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#1 2021-10-19 09:50:01

DavidD
Member
Registered: 2021-10-19
Posts: 2

Incompatibility between MKL and libgomp.so.1 library

Hi everyone,

i am trying to install Code_Aster on Ubuntu 20.04 with a conda environnement and i have trouble in doing so.

Please, find enclosed my log file

Here is my conda environnement

name: asterenv
channels:
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=4.5=1_gnu
  - blas=1.0=mkl
  - boost=1.76.0=py38hfc89cab_0
  - boost-cpp=1.76.0=h312852a_1
  - bzip2=1.0.8=h7f98852_4
  - ca-certificates=2021.10.8=ha878542_0
  - certifi=2021.10.8=py38h578d9bd_0
  - icu=68.1=h58526e2_0
  - intel-openmp=2021.3.0=h06a4308_3350
  - ld_impl_linux-64=2.35.1=h7274673_9
  - libffi=3.3=he6710b0_2
  - libgcc-ng=9.3.0=h5101ec6_17
  - libgomp=9.3.0=h5101ec6_17
  - libstdcxx-ng=9.3.0=hd4cf53a_17
  - lz4-c=1.9.3=h9c3ff4c_1
  - mkl=2021.3.0=h06a4308_520
  - mkl-service=2.4.0=py38h7f8727e_0
  - mkl_fft=1.3.0=py38h42c9631_2
  - mkl_random=1.2.2=py38h51133e4_0
  - ncurses=6.2=he6710b0_1
  - numpy=1.21.2=py38h20f2e39_0
  - numpy-base=1.21.2=py38h79a1101_0
  - openssl=1.1.1l=h7f8727e_0
  - pip=21.2.4=py38h06a4308_0
  - python=3.8.12=h12debd9_0
  - python_abi=3.8=2_cp38
  - readline=8.1=h27cfd23_0
  - setuptools=58.0.4=py38h06a4308_0
  - six=1.16.0=pyhd3eb1b0_0
  - sqlite=3.36.0=hc218d9a_0
  - tk=8.6.11=h1ccaba5_0
  - wheel=0.37.0=pyhd3eb1b0_1
  - xz=5.2.5=h7b6447c_0
  - zlib=1.2.11=h7b6447c_3
  - zstd=1.5.0=ha95c52a_0


Here are the last lines of the log file

--------------------------------------------------------------------------------
     SUMMARY OF INSTALLATION
--------------------------------------------------------------------------------

Installation of   : hdf5 1.10.3
Destination       : /home/ddanan/HSAProject/CodeAster/public/hdf5-1.10.3
Elapsed time      : 904.16 s
                                                                      [  OK  ]
Installation of   : med 4.0.0
Destination       : /home/ddanan/HSAProject/CodeAster/public/med-4.0.0
Elapsed time      : 729.07 s
                                                                      [  OK  ]
Installation of   : scotch 6.0.4
Destination       : /home/ddanan/HSAProject/CodeAster/public/scotch-6.0.4
Elapsed time      : 250.15 s
                                                                      [  OK  ]
Installation of   : astk 2020.0
Destination       : /home/ddanan/HSAProject/CodeAster/lib/python3.8/site-packages
Elapsed time      : 6.40 s
                                                                      [  OK  ]
Installation of   : metis 5.1.0
Destination       : /home/ddanan/HSAProject/CodeAster/public/metis-5.1.0
Elapsed time      : 64.47 s
                                                                      [  OK  ]
Installation of   : tfel 3.2.1
Destination       : /home/ddanan/HSAProject/CodeAster/public/tfel-3.2.1
Elapsed time      : 1871.75 s
                                                                      [  OK  ]
Installation of   : mumps 5.1.2
Destination       : /home/ddanan/HSAProject/CodeAster/public/mumps-5.1.2
Elapsed time      : 1175.32 s
                                                                      [  OK  ]
Installation of   : homard 11.12
Destination       : /home/ddanan/HSAProject/CodeAster/public/homard-11.12
Elapsed time      : 15.34 s
                                                                      [  OK  ]
Installation of   : aster 14.6.0
Destination       : /home/ddanan/HSAProject/CodeAster
Elapsed time      : 1970.51 s
                                                                     
*** Exception None raised : None
See detailed traceback in the logfile
                                                                       [FAILED]
Exit code : 4
Installation of   : Code_Aster + 9 of its prerequisites
Destination       : /home/ddanan/HSAProject/CodeAster
Elapsed time      : 7068.99 s
                                                                      [  OK  ]

And next, here is the part i am concerned about in the log

Waf: Leaving directory `/tmp/install_aster.337352/aster-14.6.0/build/std/release'
+ build the elements catalog elem.1 using installed aster (from /tmp/install_aster.337352/aster-14.6.0/build/std/release/catalo/cata_ele.ojb)
stdout:
stderr: Error: mkl-service + Intel(R) MKL: MKL_THREADING_LAYER=INTEL is incompatible with libgomp.so.1 library.
    Try to import numpy first or set the threading layer accordingly. Set MKL_SERVICE_FORCE_INTEL to force it.

I found several topics about this subject that invovles changing some environnement variables but it did not work.
Any idea? Is there anything wrong/strange in the log?
Thanks in advance for your help

David.


Attachments:
setup.log, Size: 1.38 MiB, Downloads: 26

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#2 2021-10-20 09:06:11

DavidD
Member
Registered: 2021-10-19
Posts: 2

Re: Incompatibility between MKL and libgomp.so.1 library

I guess i found the solution.

In fact, defining an environnement variable DOES work. I just did

export MKL_SERVICE_FORCE_INTEL=1

before running the setup script again.

Now i am running the sequential tests to assess whether it does work.
If it does, i will change the topic title to solve.

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