bcb03_0
    defaults/noarch::jinja2-2.11.3-pyhd3eb1b0_0
    defaults/linux-64::jsonschema-3.0.2-py37_0
    defaults/linux-64::jupyter_core-4.7.1-py37h06a4308_0
    file:///opt/intel/oneapi/conda_channel/linux-64::markdown-3.3.3-py37h06a4308_0
    defaults/noarch::prompt_toolkit-3.0.17-hd3eb1b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::protobuf-3.14.0-py37h2531618_1
    defaults/noarch::pygments-2.8.1-pyhd3eb1b0_0
    defaults/linux-64::pyqt-5.9.2-py37h05f1152_2
    file:///opt/intel/oneapi/conda_channel/linux-64::tensorboard-plugin-wit-1.6.0-py_0
    file:///opt/intel/oneapi/conda_channel/linux-64::wheel-0.36.2-py37_0
    file:///opt/intel/oneapi/conda_channel/linux-64::google-auth-1.24.0-pyhd3eb1b0_0
    defaults/linux-64::ipython-7.22.0-py37hb070fc8_0
    defaults/noarch::jupyter_client-6.1.12-pyhd3eb1b0_0
    defaults/noarch::jupyterlab_pygments-0.1.2-py_0
    defaults/noarch::nbformat-5.1.3-pyhd3eb1b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::pip-21.0.1-py37_0
    file:///opt/intel/oneapi/conda_channel/linux-64::pyjwt-1.7.1-py37_0
    file:///opt/intel/oneapi/conda_channel/linux-64::pyopenssl-20.0.1-py37_2
    defaults/linux-64::ipykernel-5.3.4-py37h5ca1d4c_0
    defaults/noarch::nbclient-0.5.3-pyhd3eb1b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::oauthlib-3.1.0-py_0
    file:///opt/intel/oneapi/conda_channel/linux-64::urllib3-1.26.3-py37_0
    defaults/noarch::jupyter_console-6.4.0-pyhd3eb1b0_0
    defaults/linux-64::nbconvert-6.0.7-py37_0
    defaults/noarch::qtconsole-5.0.3-pyhd3eb1b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::requests-2.25.1-py37_1
    defaults/linux-64::notebook-6.3.0-py37h06a4308_0
    file:///opt/intel/oneapi/conda_channel/linux-64::requests-oauthlib-1.3.0-py_0
    file:///opt/intel/oneapi/conda_channel/linux-64::google-auth-oauthlib-0.4.2-pyhd3eb1b0_2
    defaults/linux-64::widgetsnbextension-3.5.1-py37_0
    defaults/noarch::ipywidgets-7.6.3-pyhd3eb1b0_1
    defaults/linux-64::jupyter-1.0.0-py37_7
    file:///opt/intel/oneapi/conda_channel/linux-64::dpcpp_cpp_rt-2021.2.0-intel_610
    file:///opt/intel/oneapi/conda_channel/linux-64::icc_rt-2021.2.0-intel_610
    file:///opt/intel/oneapi/conda_channel/linux-64::numpy-base-1.20.1-py37hffe281f_0
    file:///opt/intel/oneapi/conda_channel/linux-64::mkl_fft-1.3.0-py37h9bd69cd_0
    file:///opt/intel/oneapi/conda_channel/linux-64::mkl_random-1.2.1-py37h3617918_2
    file:///opt/intel/oneapi/conda_channel/linux-64::mkl_umath-0.1.1-py37hc4b4d23_8
    file:///opt/intel/oneapi/conda_channel/linux-64::numpy-1.20.1-py37h288f0c4_0
    file:///opt/intel/oneapi/conda_channel/linux-64::h5py-2.8.0-py37h989c5e5_3
    file:///opt/intel/oneapi/conda_channel/linux-64::opt_einsum-3.1.0-py_0
    file:///opt/intel/oneapi/conda_channel/linux-64::scipy-1.6.1-py37haaffb16_2
    file:///opt/intel/oneapi/conda_channel/linux-64::tensorboard-2.3.0-pyh4dce500_0
    file:///opt/intel/oneapi/conda_channel/linux-64::keras-preprocessing-1.1.2-pyhd3eb1b0_0
    file:///opt/intel/oneapi/conda_channel/linux-64::tensorflow-2.3.0-py37_0


Source:      /opt/intel/oneapi/intelpython/latest/envs/tensorflow
Destination: /home/hpcadmin/fy/test_ai/tensorflow
The following packages cannot be cloned out of the root environment:
 - defaults/linux-64::conda-4.10.1-py37h06a4308_1
Packages: 166
Files: 204
Preparing transaction: ...working... done
Verifying transaction: ...working... [ClobberError: This transaction has incompatible packages due to a shared path.
  packages: file:///opt/intel/oneapi/conda_channel/linux-64::tensorboard-2.3.0-pyh4dce500_0, file:///opt/intel/oneapi/conda_channel/linux-64::tensorflow-2.3.0-py37_0
  path: 'bin/tensorboard'

]

done
Executing transaction: ...working... ===> LINKING PACKAGE: defaults::ca-certificates-2021.4.13-h06a4308_1 <===
  prefix=/home/hpcadmin/fy/test_ai/tensorflow
  source=/root/.conda/pkgs/ca-certificates-2021.4.13-h06a4308_1


===> LINKING PACKAGE: file:///opt/intel/oneapi/conda_channel::common_cmplr_lib_rt-2021.2.0-intel_610 <===
  prefix=/home/hpcadmin/fy/test_ai/tensorflow
  source=/opt/intel/oneapi/intelpython/latest/pkgs/common_cmplr_lib_rt-2021.2.0-intel_610

 

 

Please let me know if I'm missing something.Thanks.

 
 
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JananiC_Intel
Moderator
‎05-11-2021 06:35 AM
3,397 Views

Hi,


Thanks for posting in Intel forums.


We will check on this meanwhile could you share your steps followed for building AI toolkit image?


Regards,

Janani Chandran


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mpi_new_user
New Contributor II
‎05-11-2021 06:13 PM
3,384 Views
In response to JananiC_Intel

Hi,

I found this error also occurred in the conda environment which is installed directly by Intel AI Toolkit.

Here is the info :

[root@head ~]# cd /opt/intel/oneapi/
[root@head oneapi]# cd pytorch/
[root@head pytorch]# ls
1.5.0  latest
[root@head pytorch]#
[root@head pytorch]# cd latest/
[root@head latest]# ls
bin       conda-meta  etc      install_pytorch.sh  libexec    pkgs   shell  sys_check        x86_64-conda_cos6-linux-gnu
condabin  env         include  lib                 licensing  share  ssl    Untitled6.ipynb
[root@head latest]# cd bin
[root@head bin]#
[root@head bin]#
[root@head bin]# ls
2to3                    fax2ps                    jupyter-run              openssl            sqlite3     wish8.6
2to3-3.7                fax2tiff                  jupyter-serverextension  pal2rgb            tclsh8.6    wrjpgcom
activate                freetype-config           jupyter-troubleshoot     pip                tiff2bw     xml2-config
bsdcat                  idle3                     jupyter-trust            pngfix             tiff2pdf    xmlcatalog
bsdcpio                 idle3.7                   libpng16-config          png-fix-itxt       tiff2ps     xmllint
bsdtar                  iptest                    libpng-config            ppm2tiff           tiff2rgba   xz
chardetect              iptest3                   lz4                      pydoc              tiffcmp     xzcat
cjpeg                   ipython                   lz4c                     pydoc3             tiffcp      xzcmp
conda                   ipython3                  lz4cat                   pydoc3.7           tiffcrop    xzdec
conda-env               jpegtran                  lzcat                    pygmentize         tiffdither  xzdiff
convert-caffe2-to-onnx  jsonschema                lzcmp                    python             tiffdump    xzegrep
convert-onnx-to-caffe2  jupyter                   lzdiff                   python3            tiffinfo    xzfgrep
cph                     jupyter-bundlerextension  lzegrep                  python3.7          tiffmedian  xzgrep
c_rehash                jupyter-console           lzfgrep                  python3.7-config   tiffset     xzless
deactivate              jupyter-kernel            lzgrep                   python3.7m         tiffsplit   xzmore
djpeg                   jupyter-kernelspec        lzless                   python3.7m-config  tqdm        zstd
easy_install            jupyter-migrate           lzma                     python3-config     unlz4       zstdcat
easy_install-3.7        jupyter-nbconvert         lzmadec                  pyvenv             unlzma      zstdgrep
f2py                    jupyter-nbextension       lzmainfo                 pyvenv-3.7         unxz        zstdless
f2py3                   jupyter-notebook          lzmore                   raw2tiff           unzstd      zstdmt
f2py3.7                 jupyter-qtconsole         ninja                    rdjpgcom           wheel
[root@head bin]#
[root@head bin]#
[root@head bin]#
[root@head bin]# source activate
(base) [root@head bin]#
(base) [root@head bin]#
(base) [root@head bin]# conda env list
# conda environments:
#
                         /home/hpcadmin/conda
                         /home/hpcadmin/devtool_conda
                         /home/hpcadmin/fy/test_ai/pytorch
                         /home/hpcadmin/fy/test_ai/tensorflow
                         /home/hpcadmin/jupyter_test
                         /home/hpcadmin/test_tensor/pytorch
                         /home/hpcadmin/test_tensor/tensorflow
base                  *  /opt/intel/oneapi/pytorch/latest
                         /opt/miniconda
                         /tmp/hpcadmin/oneapi/pytorch/latest

(base) [root@head bin]# conda create -y -v --clone base -p /opt/pytorch
Source:      /opt/intel/oneapi/pytorch/latest
Destination: /opt/pytorch
The following packages cannot be cloned out of the root environment:
 - file:///opt/intel/oneapi/conda_channel/linux-64::conda-4.8.4-py37h926af72_10
Packages: 68
Files: 10673

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/opt/intel/oneapi/pytorch/latest/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
        return func(*args, **kwargs)
      File "/opt/intel/oneapi/pytorch/latest/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
        exit_code = do_call(args, p)
      File "/opt/intel/oneapi/pytorch/latest/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
        return getattr(module, func_name)(args, parser)
      File "/opt/intel/oneapi/pytorch/latest/lib/python3.7/site-packages/conda/cli/main_create.py", line 41, in execute
        install(args, parser, 'create')
      File "/opt/intel/oneapi/pytorch/latest/lib/python3.7/site-packages/conda/cli/install.py", line 222, in install
        clone(args.clone, prefix, json=context.json, quiet=context.quiet, index_args=index_args)
      File "/opt/intel/oneapi/pytorch/latest/lib/python3.7/site-packages/conda/cli/install.py", line 74, in clone
        index_args=index_args)
      File "/opt/intel/oneapi/pytorch/latest/lib/python3.7/site-packages/conda/misc.py", line 286, in clone_env
        force_extract=False, index_args=index_args)
      File "/opt/intel/oneapi/pytorch/latest/lib/python3.7/site-packages/conda/misc.py", line 90, in explicit
        assert not any(spec_pcrec[1] is None for spec_pcrec in specs_pcrecs)
    AssertionError

`$ /opt/intel/oneapi/pytorch/latest/bin/conda create -y -v --clone base -p /opt/pytorch`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=base
                CONDA_EXE=/opt/intel/oneapi/pytorch/latest/bin/conda
             CONDA_PREFIX=/opt/intel/oneapi/pytorch/latest
    CONDA_PROMPT_MODIFIER=(base)
         CONDA_PYTHON_EXE=/opt/intel/oneapi/pytorch/latest/bin/python
               CONDA_ROOT=/opt/intel/oneapi/pytorch/latest
              CONDA_SHLVL=1
           CURL_CA_BUNDLE=<not set>
          LD_LIBRARY_PATH=/opt/ohpc/pub/mpi/libfabric/1.10.1/lib:/opt/ohpc/pub/mpi/ucx-ohpc/1.8.
                          0/lib:/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/lib:/opt/ohpc/pub/compiler
                          /gcc/9.3.0/lib64
                  MANPATH=/opt/xcat/share/man:/opt/ohpc/pub/libs/singularity/3.4.2/share/man:/op
                          t/ohpc/pub/mpi/libfabric/1.10.1/share/man:/opt/ohpc/pub/mpi/openmpi4-g
                          nu9/4.0.4/share/man:/opt/ohpc/pub/compiler/gcc/9.3.0/share/man:/usr/lo
                          cal/share/man:/usr/share/man/overrides:/usr/share/man/en:/usr/share/ma
                          n:/opt/confluent/share/man::
               MODULEPATH=/opt/ohpc/pub/moduledeps/gnu9-openmpi4:/opt/ohpc/pub/moduledeps/gnu9:/
                          opt/ohpc/admin/modulefiles:/opt/ohpc/pub/modulefiles:/opt/intel/oneapi
                          /modulefiles
                     PATH=/opt/intel/oneapi/pytorch/latest/bin:/opt/intel/oneapi/pytorch/latest/
                          bin:/opt/miniconda/condabin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/sha
                          re/xcat/tools:/opt/ohpc/pub/libs/singularity/3.4.2/bin:/opt/ohpc/pub/m
                          pi/libfabric/1.10.1/bin:/opt/ohpc/pub/mpi/ucx-ohpc/1.8.0/bin:/opt/ohpc
                          /pub/mpi/openmpi4-gnu9/4.0.4/bin:/opt/ohpc/pub/compiler/gcc/9.3.0/bin:
                          /opt/ohpc/pub/utils/prun/2.0:/opt/ohpc/pub/bin:/opt/confluent/bin:/usr
                          /local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/bin
          PKG_CONFIG_PATH=/opt/ohpc/pub/mpi/libfabric/1.10.1/lib/pkgconfig:/opt/ohpc/pub/mpi/ucx
                          -ohpc/1.8.0/lib/pkgconfig:/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/lib/pk
                          gconfig
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>
__LMOD_REF_COUNT_LD_LIBRARY_PATH=/opt/ohpc/pub/mpi/libfabric/1.10.1/lib:1;/opt/ohpc/pub/mpi/ucx-ohpc/1.
                          8.0/lib:1;/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/lib:1;/opt/ohpc/pub/co
                          mpiler/gcc/9.3.0/lib64:1
 __LMOD_REF_COUNT_MANPATH=/opt/ohpc/pub/libs/singularity/3.4.2/share/man:1;/opt/ohpc/pub/mpi/lib
                          fabric/1.10.1/share/man:1;/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/share/
                          man:1;/opt/ohpc/pub/compiler/gcc/9.3.0/share/man:1;/usr/local/share/ma
                          n:1;/usr/share/man/overrides:1;/usr/share/man/en:1;/usr/share/man:1;/o
                          pt/confluent/share/man:1
__LMOD_REF_COUNT_MODULEPATH=/opt/ohpc/pub/moduledeps/gnu9-openmpi4:1;/opt/ohpc/pub/moduledeps/gnu9
                          :1;/opt/ohpc/admin/modulefiles:1;/opt/ohpc/pub/modulefiles:1;/opt/inte
                          l/oneapi/modulefiles:1
    __LMOD_REF_COUNT_PATH=/opt/ohpc/pub/libs/singularity/3.4.2/bin:1;/opt/ohpc/pub/mpi/libfabric
                          /1.10.1/bin:1;/opt/ohpc/pub/mpi/ucx-ohpc/1.8.0/bin:1;/opt/ohpc/pub/mpi
                          /openmpi4-gnu9/4.0.4/bin:1;/opt/ohpc/pub/compiler/gcc/9.3.0/bin:1;/opt
                          /ohpc/pub/utils/prun/2.0:1;/opt/ohpc/pub/bin:1;/opt/confluent/bin:1;/u
                          sr/local/sbin:1;/usr/local/bin:1;/usr/sbin:1;/usr/bin:1
__LMOD_REF_COUNT_PKG_CONFIG_PATH=/opt/ohpc/pub/mpi/libfabric/1.10.1/lib/pkgconfig:1;/opt/ohpc/pub/mpi/u
                          cx-ohpc/1.8.0/lib/pkgconfig:1;/opt/ohpc/pub/mpi/openmpi4-gnu9/4.0.4/li
                          b/pkgconfig:1

     active environment : base
    active env location : /opt/intel/oneapi/pytorch/latest
            shell level : 1
       user config file : /root/.condarc
 populated config files : /root/.condarc
          conda version : 4.8.4
    conda-build version : not installed
         python version : 3.7.9.final.0
       virtual packages : __glibc=2.28
       base environment : /opt/intel/oneapi/pytorch/latest  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/intel/oneapi/pytorch/latest/pkgs
                          /root/.conda/pkgs
       envs directories : /opt/intel/oneapi/pytorch/latest/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.4 requests/2.24.0 CPython/3.7.9 Linux/4.18.0-193.el8.x86_64 centos/8.2.2004 glibc/2.28
                UID:GID : 0:0
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

Upload successful.

 

In response to JananiC_Intel
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mpi_new_user
New Contributor II
‎05-11-2021 06:18 PM
3,382 Views

And  I found an alternative :

conda env export -n pytorch > pytorch_environment.yml
conda env create -f  pytorch_environment.yml -p  /clone_path

 

I hope it can help to solve this problem。

Thanks.

 

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JananiC_Intel
Moderator
‎05-14-2021 06:36 AM
3,343 Views

Hi,

 

Thanks for posting in Intel forums.

 

This is a known issue and we are working on it.

 

There are other methods to use pytorch.You can use pytorch by creating AI toolkit pytorch environment with conda(https://software.intel.com/content/www/us/en/develop/articles/installing-ai-kit-with-conda.html#gs.0sd3qn) and by installing AI analytics toolkit(https://software.intel.com/content/www/us/en/develop/tools/oneapi/ai-analytics-toolkit/download.html?operatingsystem=linux).

 

Regards,

Janani Chandran

 

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JananiC_Intel
Moderator
‎12-14-2021 04:20 AM
2,832 Views

Hi,


Sorry for the late response. This issue is been fixed. If you need any additional information, please post a new question as this thread will no longer be monitored by Intel.


Regards,

Janani Chandran


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